@article {9558,
	title = {Ancestors{\textquoteright} Gift: Parental Early Exposure to the Environmentally Realistic Pesticide Mixture Drives Offspring Phenotype in a Larger Extent Than Direct Exposure in the Pacific Oyster, Crassostrea gigas},
	journal = {Environmental Science \& Technology},
	year = {2024},
	issn = {0013-936X},
	doi = {10.1021/acs.est.3c0820110},
	url = {https://pubs.acs.org/doi/10.1021/acs.est.3c08201},
	author = {Sol-Dourdin, Thomas and Guyomard, Killian and Rabiller, Manuella and Houssais, Nina and Cormier, Alexandre and Le Monier, Pauline and Sussarellu, Rossana and Guillaume Rivi{\`e}re}
}
@article {9592,
	title = {Demography of endangered juvenile green turtles in face of environmental changes: 10 years of capture-mark-recapture efforts in Martinique},
	journal = {Biological Conservation},
	volume = {291},
	year = {2024},
	month = {Jan-03-2024},
	pages = {110471},
	issn = {00063207},
	doi = {10.1016/j.biocon.2024.110471},
	url = {https://authors.elsevier.com/c/1icDh1R~eWZv6},
	author = {Lelong, Pierre and Besnard, Aur{\'e}lien and Girondot, Marc and Habold, Caroline and Priam, Fabienne and Giraudeau, Mathieu and Le Loc{\textquoteright}h, Guillaume and Le Loc{\textquoteright}h, Aur{\'e}lie and Fournier, Pascal and Fournier-Chambrillon, Christine and Bustamante, Paco and Dupont, Sophie M. and Vincze, Orsolya and Gros-Desormeaux, Jean-Rapha{\"e}l and Martin, Jordan and Bourgeois, Ouv{\'e}a and Lepori, Muriel and R{\'e}gis, Sidney and Lecerf, Nicolas and Lefebvre, Fabien and Aubert, Nathalie and Frouin, C{\'e}dric and Flora, Fr{\'e}d{\'e}ric and Pimentel, Esteban and Pimentel, Manon and Siegwalt, Flora and Jeantet, Lor{\`e}ne and Chambault, Philippine and Hielard, Ga{\"e}lle and Arqu{\'e}, Alexandre and Arthus, Mosiah and Louis-Jean, Laurent and Brador, Aude and Giannasi, Paul and Etienne, Denis and Lecerf, Natha{\"e}l and Chevallier, Pascale and Chevallier, Tao and Meslier, St{\'e}phane and Landreau, Anthony and Maceno, Myriane and Larcher, Eug{\`e}ne and Le Maho, Yvon and Chevallier, Damien}
}
@article {9457,
	title = {Intraspecific genetic lineages of a marine mussel show behavioural divergence when exposed to microplastic leachates},
	journal = {Environmental Pollution},
	volume = {340},
	year = {2024},
	month = {2024},
	issn = {ISSN 0269-7491},
	doi = {https://doi.org/10.1016/j.envpol.2023.122779},
	author = {Lorenzo Cozzolino and Nicastro, Katy R. and Hubbard, P C and Seuront, Laurent and Christopher D. McQuaid and Zardi, Gerardo I.}
}
@article {9525,
	title = {The metabolites of light: Untargeted metabolomic approaches bring new clues to understand light-driven acclimation of intertidal mudflat biofilm},
	journal = {Science of The Total Environment},
	volume = {912},
	year = {2024},
	month = {Jan-02-2024},
	pages = {168692},
	abstract = {The\&nbsp;microphytobenthos\&nbsp;(MPB), a\&nbsp;microbial community\&nbsp;of primary producers, play a key role in\&nbsp;coastal ecosystem\&nbsp;functioning, particularly in intertidal mudflats. These mudflats experience challenging variations of irradiance, forcing the micro-organisms to develop photoprotective mechanisms to survive and thrive in this dynamic environment. Two major adaptations to light are well described in literature: the excess of light\&nbsp;energy dissipation\&nbsp;through non-photochemical quenching (NPQ), and the vertical migration in the sediment. These mechanisms trigger considerable scientific interest, but the biological processes and metabolic mechanisms involved in light-driven vertical migration remain largely unknown. To our knowledge, this study investigates for the first time metabolomic responses of a migrational mudflat biofilm exposed for 30\&nbsp;min to a light gradient of photosynthetically active radiation (PAR) from 50 to 1000\&nbsp;μmol photons m-2\&nbsp;s-1. The untargeted metabolomic analysis allowed to identify metabolites involved in two types of responses to light irradiance levels. On the one hand, the production of SFAs and MUFAs, primarily derived from bacteria, indicates a healthy photosynthetic state of MPB under low light (LL; 50 and 100 PAR) and medium light (ML; 250 PAR) conditions. Conversely, when exposed to high light (HL; 500, 750 and 1000 PAR), the MPB experienced light-induced stress, triggering the production of alka(e)nes and fatty alcohols. The physiological and ecological roles of these compounds are poorly described in literature. This study sheds new light on the topic, as it suggests that these compounds may play a crucial and previously unexplored role in light-induced stress\&nbsp;acclimation\&nbsp;of migrational MPB biofilms. Since alka(e)nes are produced from FAs\&nbsp;decarboxylation, these results thus emphasize for the first time the importance of FAs pathways in microphytobenthic biofilms acclimation to light.},
	issn = {00489697},
	doi = {10.1016/j.scitotenv.2023.168692},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969723073205},
	author = {Caroline Doose and C{\'e}dric Hubas}
}
@article {9528,
	title = {Tracing the fate of seabird-derived nitrogen in a coral reef using nitrate and coral skeleton nitrogen isotopes},
	journal = {Limnology and Oceanography},
	year = {2024},
	month = {Mar-01-2024},
	issn = {0024-3590},
	doi = {10.1002/lno.12485},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lno.12485},
	author = {Choisnard, No{\'e}mie and Duprey, Nicolas Noel and Wald, Tanja and Thibault, Martin and Houlbr{\`e}que, Fanny and Foreman, Alan D. and Cuet, Pascale and Mireille M.M. Guillaume and Vonhof, Hubert and Sigman, Daniel M. and Haug, Gerald H. and Maguer, Jean-Fran{\c c}ois and L{\textquoteright}Helguen, St{\'e}phane and Mart{\'\i}nez-Garc{\'\i}a, Alfredo and Lorrain, Anne}
}
@article {9290,
	title = {Artificial reef effectiveness changes among types as revealed by underwater hyperspectral imagery},
	journal = {Restoration Ecology},
	year = {2023},
	month = {Dec-07-2024},
	pages = {e13978},
	abstract = {Artificial reefs (ARs) are designed to mimic natural habitats and promote marine life. Their effectiveness is however debatable and can depend on factors such as structural complexity and construction material. Old artificial reefs (OARs) were made of concrete mold of simple geometric shapes, limiting their ability to mimic the complexity of natural reefs. Recent advancements in three-dimentional (3D)-printing technology have enabled the creation of 3D-printed artificial reefs (3DRs) with biocompatible material and complex structures that can better simulate the natural habitats. We employed underwater hyperspectral technology to estimate the performance of these reefs and compare the benthic photosynthetic signal of natural reefs (NATs) with those of ARs (OARs and 3DRs) in coastal area of the north-western Mediterranean (France and Monaco Principality). We expected differences in reflectance signals between OARs and NATs, and signals closer to NATs in 3DRs than OARs. Underwater hyperspectral technology was able to detect higher chlorophyll-a\&nbsp;derived signals on NATs than OARs. Moreover, the magnitude of differences between 3DRs and NATs was smaller than that between OARs and NATs. Although ARs were not capable of mimicking natural reefs, the use of 3D-printed ARs might ameliorate their effectiveness for coastal reconciliation.},
	issn = {1061-2971},
	doi = {10.1111/rec.13978},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/rec.13978},
	author = {Elisabeth Riera and C{\'e}dric Hubas and Ungermann, Mischa and Rigot, Guy and Pey, Alexis and Patrice Francour and Rossi, Fracesca}
}
@article {9524,
	title = {A benchmark for computational analysis of animal behavior, using animal-borne tags},
	journal = {arXiv},
	year = {2023},
	month = {05/2023},
	abstract = {Animal-borne sensors ({\textquoteleft}bio-loggers{\textquoteright}) can record a suite of kinematic and environmental data, which can elucidate animal ecophysiology and improve conservation efforts. Machine learning techniques are useful for interpreting the large amounts of data recorded by bio-loggers, but there exists no standard for comparing the different machine learning techniques in this domain. To address this, we present the Bio-logger Ethogram Benchmark (BEBE), a collection of datasets with behavioral annotations, standardized modeling tasks, and evaluation metrics. BEBE is to date the largest, most taxonomically diverse, publicly available benchmark of this type, and includes 1654 hours of data collected from 149 individuals across nine taxa. We evaluate the performance of ten different machine learning methods on BEBE, and identify key challenges to be addressed in future work. Datasets, models, and evaluation code are made publicly available at https://github.com/earthspecies/ BEBE, to enable community use of BEBE as a point of comparison in methods development.},
	keywords = {Accelerometers, animal behavior, Bio-loggers, Clustering, Machine Learning, Time series},
	author = {Benjamin Hoffman and Maddie Cusimano and Vittorio Baglione and Daniela Canestrari and Chevallier, Damien and Dominic L. DeSantis and Lor{\`e}ne Jeantet and Monique A. Ladds and Takuya Maekawa and Vicente Mata-Silva and V{\'\i}ctor Moreno-Gonz{\'a}lez and Eva Trapote and Outi Vainio and Antti Vehkaoja and Ken Yoda and Katherine Zacarian and Ari Friedlaender and Christian Rutz}
}
@article {9192,
	title = {Data quality control considerations in multivariate environmental monitoring: experience of the French coastal network SOMLIT},
	journal = {Frontiers in Marine Science},
	volume = {10},
	year = {2023},
	month = {Feb-04-2025},
	doi = {doi.org/10.3389/fmars.2023.1135446},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2023.1135446/full},
	author = {Breton, Elsa and Savoye, Nicolas and Rimmelin-Maury, Peggy and Sautour, Benoit and Goberville, Eric and Lheureux, Arnaud and Cariou, Thierry and Ferreira, Sophie and Agogue, Helene and Alliouane, Samir and Aubert, Fabien and Aubin, S{\'e}bastien and Berthebaud, Eric and Blayac, Hadrien and Blondel, Lucie and Boulart, C{\'e}dric and Bozec, Yann and Bureau, Sarah and Caillo, Arnaud and Cauvin, Arnaud and Cazes, Jean-Baptiste and Chasselin, L{\'e}o and Pascal Claquin and Conan, Pascal and Cordier, Marie-Ange and Costes, Laurence and Crec{\textquoteright}hriou, Romain and Crispi, Olivier and Crouvoisier, Muriel and David, Val{\'e}rie and Del Amo, Yolanda and De Lary, Hortense and Delebecq, Gaspard and Devesa, J{\'e}r{\'e}my and Domeau, Aur{\'e}lien and Durozier, Maria and Emery, Claire and Eric Feunteun and Juliette Fauchot and Gentilhomme, Val{\'e}rie and Geslin, Sandrine and Giraud, M{\'e}lanie and Granger{\'e}, Karine and Gr{\'e}gori, Gerald and Grossteffan, Emilie and Gueux, Aurore and Guillaudeau, Julien and Guillou, Ga{\"e}l and Harrewyn, Manon and Jolly, Orianne and Jude-Lemeilleur, Florence and Labatut, Paul and Labourdette, Nathalie and Lachauss{\'e}e, Nicolas and Lafont, Michel and Lagadec, V{\'e}ronique and Lambert, Christophe and Lamoureux, Jezebel and Lanceleur, Laurent and Lebreton, Beno{\^\i}t and Lecuyer, Eric and Lemeille, David and Leredde, Yann and Leroux, C{\'e}dric and Leynaert, Aude and L{\textquoteright}Helguen, St{\'e}phane and Li{\'e}nart, Camilla and Mac{\'e}, Eric and Maria, Eric and Marie, Barbara and Marie, Dominique and Mas, S{\'e}bastien and Mendes, Fabrice and Mornet, Line and Mostajir, Behzad and Mousseau, Laure and Nowaczyk, Antoine and Nunige, Sandra and Parra, Ren{\'e} and Paulin, Thomas and Pecqueur, David and Petit, Franck and Pineau, Philippe and Raimbault, Patrick and Rigaut-Jalabert, Fabienne and Salmeron, Christophe and Salter, Ian and Sauriau, Pierre-Guy and Seuront, Laurent and Sultan, Emmanuelle and Vald{\`e}s, R{\'e}mi and Vantrepotte, Vincent and Vidussi, Francesca and Voron, Florian and Vuillemin, Renaud and Zudaire, Laurent. and Garcia, Nicole}
}
@article {9302,
	title = {Discovery of a Digenean (Cryptogonimidae) Living in a Cleft-Lipped Goby, Sicyopterus cynocephalus (Teleostei: Gobiidae) from Ranongga Island, Solomon Islands: Analysis of Multiple Ribosomal DNA Regions},
	journal = {Pathogens},
	volume = {12},
	year = {2023},
	month = {Jan-07-2023},
	pages = {923},
	doi = {10.3390/pathogens12070923},
	url = {https://www.mdpi.com/2076-0817/12/7/923},
	author = {Mathews, Patrick D. and Nicolas Rabet and L. Espinoza, Luis and Vincent Ha{\"y} and Bonillo, C{\'e}line and Philippe Keith and Clara Lord and Audebert, Fabienne}
}
@article {9466,
	title = {An ecosystem-wide approach for assessing the spatialized cumulative effects of local and global changes on coastal ecosystem functioningAbstract},
	journal = {ICES Journal of Marine Science},
	volume = {80},
	year = {2023},
	month = {May-03-2025},
	pages = {1129 - 1142},
	issn = {1054-3139},
	doi = {10.1093/icesjms/fsad043},
	url = {https://academic.oup.com/icesjms/article/80/4/1129/7092991},
	author = {Nogues, Quentin and Bourdaud, Pierre and Araignous, Emma and Halouani, Ghassen and Ben~Rais~Lasram, Frida and Dauvin, Jean-Claude and Le~Loc{\textquoteright}h, Fran{\c c}ois and Nathalie Niquil},
	editor = {Coll, Marta}
}
@book {9396,
	title = {El Observatorio permanente del Lago Titicaca (OLT) {\textendash} Investigaci{\'o}n y monitoreo de la eutrofizaci{\'o}n del Lago Menor con estaciones limnol{\'o}gicas, boya HydroMet y teledetecci{\'o}n satelital.},
	series = {IRD/BOREA, UMSA/IE \& UMSA/IIGEO.},
	year = {2023},
	pages = {370},
	publisher = {Proyecto Piloto PNUD/GEF 05-B-05 (2019-2022). Concep Trazzos - Proyectos Gr{\'a}ficos, La Paz, Bolivia},
	organization = {Proyecto Piloto PNUD/GEF 05-B-05 (2019-2022). Concep Trazzos - Proyectos Gr{\'a}ficos, La Paz, Bolivia},
	edition = {Registro de Deposito Legal de Obras Impresas},
	issn = {978-9917-0-3035-5},
	author = {Xavier Lazzaro and Viviana Edith Cruz Hern{\'a}ndez and Marcela Andrea Ormachea Rojas and William Gustavo Lanza Aguilar and Javier Alberto Maldonado Alfaro and Javier N{\'u}{\~n}ez Villalba}
}
@article {9279,
	title = {First isolation of Francisella halioticida strains from blue mussel (Mytilus edulis) in Normandy, France},
	journal = {Journal of Invertebrate Pathology},
	volume = {200},
	year = {2023},
	month = {09/2023},
	pages = {107950},
	issn = {00222011},
	doi = {10.1016/j.jip.2023.107950},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022201123000678},
	author = {Bouras, H{\'e}l{\`e}ne and Quesnelle, Yann and Barozet, Alix and Goux, Didier and Blin, Jean-Louis and Savary, Manuel and C{\'e}line Zatylny-Gaudin and Maryline Houssin}
}
@article {9526,
	title = {Identification of microbial exopolymer producers in sandy and muddy intertidal sediments by compound-specific isotope analysis},
	journal = {Peer Community Journal},
	volume = {3},
	year = {2023},
	month = {Jan-01-2023},
	abstract = {Extracellular polymeric substances (EPS) refer to a wide variety of high molecular weight molecules secreted outside the cell membrane by biofilm microorganisms. In the present study, EPS from marine microphytobenthic biofilms were extracted and their isotope ratios were analysed. A comparison of these ratios with the carbon isotope ratios of fatty acid biomarkers allowed the identification of the main EPS producers of two contrasting types of intertidal marine sediments. Our study reveals that EPS sources are more diverse in sandy sediments than in muddy sediments. We also found distinct patterns in the production and breakdown of EPS in sandy and muddy environments. The main difference observed was in how epipelic and epipsammic diatoms affected the chemistry of EPS, which had significant implications for the growth of bacteria specialized in utilizing EPS. These differences were likely linked to variations in the functioning of epipelic and epipsammic communities, specifically in how EPS was used either for motility or for cell attachment.},
	doi = {10.24072/pcjournal.336},
	url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.336/},
	author = {C{\'e}dric Hubas and Gaubert-Boussarie, Julie and D{\textquoteright}Hondt, An-Sofie and Bruno Jesus and Lamy, Dominique and Meleder, Vona and Prins, Antoine and Rosa, Philippe and Stock, Willem and Sabbe, Koen}
}
@article {9523,
	title = {Key issues in assessing threats to sea turtles: knowledge gaps and future directions},
	journal = {Endangered Species Research},
	volume = {52},
	year = {2023},
	month = {Feb-12-2024},
	pages = {303 - 341},
	issn = {1863-5407},
	doi = {10.3354/esr01278},
	url = {https://www.int-res.com/abstracts/esr/v52/p303-341/},
	author = {Fuentes, MMPB and McMichael, E and Kot, CY and Silver-Gorges, I and Wallace, BP and Godley, BJ and Brooks, AML and Ceriani, SA and Cort{\'e}s-G{\'o}mez, AA and Dawson, TM and Dodge, KL and Flint, M and Jensen, MP and Komoroske, LM and Kophamel, S and Lettrich, MD and Long, CA and Nelms, SE and Patr{\'\i}cio, AR and Robinson, NJ and Seminoff, JA and Ware, M and Whitman, ER and Chevallier, Damien and Clyde-Brockway, CE and Korgaonkar, SA and Mancini, A and Mello-Fonseca, J and Monsinjon, JR and Neves-Ferreira, I and Ortega, AA and Patel, SH and Pfaller, JB and Ramirez, MD and Raposo, C and Smith, CE and Abreu-Grobois, FA and Hays, GC}
}
@article {9070,
	title = {Local Food Systems under Global Influence: The Case of Food, Health and Environment in Five Socio-Ecosystems},
	journal = {Sustainability},
	volume = {15},
	year = {2023},
	month = {Jan-02-2023},
	pages = {2376},
	doi = {10.3390/su15032376},
	url = {https://www.mdpi.com/2071-1050/15/3/2376},
	author = {Rapinski, Michael and Raymond, Richard and Davy, Damien and Herrmann, Thora and Bedell, Jean-Philippe and Ka, Abdou and Odonne, Guillaume and Chanteloup, Laine and Pascal Jean Lopez and Foulquier, Eric and da Silva, Eduardo Ferreira and El Deghel, Nathalie and Bo{\"e}tsch, Gilles and Coxam, V{\'e}ronique and Joliet, Fabienne and Guihard-Costa, Anne-Marie and Tib{\`e}re, Laurence and Nazare, Julie-Anne and Duboz, Priscilla}
}
@article {9277,
	title = {Major declines in NE Atlantic plankton contrast with more stable populations in the rapidly warming North Sea},
	journal = {Science of The Total Environment},
	year = {2023},
	month = {Jan-07-2023},
	pages = {165505},
	abstract = {Plankton form the base of marine food webs, making them important indicators of ecosystem status. Changes in the abundance of plankton functional groups, or lifeforms, can affect higher trophic levels and can indicate important shifts in ecosystem functioning. Here, we extend this knowledge by combining data from Continuous Plankton Recorder and fixed-point stations to provide the most comprehensive analysis of plankton time-series for the North-East Atlantic and North-West European shelf to date. We analysed 24 phytoplankton and zooplankton datasets from 15 research institutions to map 60-year abundance trends for 8 planktonic lifeforms. Most lifeforms decreased in abundance (e.g. dinoflagellates: -5 \%, holoplankton: -7 \% decade-1), except for meroplankton, which increased 12 \% decade-1, reflecting widespread changes in large-scale and localised processes. K-means clustering of assessment units according to abundance trends revealed largely opposing trend direction between shelf and oceanic regions for most lifeforms, with North Sea areas characterised by increasing coastal abundance, while abundance decreased in North-East Atlantic areas. Individual taxa comprising each phytoplankton lifeform exhibited similar abundance trends, whereas taxa grouped within zooplankton lifeforms were more variable. These regional contrasts are counterintuitive, since the North Sea which has undergone major warming, changes in nutrients, and past fisheries perturbation has changed far less, from phytoplankton to fish larvae, as compared to the more slowly warming North-East Atlantic with lower nutrient supply and fishing pressure. This more remote oceanic region has shown a major and worrying decline in the traditional food web. Although the causal mechanisms remain unclear, declining abundance of key planktonic lifeforms in the North-East Atlantic, including diatoms and copepods, are a cause of major concern for the future of food webs and should provide a red flag to politicians and policymakers about the prioritisation of future management and adaptation measures required to ensure future sustainable use of the marine ecosystem.},
	issn = {00489697},
	doi = {10.1016/j.scitotenv.2023.165505},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969723041281},
	author = {Holland, Matthew M. and Louchart, Arnaud and Artigas, Luis Felipe and Ostle, Clare and Atkinson, Angus and Rombouts, Isabelle and Graves, Carolyn A. and Devlin, Michelle and Heyden, Birgit and Machairopoulou, Margarita and Bresnan, Eileen and Schilder, Jos and Jakobsen, Hans H. and Llody-Hartley, Hannah and Tett, Paul and Best, Mike and Goberville, Eric and McQuatters-Gollop, Abigail}
}
@article {9108,
	title = {Marine invertebrates and noise},
	journal = {Frontiers in Marine Science},
	volume = {10},
	year = {2023},
	month = {March-07-2023},
	abstract = {Within the set of risk factors that compromise the conservation of marine biodiversity, one of the least understood concerns is the noise produced by human operations at sea and from land. Many aspects of how noise and other forms of energy may impact the natural balance of the oceans are still unstudied. Substantial attention has been devoted in the last decades to determine the sensitivity to noise of marine mammals{\textemdash}especially cetaceans and pinnipeds{\textemdash} and fish because they are known to possess hearing organs. Recent studies have revealed that a wide diversity of invertebrates are also sensitive to sounds, especially via sensory organs whose original function is to allow maintaining equilibrium in the water column and to sense gravity. Marine invertebrates not only represent the largest proportion of marine biomass and are indicators of ocean health but many species also have important socio-economic values. This review presents the current scientific knowledge on invertebrate bioacoustics (sound production, reception, sensitivity), as well as on how marine invertebrates are affected by anthropogenic noises. It also critically revisits the literature to identify gaps that will frame future research investigating the tolerance to noise of marine ecosystems.},
	keywords = {marine invertebrates, marine noise pollution, noise effects, particle motion, sound detection, sound pressure, sound production, statocyst},
	doi = {10.3389/fmars.2023.1129057},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2023.1129057/full},
	author = {Sol{\'e}, Marta and Kaifu, Kenzo and Mooney, T. Aran and Nedelec, Sophie L. and Olivier, Fr{\'e}d{\'e}ric and Radford, Andrew N. and Vazzana, Mirella and Wale, Matthew A. and Semmens, Jayson M. and Simpson, Stephen D. and Buscaino, Giuseppa and Hawkins, Anthony and Aguilar de Soto, Natacha and Akamatsu, Tomoari and Chauvaud, Laurent and Day, Ryan D. and Fitzgibbon, Quinn and McCauley, Robert D. and Andr{\'e}, Michel}
}
@article {9215,
	title = {Sex-specific seasonal variations in the fatty acid and carotenoid composition of sea cucumber gonads and implications for aquaculture},
	journal = {Marine Biology},
	volume = {170},
	year = {2023},
	month = {Jan-04-2023},
	issn = {0025-3162},
	doi = {10.1007/s00227-023-04198-0},
	url = {https://link.springer.com/10.1007/s00227-023-04198-0},
	author = {Frank David and Herault, Gwen and Ameziane, Nadia and Tarik Meziane and Badou, Aicha and C{\'e}dric Hubas}
}
@article {9467,
	title = {Structure of planktonic food web in the Gulf of Gab{\`e}s (Southeastern Mediterranean): potential importance of heterotrophic and mixotrophic microzooplankton},
	journal = {Aquatic Sciences},
	volume = {85},
	year = {2023},
	month = {Jan-04-2023},
	issn = {1015-1621},
	doi = {10.1007/s00027-023-00954-y},
	url = {https://link.springer.com/10.1007/s00027-023-00954-y},
	author = {Mejri Kousri, Kaouther and Belaaj Zouari, Amel and Meddeb, Marouan and Chkili, Oumayma and Nathalie Niquil and Tedetti, Marc and Pagano, Marc and Sammari, Cherif and Khammeri, Yosra and Bel Hassen, Malika and Sakka Hlaili, Asma}
}
@article {9064,
	title = {Temporal pesticide dynamics alter specific eukaryotic taxa in a coastal transition zone},
	journal = {Science of The Total Environment},
	volume = {866},
	year = {2023},
	month = {Jan-03-2023},
	pages = {161205},
	issn = {00489697},
	doi = {10.1016/j.scitotenv.2022.161205},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969722083097},
	author = {Herv{\'e}, Vincent and Sabatier, Pierre and Lambourdi{\`e}re, Josie and Poulenard, J{\'e}r{\^o}me and Pascal Jean Lopez}
}
@article {9299,
	title = {Unmasking pipefish otolith using synchrotron-based scanning X-ray fluorescenceAbstract},
	journal = {Scientific Reports},
	volume = {13},
	year = {2023},
	month = {Jan-12-2023},
	doi = {10.1038/s41598-023-31798-z},
	url = {https://www.nature.com/articles/s41598-023-31798-z},
	author = {Ha{\"y}, Vincent and Berland, Sophie and Medjoubi, Kadda and Somogyi, Andrea and Mennesson, Marion I. and Philippe Keith and Lord, Clara}
}
@article {9126,
	title = {Unmasking pipefish otolith using synchrotron-based scanning X-ray fluorescenceAbstract},
	journal = {Scientific Reports},
	volume = {13},
	year = {2023},
	month = {Jan-12-2023},
	doi = {10.1038/s41598-023-31798-z},
	url = {https://www.nature.com/articles/s41598-023-31798-z},
	author = {Ha{\"y}, Vincent and Berland, Sophie and Medjoubi, Kadda and Somogyi, Andrea and Mennesson, Marion I. and Keith, Philippe and Lord, Clara}
}
@article {9465,
	title = {The usefulness of food web models in the ecosystem services framework: Quantifying, mapping, and linking services supply},
	journal = {Ecosystem Services},
	volume = {63},
	year = {2023},
	month = {Jan-10-2023},
	pages = {101550},
	issn = {22120416},
	doi = {10.1016/j.ecoser.2023.101550},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2212041623000438},
	author = {Nogues, Quentin and Baulaz, Yoann and Clavel, Joanne and Araignous, Emma and Bourdaud, Pierre and Ben Rais Lasram, Frida and Dauvin, Jean-Claude and Girardin, Valerie and Halouani, Ghassen and Le Loc{\textquoteright}h, Francois and Loew-Turbout, Fr{\'e}d{\'e}rique and Raoux, Aurore and Nathalie Niquil}
}
@article {9118,
	title = {What are the toxicity thresholds of chemical pollutants for tropical reef-building corals? A systematic review},
	journal = {Environmental Evidence},
	volume = {12},
	year = {2023},
	month = {Jan-12-2023},
	doi = {10.1186/s13750-023-00298-y},
	url = {https://environmentalevidencejournal.biomedcentral.com/articles/10.1186/s13750-023-00298-y},
	author = {Ou{\'e}draogo, Dakis-Yaoba and Mell, Hugo and Perceval, Olivier and Burga, Karen and Domart-Coulon, Isabelle and H{\'e}douin, Laetitia and Delaunay, Mathilde and Mireille M.M. Guillaume and Castelin, Magalie and Calvayrac, Christophe and Kerkhof, Odile and Sordello, Romain and Reyjol, Yorick and Ferrier-Pages, Christine}
}
@article {9301,
	title = {Why several when one can unite them all? Integrative taxonomic revision of Indo-Pacific freshwater pipefish (Nerophinae)Abstract},
	journal = {Zoological Journal of the Linnean Society},
	year = {2023},
	month = {May-06-2023},
	issn = {0024-4082},
	doi = {10.1093/zoolinnean/zlad007},
	url = {https://academic.oup.com/zoolinnean/advance-article/doi/10.1093/zoolinnean/zlad007/7190493},
	author = {Vincent Ha{\"y} and Marion Mennesson and Clara Lord and Philippe Keith}
}
@article {9182,
	title = {Additional records of Sicyopus discordipinnis (Watson, 1995) (Oxudercidae: Sicydiinae) in Central Sulawesi, Indonesia.},
	journal = {Cybium},
	volume = {46},
	year = {2022},
	month = {02/2022},
	pages = {41-43},
	author = {Nurjirana and Burhanuddin, A I and Philippe Keith and Haris, A}
}
@article {8832,
	title = {Assessing the state of marine biodiversity in the Northeast Atlantic},
	journal = {Ecological Indicators},
	volume = {141},
	year = {2022},
	month = {Jan-08-2022},
	pages = {109148},
	issn = {1470160X},
	doi = {10.1016/j.ecolind.2022.109148},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1470160X22006203},
	author = {McQuatters-Gollop, A. and Gu{\'e}rin, L. and Arroyo, N.L. and Aubert, A. and Artigas, L.F. and Bedford, J. and Corcoran, E. and Dierschke, V. and Elliott, S.A.M. and Geelhoed, S.C.V. and Gilles, A. and Gonz{\'a}lez-Irusta, J.M. and Haelters, J. and Johansen, M. and Le Loc{\textquoteright}h, F. and Lynam, C.P. and Nathalie Niquil and Meakins, B. and Mitchell, I. and Padegimas, B. and Pesch, R. and Preciado, I. and Rombouts, I. and Safi, G. and Schmitt, P. and Sch{\"u}ckel, U. and Serrano, A. and Stebbing, P. and De la Torriente, A. and Vina-Herbon, C.}
}
@article {8804,
	title = {Biologging of emperor penguins {\textendash} attachment techniques and associated deployment performance},
	journal = {PLoS ONE},
	year = {2022},
	doi = {10.1101/2021.06.08.446548},
	url = {https://hal.archives-ouvertes.fr/hal-03409952},
	author = {Houstin, Aymeric and Zitterbart, Daniel and Winterl, Alexander and Richter, Sebastian and Planas-Bielsa, V{\'\i}ctor and Chevallier, Damien and Ancel, Andr{\'e} and Fournier, J{\'e}r{\^o}me and Fabry, Ben and Le Bohec, C{\'e}line}
}
@article {8991,
	title = {Cephalopod palaeobiology: evolution and life history of the most intelligent invertebratesAbstract},
	journal = {Swiss Journal of Palaeontology},
	volume = {141},
	year = {2022},
	month = {Jan-12-2022},
	issn = {1664-2376},
	doi = {10.1186/s13358-022-00247-1},
	url = {https://sjpp.springeropen.com/articles/10.1186/s13358-022-00247-1},
	author = {Klug, Christian and Laure Bonnaud-Ponticelli and Nabhitabhata, Jaruwat and Fuchs, Dirk and De Baets, Kenneth and Cheng, Ji and Hoffmann, Ren{\'e}}
}
@book {8753,
	title = {Chapter 6 - Fishes and Estuarine Environmental Health},
	year = {2022},
	pages = {332 - 379},
	publisher = {Wiley},
	organization = {Wiley},
	edition = {1},
	abstract = {This chapter addresses the use of fish as indicators of environmental health. The main anthropogenic pressures impacting estuarine fishes are reviewed, as well as the main types of responses by fishes at different levels of biological organisation. Fishes have been widely used to assess estuarine health through different methodological approaches, namely comparisons with historical data or reference conditions, experimental approaches, environmental impact or risk assessment methods, as well as qualitative or quantitative indicators and models. A large number of multi-metric indices based on fish have been proposed and are routinely used in environmental assessments, although to disentangle natural variability from anthropogenic pressures in a multi-stress context of global change is still a major challenge.},
	isbn = {9781444336672},
	doi = {10.1002/978111970534510.1002/9781119705345.ch6},
	url = {https://onlinelibrary.wiley.com/doi/book/10.1002/9781119705345},
	author = {Cabral, Henrique N. and Borja, Angel and Fonseca, Vanessa F. and Harrison, Trevor D. and Teichert, Nils and Lepage, Mario and Leal, Miguel C.},
	editor = {Whitfield, Alan K. and Able, Kenneth W. and Blaber, Stephen J.M. and Elliott, Michael}
}
@article {8534,
	title = {Chlordecone-contaminated epilithic biofilms show increased adsorption capacities},
	journal = {Science of The Total Environment},
	volume = {825},
	year = {2022},
	month = {Jan-06-2022},
	pages = {153942},
	issn = {00489697},
	doi = {10.1016/j.scitotenv.2022.153942},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969722010348},
	author = {C{\'e}dric Hubas and Monti, Dominique and Jean-Michel Mortillaro and Augagneur, Sylvie and Carbon, Anne and Duran, Robert and Karama, Solange and Tarik Meziane and Pardon, Patrick and Risser, Th{\'e}o and Tapie, Nathalie and Najet Thiney and Budzinski, H{\'e}l{\`e}ne and Lauga, B{\'e}atrice}
}
@article {8121,
	title = {Climate change influences chlorophylls and bacteriochlorophylls metabolism in hypersaline microbial mat},
	journal = {Science of The Total Environment},
	volume = {802},
	year = {2022},
	month = {Jan-01-2022},
	pages = {149787},
	issn = {00489697},
	doi = {10.1016/j.scitotenv.2021.149787},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969721048622},
	author = {Mazi{\`e}re, C. and Bodo, M. and Perdrau, M.A. and Cravo-Laureau, C. and Duran, Robert and Christine Dupuy and C{\'e}dric Hubas}
}
@article {8944,
	title = {Detection of the protistan parasite, Haplosporidium costale in Crassostrea gigas oysters from the French coast: A retrospective study},
	journal = {Journal of Invertebrate Pathology},
	volume = {195},
	year = {2022},
	month = {Oct-17-2022},
	pages = {107831},
	issn = {00222011},
	doi = {10.1016/j.jip.2022.107831},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022201122001161},
	author = {Cherif--Feildel, Ma{\"e}va and Lagy, Coralie and Quesnelle, Yann and Bouras, H{\'e}l{\`e}ne and Trancart, Suzanne and Maryline Houssin}
}
@article {8530,
	title = {Estimation of the Maternal Investment of Sea Turtles by Automatic Identification of Nesting Behavior and Number of Eggs Laid from a Tri-Axial Accelerometer},
	journal = {Animals},
	volume = {12},
	year = {2022},
	month = {Jan-02-2022},
	pages = {520},
	doi = {10.3390/ani12040520},
	url = {https://www.mdpi.com/2076-2615/12/4/520},
	author = {Jeantet, Lor{\`e}ne and Hadetskyi, Vadym and Vigon, Vincent and Korysko, Fran{\c c}ois and Paranthoen, Nicolas and Chevallier, Damien}
}
@article {8713,
	title = {Fibropapillomatosis Prevalence and Distribution in Immature Green Turtles (Chelonia mydas) in Martinique Island (Lesser Antilles)},
	journal = {EcoHealth},
	year = {2022},
	month = {Mar-06-2022},
	issn = {1612-9202},
	doi = {10.1007/s10393-022-01601-y},
	url = {https://link.springer.com/10.1007/s10393-022-01601-y},
	author = {Roost, Thibaut and Schies, Jo-Ann and Girondot, Marc and Robin, Jean-Patrice and Lelong, Pierre and Martin, Jordan and Siegwalt, Flora and Jeantet, Lor{\`e}ne and Giraudeau, Mathieu and Le Loch, Guillaume and Bejarano, Manola and Bonola, Marc and Benhalilou, Abdelwahab and Murgale, C{\'e}line and Andreani, Lucas and Jacaria, Fran{\c c}ois and Campistron, Guilhem and Lathi{\`e}re, Anthony and Martial, Fran{\c c}ois and Hielard, Ga{\"e}lle and Arqu{\'e}, Alexandre and R{\'e}gis, Sidney and Lecerf, Nicolas and Frouin, C{\'e}dric and Lefebvre, Fabien and Aubert, Nathalie and Flora, Fr{\'e}d{\'e}ric and Pimentel, Esteban and Lafolle, Rachelle and Thobor, Florence and Arthus, Mosiah and Etienne, Denis and Lecerf, Natha{\"e}l and All{\'e}nou, Jean-Pierre and Desigaux, Florian and Larcher, Eug{\`e}ne and Larcher, Christian and Curto, Alberto Lo and Befort, Joanne and Maceno-Panevel, Myriane and Lepori, Muriel and Chevallier, Pascale and Chevallier, Tao and Meslier, St{\'e}phane and Landreau, Anthony and Habold, Caroline and Le Maho, Yvon and Chevallier, Damien}
}
@article {9187,
	title = {First record of Hippichthys albomaculosus Jenkins \& Mailautoka, 2010 (Syngnathidae) in New Caledonia. Cybium, 46(1): 53-55.},
	journal = {Cybium},
	volume = {46},
	year = {2022},
	month = {02/2022},
	pages = {53-55},
	author = {Vincent Ha{\"y} and Charpin Nicolas and Philippe Keith and Clara Lord and Marion Mennesson}
}
@article {8714,
	title = {Food selection and habitat use patterns of immature green turtles (Chelonia mydas) on Caribbean seagrass beds dominated by the alien species Halophila stipulacea},
	journal = {Global Ecology and Conservation},
	volume = {37},
	year = {2022},
	month = {Jan-09-2022},
	pages = {e02169},
	issn = {23519894},
	doi = {10.1016/j.gecco.2022.e02169},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2351989422001718},
	author = {Siegwalt, Flora and Jeantet, Lor{\`e}ne and Lelong, Pierre and Martin, Jordan and Girondot, Marc and Bustamante, Paco and Benhalilou, Abdelwahab and Murgale, C{\'e}line and Andreani, Lucas and Jacaria, Fran{\c c}ois and Campistron, Guilhem and Lathi{\`e}re, Anthony and Barotin, Charl{\`e}ne and Buret-Rochas, Ga{\"e}lle and Barre, Philippe and Hielard, Ga{\"e}lle and Arqu{\'e}, Alexandre and R{\'e}gis, Sidney and Lecerf, Nicolas and Frouin, C{\'e}dric and Lefebvre, Fabien and Aubert, Nathalie and Arthus, Mosiah and Etienne, Denis and All{\'e}nou, Jean-Pierre and Delnatte, C{\'e}sar and Lafolle, Rachelle and Thobor, Florence and Chevallier, Pascale and Chevallier, Tao and Lepori, Muriel and Assio, Cindy and Grand, Cl{\'e}ment and Bonola, Marc and Tursi, Yannick and Varkala, Pierre-Walter and Meslier, St{\'e}phane and Landreau, Anthony and Le Maho, Yvon and Habold, Caroline and Robin, Jean-Patrice and Chevallier, Damien}
}
@article {8882,
	title = {Geographic and taxonomic trends of rising biological invasion costs},
	journal = {Science of The Total Environment},
	volume = {817},
	year = {2022},
	month = {Jan-04-2022},
	pages = {152948},
	issn = {00489697},
	doi = {10.1016/j.scitotenv.2022.152948},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969722000377},
	author = {Haubrock, Phillip J. and Cuthbert, Ross N. and Hudgins, Emma J. and Crystal-Ornelas, Robert and Kourantidou, Melina and Moodley, Desika and Liu, Chunlong and Turbelin, Anna J. and Leroy, Boris and Courchamp, Franck}
}
@article {8726,
	title = {Identification of a New Set of Polypeptidic Sex Pheromones from Cuttlefish (Sepia officinalis)},
	journal = {Marine Biotechnology},
	year = {2022},
	month = {Sep-04-2022},
	issn = {1436-2228},
	doi = {10.1007/s10126-022-10126-y},
	url = {https://link.springer.com/10.1007/s10126-022-10126-y},
	author = {C{\'e}line Zatylny-Gaudin and Corre, Erwan and Zanuttini, Bruno and Endress, Maxime and Bernay, Beno{\^\i}t and Pontin, Julien and Leduc, Alexandre and Jo{\"e}l Henry}
}
@article {8869,
	title = {Immuno-Enzymatic and Proteomic Approaches for Sexing the African Bonytongue (Heterotis niloticus Cuvier, 1829)},
	journal = {Fishes},
	volume = {7},
	year = {2022},
	month = {Jan-06-2022},
	pages = {106},
	doi = {10.3390/fishes7030106},
	url = {https://www.mdpi.com/2410-3888/7/3/106},
	author = {Koua, N{\textquoteright}Zi Daniel and Henry, Jo{\"e}l and Corre, Erwan and Pontin, Julien and Bernay, Beno{\^\i}t and N{\'u}{\~n}ez-Rodr{\'\i}guez, Jes{\'u}s}
}
@article {9178,
	title = {An integrative phylogenetic approach for inferring relationships of fossil gobioids},
	journal = {PLOS ONE},
	volume = {17},
	year = {2022},
	month = {Aug-07-2022},
	pages = {e0271121},
	doi = {10.1371/journal.pone.0271121},
	url = {https://dx.plos.org/10.1371/journal.pone.0271121},
	author = {Gierl, Christoph and Dohrmann, Martin and Philippe Keith and Humphreys, William and Esmaeili, Hamid R. and Vuki{\'c}, Jasna and {\v S}anda, Radek and Reichenbacher, Bettina},
	editor = {Mirande, Juan Marcos}
}
@article {8146,
	title = {Knowledge gaps in economic costs of invasive alien fish worldwide},
	journal = {Science of The Total Environment},
	volume = {803},
	year = {2022},
	month = {Jan-01-2022},
	pages = {149875},
	issn = {00489697},
	doi = {10.1016/j.scitotenv.2021.149875},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969721049500},
	author = {Haubrock, Phillip J. and Bernery, Camille and Cuthbert, Ross N. and Liu, Chunlong and Kourantidou, Melina and Leroy, Boris and Turbelin, Anna J. and Kramer, Andrew M. and Verbrugge, Laura N.H. and Diagne, Christophe and Courchamp, Franck and Gozlan, Rodolphe E.}
}
@article {8356,
	title = {Macrozooplankton and micronekton diversity and associated carbon vertical patterns and fluxes under distinct productive conditions around the Kerguelen Islands},
	journal = {Journal of Marine Systems},
	volume = {226},
	year = {2022},
	month = {Jan-02-2022},
	pages = {103650},
	issn = {09247963},
	doi = {10.1016/j.jmarsys.2021.103650},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0924796321001457},
	author = {Cott{\'e}, C. and Ariza, A. and Berne, A. and Habasque, J. and Lebourges-Dhaussy, A. and Roudaut, G. and Espinasse, B. and Hunt, B.P.V. and Pakhomov, E.A. and Henschke, N. and Clara P{\'e}ron and Conchon, A. and Koedooder, C. and Izard, L. and Cherel, Y.}
}
@article {8884,
	title = {Managing biological invasions: the cost of inaction},
	journal = {Biological Invasions},
	volume = {24},
	year = {2022},
	month = {Jan-07-2022},
	pages = {1927 - 1946},
	issn = {1387-3547},
	doi = {10.1007/s10530-022-02755-0},
	url = {https://link.springer.com/10.1007/s10530-022-02755-0},
	author = {Ahmed, Danish A. and Hudgins, Emma J. and Cuthbert, Ross N. and Kourantidou, Melina and Diagne, Christophe and Haubrock, Phillip J. and Leung, Brian and Liu, Chunlong and Leroy, Boris and Petrovskii, Sergei and Beidas, Ayah and Courchamp, Franck}
}
@article {8923,
	title = {Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators},
	journal = {Science of The Total Environment},
	volume = {807},
	year = {2022},
	month = {Jan-02-2022},
	pages = {150667},
	issn = {00489697},
	doi = {10.1016/j.scitotenv.2021.150667},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969721057454},
	author = {Fiard, Maud and Cuny, Philippe and Sylvi, L{\'e}a and C{\'e}dric Hubas and J{\'e}z{\'e}quel, Ronan and Lamy, Dominique and Walcker, Romain and El Houssainy, Amonda and Heimb{\"u}rger-Boavida, Lars-Eric and Robinet, Tony and Bihannic, Isabelle and Gilbert, Franck and Michaud, Emma and Guillaume Dirberg and Militon, C{\'e}cile}
}
@article {9027,
	title = {Myctobase, a circumpolar database of mesopelagic fishes for new insights into deep pelagic prey fields},
	journal = {Scientific Data},
	volume = {9},
	year = {2022},
	month = {Jan-12-2022},
	doi = {10.1038/s41597-022-01496-y},
	url = {https://www.nature.com/articles/s41597-022-01496-y},
	author = {Woods, Briannyn and Trebilco, Rowan and Walters, Andrea and Hindell, Mark and Guy Duhamel and Flores, Hauke and Moteki, Masato and Patrice Pruvost and Reiss, Christian and Saunders, Ryan A. and Sutton, Caroline and Gan, Yi-Ming and Van de Putte, Anton}
}
@article {8995,
	title = {The response of microphytobenthos to physical disturbance, herbicide, and titanium dioxide nanoparticle exposure},
	journal = {Marine Pollution Bulletin},
	volume = {185},
	year = {2022},
	month = {Jan-12-2022},
	pages = {114348},
	abstract = {The microphytobenthos that form transient biofilms are important primary producers in intertidal, depositional habitats, yet we have only a limited understanding of how they respond to the cumulative impacts of the growing range of anthropogenic stressors to which they are exposed. We know even less about how the temporal alignment of exposure {\textendash} such as duration and exposure sequence {\textendash} may affect the response. Estuarine biofilms were cultured in mesocosms and exposed to the herbicide glyphosate and titanium dioxide (TiO2) nanoparticles in different sequences (glyphosate-first or TiO2-first), as well as in the presence and absence of physical disturbance. We found that at environmentally realistic chemical concentrations, the order of exposure was less important than the total stressor scenario in terms of impacts on key functional attributes and diatom community structure. Physical disturbance did not have an impact on functional attributes, regardless of exposure sequence.},
	issn = {0025326X},
	doi = {10.1016/j.marpolbul.2022.114348},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0025326X2201030X},
	author = {Rimmer, James E.V. and C{\'e}dric Hubas and Wyness, Adam J. and Bruno Jesus and Hartley, Morgan and Blight, Andrew J. and Prins, Antoine and Paterson, David M}
}
@article {8835,
	title = {The Response of North Sea Ecosystem Functional Groups to Warming and Changes in Fishing},
	journal = {Frontiers in Marine Science},
	volume = {9},
	year = {2022},
	month = {Apr-04-2022},
	doi = {10.3389/fmars.2022.841909},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2022.841909/full},
	author = {Thorpe, Robert B. and Arroyo, Nina L. and Safi, Georges and Nathalie Niquil and Preciado, Izaskun and Heath, Michael and Pace, Matthew C. and Lynam, Christopher P.}
}
@article {9177,
	title = {Revision of the Genus Rhyacichthys Using Integrative Taxonomy},
	journal = {Pacific Science},
	volume = {76},
	year = {2022},
	month = {Jan-04-2022},
	doi = {10.2984/76.2.3},
	url = {https://bioone.org/journals/pacific-science/volume-76/issue-2/76.2.3/Revision-of-the-Genus-Rhyacichthys-Using-Integrative-Taxonomy/10.2984/76.2.3.full},
	author = {Ha{\"y}, Vincent and Marion Mennesson and Philippe Keith and Lord, Clara}
}
@article {8883,
	title = {On the road: Anthropogenic factors drive the invasion risk of a wild solitary bee species},
	journal = {Science of The Total Environment},
	volume = {827},
	year = {2022},
	month = {Jan-06-2022},
	pages = {154246},
	issn = {00489697},
	doi = {10.1016/j.scitotenv.2022.154246},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969722013389},
	author = {Lanner, Julia and Dubos, Nicolas and Geslin, Beno{\^\i}t and Leroy, Boris and Hern{\'a}ndez-Castellano, Carlos and Dubai{\'c}, Jovana Bila and Bortolotti, Laura and Calafat, Joan Diaz and {\'C}etkovi{\'c}, Aleksandar and Flaminio, Simone and Le F{\'e}on, Violette and Margalef-Marrase, Jordi and Orr, Michael and Pachinger, B{\"a}rbel and Ruzzier, Enrico and Smagghe, Guy and Tuerlings, Tina and Vereecken, Nicolas J. and Meimberg, Harald}
}
@article {8696,
	title = {Seasonal dynamics of marine protist communities in tidally mixed coastal waters},
	journal = {Molecular Ecology},
	year = {2022},
	month = {Aug-05-2023},
	abstract = {Major seasonal community reorganizations and associated biomass variations are landmarks of plankton ecology. However, the processes of plankton community turnover rates have not been fully elucidated so far. Here, we analyse patterns of planktonic protist community succession in temperate latitudes, based on quantitative taxonomic data from both microscopy counts (cells \&gt; 10 μm) and ribosomal DNA metabarcoding (size fraction \&gt; 3 μm, 18S rRNA gene) from plankton samples collected biweekly over 8 years (2009-2016) at the SOMLIT-Astan station (Roscoff, Western English Channel). Based on morphology, diatoms were clearly the dominating group all year round and over the study period. Metabarcoding uncovered a wider diversity spectrum and revealed the prevalence of Dinophyceae and diatoms but also of Cryptophyta, Chlorophyta, Cercozoa, Syndiniales and Ciliophora in terms of read counts and or richness. The use of morphological and molecular analyses in combination allowed improving the taxonomic resolution and to identify the sequence of the dominant species and OTUs (18S V4 rDNA-derived taxa) that drive annual plankton successions. We detected that some of these dominant OTUs were benthic as a result of the intense tidal mixing typical of the French coasts in the English Channel. Our analysis of the temporal structure of community changes point to a strong seasonality and resilience. The temporal structure of environmental variables (especially Photosynthetic Active Radiation, temperature and macronutrients) and temporal structures generated by species life cycles and or species interactions, are key drivers of the observed cyclic annual plankton turnover.},
	issn = {0962-1083},
	doi = {10.1111/mec.16539},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/mec.16539},
	author = {Caracciolo, Mariarita and Rigaut-Jalabert, Fabienne and Romac, Sarah and Mah{\'e}, Fr{\'e}d{\'e}ric and Forsans, Samuel and Gac, Jean-Philippe and Arsenieff, Laure and Manno, Maxime and Chaffron, Samuel and Cariou, Thierry and Hoebeke, Mark and Bozec, Yann and Goberville, Eric and Le Gall, Florence and Guilloux, Lo{\"\i}c and Baudoux, Anne-Claire and de Vargas, Colomban and Not, Fabrice and Thi{\'e}baut, Eric and Henry, Nicolas and Simon, Nathalie}
}
@article {8440,
	title = {Similar trait structure and vulnerability in pelagic fish faunas on two remote island systems},
	journal = {Marine Biology},
	volume = {169},
	year = {2022},
	month = {Jan-01-2022},
	abstract = {The link between biodiversity and ecosystem functioning has been the topic of considerable research, but it remains unclear how biodiversity decline is compromising ecosystem functionality, particularly in the pelagic realm. Here, we explore how pelagic fish species diversity relates to functional diversity by sampling two locations, which, on the basis of biogeography, environmental conditions and human pressures, were expected to host pronounced differences in species composition and abundances and therefore functionality. Strings of five drifting mid-water Baited Remote Underwater Video Systems were used to survey pelagic vertebrate diversity and abundance in two isolated oceanic island systems, the Malpelo Fauna and Flora Sanctuary{\textemdash}a large, 25-year-old marine protected area{\textemdash}and an unprotected area in Cape Verde. Functional diversity, which offers insight into a community{\textquoteright}s resilience against disturbance, was analysed using six key functional traits of marine fishes. Abundance was recorded as MaxN, the maximum number of individuals of a given species in a single frame during the 2-h deployment time. Cape Verde showed high overall abundance (Total MaxN\&nbsp;873) and low biomass (3559\&nbsp;kg), with a predominance of smaller fishes. Malpelo showed high biomass (7839\&nbsp;kg) but lower abundance (Total MaxN\&nbsp;465), with a predominance of large species. Species and functional diversity were marginally different between locations. Multivariate analysis of species relative abundances showed significant divergence between locations, although community functional traits overlapped strongly, suggesting that both communities share a similar structure and vulnerability. The existence of a common functional {\textquoteleft}backbone{\textquoteright} in diverging species communities across the oceans, under different productivity regimes, and under different protection levels, suggests that although pelagic communities may differ considerably in terms of species composition, this does not translate into a differing functional structure and resilience potential. Whether this vulnerability is a common feature of pelagic communities and how this contrasts with benthic systems warrants further research.},
	issn = {0025-3162},
	doi = {10.1007/s00227-021-03998-6},
	url = {https://link.springer.com/10.1007/s00227-021-03998-6},
	author = {Steinberg, Madeline and Juhel, Jean-Baptiste and Marques, Virginie and Clara P{\'e}ron and Hocd{\'e}, R{\'e}gis and Polanco Fern{\'a}ndez, Andr{\'e}a and Pellissier, Lo{\"\i}c and Villeger, Sebastien and Mouillot, David and Letessier, Tom B.}
}
@article {8833,
	title = {Spatialized ecological network analysis for ecosystem-based management: effects of climate change, marine renewable energy, and fishing on ecosystem functioning in the Bay of SeineAbstract},
	journal = {ICES Journal of Marine Science},
	volume = {79},
	year = {2022},
	month = {Dec-02-2023},
	pages = {1098 - 1112},
	issn = {1054-3139},
	doi = {10.1093/icesjms/fsac026},
	url = {https://academic.oup.com/icesjms/article/79/4/1098/6535870},
	author = {Nogues, Quentin and Araignous, Emma and Bourdaud, Pierre and Halouani, Ghassen and Raoux, Aurore and Foucher, Eric and Loc{\textquoteright}h, Fran{\c c}ois Le and Loew-Turbout, Fr{\'e}d{\'e}rique and Ben~Rais~Lasram, Frida and Dauvin, Jean-Claude and Nathalie Niquil}
}
@article {8868,
	title = {Structural and Functional Characterization of Orcokinin B-like Neuropeptides in the Cuttlefish (Sepia officinalis)},
	journal = {Marine Drugs},
	volume = {20},
	year = {2022},
	month = {Jan-08-2022},
	pages = {505},
	doi = {10.3390/md20080505},
	url = {https://www.mdpi.com/1660-3397/20/8/505},
	author = {Endress, Maxime and C{\'e}line Zatylny-Gaudin and Leprince, J{\'e}r{\^o}me and Lefranc, Benjamin and Corre, Erwan and Le Corguill{\'e}, Gildas and Bernay, Beno{\^\i}t and Leduc, Alexandre and Rangama, Jimmy and Mouret, Liza and Lafont, Anne-Gaelle and Bondon, Arnaud and Jo{\"e}l Henry}
}
@article {7654,
	title = {Annual phytoplankton succession results from niche-environment interactionAbstract},
	journal = {Journal of Plankton Research},
	volume = {43},
	year = {2021},
	month = {12/2020},
	pages = {85{\textendash}102},
	abstract = {Annual plankton succession has been investigated for many decades with hypotheses ranging from abiotic to biotic mechanisms being proposed to explain these recurrent patterns. Here, using data collected by the Continuous Plankton Recorder (CPR) survey and models originating from the MacroEcological Theory on the Arrangement of Life, we investigate Annual Phytoplankton Succession (APS) in the North Sea at a species level. Our results show that this phenomenon can be predicted well by models combining photosynthetically active radiation, temperature and macro-nutrients. Our findings suggest that APS originates from the interaction between species{\textquoteright} ecological niches and the annual environmental fluctuations at a community level. We discuss our results in the context of traditional hypotheses formulated to explain this recurrent pattern in the marine field.},
	issn = {0142-7873},
	doi = {10.1093/plankt/fbaa060},
	url = {https://academic.oup.com/plankt/advance-article/doi/10.1093/plankt/fbaa060/6043723},
	author = {Caracciolo, Mariarita and Gr{\'e}gory Beaugrand and Pierre H{\'e}laou{\"e}t and Gevaert, Francois and Martin Edwards and Lizon, Fabrice and Kl{\'e}parski, Lo{\"\i}ck and Goberville, Eric}
}
@article {8426,
	title = {Anthropogenic pressures coincide with Neotropical biodiversity hotspots in a flagship butterfly group},
	journal = {Diversity and Distributions},
	year = {2021},
	month = {12/2021},
	issn = {1366-9516},
	doi = {10.1111/ddi.13455},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ddi.13455},
	author = {Dor{\'e}, Ma{\"e}l and Willmott, Keith and Leroy, Boris and Chazot, Nicolas and Mallet, James and Freitas, Andr{\'e} V. L. and Hall, Jason P. W. and Lamas, Gerardo and Dasmahapatra, Kanchon K. and Fontaine, Colin and Elias, Marianne}
}
@article {8707,
	title = {Are we ready to track climate-driven shifts in marine species across international boundaries? - A global survey of scientific bottom trawl data},
	journal = {Global Change Biology},
	volume = {27},
	year = {2021},
	month = {Jan-01-2021},
	pages = {220 - 236},
	issn = {1354-1013},
	doi = {10.1111/gcb.v27.210.1111/gcb.15404},
	url = {https://onlinelibrary.wiley.com/toc/13652486/27/2},
	author = {Maureaud, Aurore and Frelat, Romain and P{\'e}cuchet, Laur{\`e}ne and Shackell, Nancy and M{\'e}rigot, Bastien and Pinsky, Malin L. and Amador, Kofi and Anderson, Sean C. and Arkhipkin, Alexander and Auber, Arnaud and Barri, I{\c c}a and Bell, Richard J. and Belmaker, Jonathan and Beukhof, Esther and Camara, Mohamed L. and Guevara-Carrasco, Renato and Choi, Junghwa and Christensen, Helle T. and Conner, Jason and Cubillos, Luis A. and Diadhiou, Hamet D. and Edelist, Dori and Emblemsv{\r a}g, Margrete and Ernst, Billy and Fairweather, Tracey P. and Fock, Heino O. and Friedland, Kevin D. and Garcia, Camilo B. and Gascuel, Didier and Gislason, Henrik and Goren, Menachem and Guitton, J{\'e}r{\^o}me and Jouffre, Didier and Hattab, Tarek and Hidalgo, Manuel and Kathena, Johannes N. and Knuckey, Ian and Kid{\'e}, Sa{\"\i}kou O. and Koen-Alonso, Mariano and Koopman, Matt and Kulik, Vladimir and Le{\'o}n, Jacqueline Palacios and Levitt-Barmats, Ya{\textquoteright}arit and Lindegren, Martin and Llope, Marcos and Massiot-Granier, F{\'e}lix and Masski, Hicham and McLean, Matthew and Meissa, Beyah and M{\'e}rillet, Laur{\`e}ne and Mihneva, Vesselina and Nunoo, Francis K. E. and O{\textquoteright}Driscoll, Richard and O{\textquoteright}Leary, Cecilia A. and Petrova, Elitsa and Ramos, Jorge E. and Refes, Wahid and Rom{\'a}n-Marcote, Esther and Siegstad, Helle and Sobrino, Ignacio and S{\'o}lmundsson, J{\'o}n and Sonin, Oren and Spies, Ingrid and Steingrund, Petur and Stephenson, Fabrice and Stern, Nir and Tserkova, Feriha and Tserpes, Georges and Tzanatos, Evangelos and Rijn, Itai and Zwieten, Paul A. M. and Vasilakopoulos, Paraskevas and Yepsen, Daniela V. and Ziegler, Philippe and Thorson, James}
}
@article {9364,
	title = {Conservative route to genome compaction in a miniature annelidAbstract},
	journal = {Nature Ecology \& Evolution},
	volume = {5},
	year = {2021},
	month = {Jan-02-2021},
	pages = {231 - 242},
	doi = {10.1038/s41559-020-01327-6},
	url = {https://www.nature.com/articles/s41559-020-01327-6},
	author = {Mart{\'\i}n-Dur{\'a}n, Jos{\'e} M. and Vellutini, Bruno C. and Marl{\'e}taz, Ferdinand and Cetrangolo, Viviana and Cvetesic, Nevena and Thiel, Daniel and Henriet, Simon and Grau-Bov{\'e}, Xavier and Carrillo-Baltodano, Allan M. and Gu, Wenjia and Kerbl, Alexandra and Marquez, Yamile and Bekkouche, Nicolas and Chourrout, Daniel and G{\'o}mez-Skarmeta, Jose Luis and Irimia, Manuel and Lenhard, Boris and Worsaae, Katrine and Hejnol, Andreas}
}
@article {8143,
	title = {Cumulative effects of marine renewable energy and climate change on ecosystem properties: Sensitivity of ecological network analysis},
	journal = {Ecological Indicators},
	volume = {121},
	year = {2021},
	month = {Jan-02-2021},
	pages = {107128},
	issn = {1470160X},
	doi = {10.1016/j.ecolind.2020.107128},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1470160X20310670},
	author = {Nogues, Quentin and Raoux, Aurore and Araignous, Emma and Chaalali, Aur{\'e}lie and Hattab, Tarek and Leroy, Boris and Ben Rais Lasram, Frida and David, Val{\'e}rie and Le Loc{\textquoteright}h, Francois and Dauvin, Jean-Claude and Nathalie Niquil}
}
@article {8020,
	title = {Decadal trajectories of phytoplankton communities in contrasted estuarine systems in an epicontinental sea},
	journal = {Estuarine, Coastal and Shelf Science},
	volume = {258},
	year = {2021},
	month = {Jan-09-2021},
	pages = {107409},
	abstract = {In coastal areas, global changes are known to affect estuaries and their plume leading to water temperature increase and river discharge variations, which are two of the main drivers controlling phytoplankton dynamics. This paper aims at understanding the past 10 years{\textquoteright} variations in term of communities{\textquoteright} stability and trajectories along with their relationship with the environment. Considering the high environmental variability along coastal areas, we focused our study on six contrasted estuarine systems from the eastern English Channel. Using monthly monitoring from 2008 to 2019, the response of the micro-phytoplankton compartment was investigated through the abundances of a hundred taxa and several abiotic parameters{\textquoteright} records. The results indicate an overall stability in community composition with an average of 30{\textendash}40\% similarity between pairs of samples over the study period. The phytoplankton assemblages also display greater spatial heterogeneity during summer in comparison with other seasons. The co-inertia analysis highlighted four separate systems linked to major drivers; a system under strong river and nutrient flows influence, a well-mixed and oxygenized estuary, a system challenged by offshore marine waters, and finally a system under shellfish farms pressure. This structuration is built from the dominance of a handful of species that differs from one place to another, which explains why phytoplankton is mostly site specific. Additionally, the low variations led a by few species{\textquoteright} dominance also explains the interannual stability noticed during summer at each area, in spite of the high diversity observed.},
	issn = {02727714},
	doi = {10.1016/j.ecss.2021.107409},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0272771421002626},
	author = {Lefran, Ang{\'e}line and Hern{\'a}ndez-Fari{\~n}as, Tania and Gohin, Francis and Pascal Claquin}
}
@article {8886,
	title = {Detailed assessment of the reported economic costs of invasive species in Australia},
	journal = {NeoBiota},
	volume = {67},
	year = {2021},
	month = {May-07-2023},
	pages = {511 - 550},
	issn = {1619-0033},
	doi = {10.3897/neobiota.67.5883410.3897/neobiota.67.58834.suppl1},
	url = {https://neobiota.pensoft.net/article/58834/},
	author = {Bradshaw, Corey J. A. and Hoskins, Andrew J. and Haubrock, Phillip J. and Cuthbert, Ross N. and Diagne, Christophe and Leroy, Boris and Andrews, Lindell and Page, Brad and Cassey, Phill and Sheppard, Andy W. and Courchamp, Franck}
}
@article {8161,
	title = {Disentangling tropicalization and deborealization in marine ecosystems under climate change},
	journal = {Current Biology},
	year = {2021},
	abstract = {Summary As climate change accelerates, species are shifting poleward and subtropical and tropical species are colonizing temperate environments.1, 2, 3 A popular approach for characterizing such responses is the community temperature index (CTI), which tracks the mean thermal affinity of a community. Studies in marine,4 freshwater,5 and terrestrial6 ecosystems have documented increasing CTI under global warming. However, most studies have only linked increasing CTI to increases in warm-affinity species. Here, using long-term monitoring of marine fishes across the Northern Hemisphere, we decomposed CTI changes into four underlying processes{\textemdash}tropicalization (increasing warm-affinity), deborealization (decreasing cold-affinity), borealization (increasing cold-affinity), and detropicalization (decreasing warm-affinity){\textemdash}for which we examined spatial variability and drivers. CTI closely tracked changes in sea surface temperature, increasing in 72\% of locations. However, 31\% of these increases were primarily due to decreases in cold-affinity species, i.e., deborealization. Thus, increases in warm-affinity species were prevalent, but not ubiquitous. Tropicalization was stronger in areas that were initially warmer, experienced greater warming, or were deeper, while deborealization was stronger in areas that were closer to human population centers or that had higher community thermal diversity. When CTI (and temperature) increased, species that decreased were more likely to be living closer to their upper thermal limits or to be commercially fished. Additionally, warm-affinity species that increased had smaller body sizes than those that decreased. Our results show that CTI changes arise from a variety of underlying community responses that are linked to environmental conditions, human impacts, community structure, and species characteristics.},
	keywords = {bottom trawl, community temperature index, Fisheries, marine ecology, thermal affinity},
	issn = {0960-9822},
	doi = {https://doi.org/10.1016/j.cub.2021.08.034},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982221011386},
	author = {Matthew McLean and David Mouillot and Aurore A. Maureaud and Tarek Hattab and M. Aaron MacNeil and Goberville, Eric and Martin Lindegren and Georg Engelhard and Malin Pinsky and Arnaud Auber}
}
@article {8656,
	title = {Economic costs of biological invasions within North America},
	journal = {NeoBiota},
	volume = {67},
	year = {2021},
	month = {07/2021},
	pages = {485-510},
	author = {Crystal-Ornelas, Rob and Hudgins, Emma J and Cuthbert, Ross N. and Haubrock, Phillip J. and Fantle-Lepczyk, J and Angulo, Elena and Kramer, Andrew M. and Ballesteros-Mejia, Liliana and Leroy, Boris and Leung, Brian and L{\'o}pez-L{\'o}pez, E and Diagne, Christophe and Courchamp, Franck}
}
@article {8144,
	title = {Economic costs of invasive alien species across Europe},
	journal = {NeoBiota},
	volume = {67},
	year = {2021},
	month = {May-07-2023},
	pages = {153 - 190},
	issn = {1619-0033},
	doi = {10.3897/neobiota.67.58196},
	url = {https://neobiota.pensoft.net/article/58196/},
	author = {Haubrock, Phillip J. and Turbelin, Anna J. and Cuthbert, Ross N. and Novoa, Ana and Taylor, Nigel G. and Angulo, Elena and Ballesteros-Mejia, Liliana and Bodey, Thomas W. and Capinha, C{\'e}sar and Diagne, Christophe and Essl, Franz and Golivets, Marina and Kirichenko, Natalia and Kourantidou, Melina and Leroy, Boris and Renault, David and Verbrugge, Laura and Courchamp, Franck}
}
@article {8653,
	title = {Economic costs of invasive alien species in the Mediterranean basin},
	journal = {NeoBiota},
	volume = {67},
	year = {2021},
	month = {May-07-2023},
	pages = {427 - 458},
	issn = {1619-0033},
	doi = {10.3897/neobiota.67.5892610.3897/neobiota.67.58926.suppl110.3897/neobiota.67.58926.suppl2},
	url = {https://neobiota.pensoft.net/article/58926/},
	author = {Kourantidou, Melina and Cuthbert, Ross N. and Haubrock, Phillip J. and Novoa, Ana and Taylor, Nigel G. and Leroy, Boris and Capinha, C{\'e}sar and Renault, David and Angulo, Elena and Diagne, Christophe and Courchamp, Franck}
}
@article {7883,
	title = {Effects of Melatonin on Anterior Pituitary Plasticity: A Comparison Between Mammals and Teleosts},
	journal = {Frontiers in Endocrinology},
	volume = {11},
	year = {2021},
	month = {Nov-01-2021},
	abstract = {Melatonin is a key hormone involved in the photoperiodic signaling pathway. In both teleosts and mammals, melatonin produced in the pineal gland at night is released into the blood and cerebrospinal fluid, providing rhythmic information to the whole organism. Melatonin acts\&nbsp;via\&nbsp;specific receptors, allowing the synchronization of daily and annual physiological rhythms to environmental conditions. The pituitary gland, which produces several hormones involved in a variety of physiological processes such as growth, metabolism, stress and reproduction, is an important target of melatonin. Melatonin modulates pituitary cellular activities, adjusting the synthesis and release of the different pituitary hormones to the functional demands, which changes during the day, seasons and life stages. It is, however, not always clear whether melatonin acts directly or indirectly on the pituitary. Indeed, melatonin also acts both upstream, on brain centers that control the pituitary hormone production and release, as well as downstream, on the tissues targeted by the pituitary hormones, which provide positive and negative feedback to the pituitary gland. In this review, we describe the known pathways through which melatonin modulates anterior pituitary hormonal production, distinguishing indirect effects mediated by brain centers from direct effects on the anterior pituitary. We also highlight similarities and differences between teleosts and mammals, drawing attention to knowledge gaps, and suggesting aims for future research.},
	doi = {10.3389/fendo.2020.605111},
	url = {https://www.frontiersin.org/articles/10.3389/fendo.2020.605111/full},
	author = {Ciani, Elia and Haug, Trude M. and Maugars, Gersende and Weltzien, Finn-Arne and Falc{\'o}n, Jack and Fontaine, Romain}
}
@article {7915,
	title = {Electron \& Biomass Dynamics of Cyanothece Under Interacting Nitrogen \& Carbon Limitations},
	journal = {Frontiers in Microbiology},
	volume = {12},
	year = {2021},
	month = {04/2021},
	doi = {10.3389/fmicb.2021.61780210.3389/fmicb.2021.617802.s001},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2021.617802/full},
	author = {Rabouille, Sophie and Campbell, Douglas A. and Masuda, Takako and Zav{\v r}el, Tomas and Bern{\'a}t, Gabor and Polerecky, Lubos and Halsey, Kimberly and Eichner, Meri and Kotabov{\'a}, Eva and Stephan, Susanne and Luke{\v s}, Martin and Pascal Claquin and Bonomi-Barufi, Jose and Lombardi, Ana Teresa and {\v C}erven{\'y}, Jan and Suggett, David J. and Giordano, Mario and Kromkamp, Jacco C. and Pr{\'a}{\v s}il, Ondrej}
}
@article {8404,
	title = {Eleotris (Teleostei: Eleotridae) from Indonesia with description of three news species},
	journal = {Pacific Science},
	volume = {75},
	year = {2021},
	month = {11/2021},
	pages = {469-496},
	abstract = {The species of Eleotris from Indonesia are reviewed and compared to the known species described from the area. Nine species are recognized including three new species in the {\textquoteleft}melanosoma{\textquoteright} neuromast pattern group. These are described using genetic and morpho-meristic approaches. The new species differ by a high percentage of genetic divergence in partial COI gene (652 bp) and by several characters including the number of pectoral fin rays, the number of scales in lateral, predorsal, forward and zigzag series. The main characteristics of the other known species in the area in the {\textquoteleft}melanosoma{\textquoteright} group, Eleotris melanosoma Bleeker, 1853 and Eleotris macrolepis (Bleeker, 1875), both belonging to this group, are given for comparison. A key for Eleotris species from Indonesia is provided.},
	doi = {https://doi.org/10.2984/75.4.2},
	author = {Marion Mennesson and Philippe Keith and Hubert, Nicolas}
}
@article {7995,
	title = {Environmental heterogeneity drives phytoplankton community assembly patterns in a tropical riverine system},
	journal = {Peer Community In Ecology},
	year = {2021},
	month = {Jan-05-2023},
	doi = {10.24072/pci.ecology.100083},
	url = {https://ecology.peercommunityin.org/articles/rec?id=86},
	author = {C{\'e}dric Hubas and Goberville, Eric}
}
@article {8466,
	title = {Estimating ecotoxicological effects of chemicals on tropical reef-building corals; a systematic review protocol},
	journal = {Environmental Evidence},
	volume = {10},
	year = {2021},
	month = {Dec-11-2021},
	doi = {10.1186/s13750-021-00250-y},
	url = {https://environmentalevidencejournal.biomedcentral.com/articles/10.1186/s13750-021-00250-y},
	author = {Ou{\'e}draogo, Dakis-Yaoba and Perceval, Olivier and Ferrier-Pages, Christine and Domart-Coulon, Isabelle and H{\'e}douin, Laetitia and Burga, Karen and Mireille M.M. Guillaume and Calvayrac, Christophe and Castelin, Magalie and Reyjol, Yorick and Sordello, Romain}
}
@article {7412,
	title = {European small pelagic fish distribution under global change scenarios},
	journal = {Fish and Fisheries},
	volume = {22},
	year = {2021},
	month = {10/2020},
	pages = {212-225},
	abstract = {The spectre of increasing impacts on exploited fish stocks in consequence of warmer climate conditions has become a major concern over the last decades. It is now imperative to improve the way we project the effects of future climate warming on fisheries. While estimating future climate-induced changes in fish distribution is an important contribution to sustainable resource management, the impacts on European small pelagic fish{\textemdash}representing over 50\% of the landings in the Mediterranean and Black Sea between 2000 and 2013{\textemdash}are yet largely understudied. Here, we investigated potential changes in the spatial distribution of seven of the most harvested small pelagic fish species in Europe under several climate change scenarios over the 21st century. For each species, we considered eight Species Distribution Models (SDMs), five General Circulation Models (GCMs) and three emission scenarios (the IPCC Representative Concentration Pathways; RCPs). Under all scenarios, our results revealed that the environmental suitability for most of the seven species may strongly decrease in the Mediterranean and western North Sea while increasing in the Black and Baltic Seas. This potential northward range expansion of species is supported by a strong convergence among projections and a low variability between RCPs. Under the most pessimistic scenario (RCP8.5), climate-related local extinctions were expected in the south-eastern Mediterranean basin. Our results highlight that a multi-SDM, multi-GCM, multi-RCP approach is needed to produce more robust ecological scenarios of changes in exploited fish stocks in order to better anticipate the economic and social consequences of global climate change.},
	issn = {1467-2960},
	doi = {10.1111/faf.12515},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/faf.12515},
	author = {Schickele, Alexandre and Goberville, Eric and Leroy, Boris and Gr{\'e}gory Beaugrand and Hattab, Tarek and Patrice Francour and Virginie Raybaud}
}
@article {8200,
	title = {Evidence on the impacts of chemicals arising from human activity on tropical reef-building corals; a systematic map},
	journal = {Environmental Evidence},
	volume = {10},
	year = {2021},
	month = {Sep-22-2021},
	doi = {10.1186/s13750-021-00237-9},
	url = {https://environmentalevidencejournal.biomedcentral.com/articles/10.1186/s13750-021-00237-9},
	author = {Ou{\'e}draogo, Dakis-Yaoba and Delaunay, Mathilde and Sordello, Romain and H{\'e}douin, L. and Castelin, Magalie and Perceval, Olivier and Domart-Coulon, Isabelle and Burga, Karen and Ferrier-Pages, Christine and Multon, Romane and Mireille M.M. Guillaume and L{\'e}ger, Cl{\'e}ment and Calvayrac, Christophe and Joannot, Pascale and Reyjol, Yorick}
}
@article {7965,
	title = {First Assessment of the Benthic Meiofauna Sensitivity to Low Human-Impacted Mangroves in French Guiana},
	journal = {Forests},
	volume = {12},
	year = {2021},
	month = {Jan-03-2021},
	pages = {338},
	doi = {10.3390/f12030338},
	url = {https://www.mdpi.com/1999-4907/12/3/338},
	author = {Michelet, Claire and Zeppilli, Daniela and C{\'e}dric Hubas and Baldrighi, Elisa and Cuny, Philippe and Guillaume Dirberg and Militon, C{\'e}cile and Walcker, Romain and Lamy, Dominique and J{\'e}z{\'e}quel, Ronan and Receveur, Justine and Gilbert, Franck and Houssainy, Amonda El and Dufour, Aur{\'e}lie and Heimb{\"u}rger-Boavida, Lars-Eric and Bihannic, Isabelle and Sylvi, L{\'e}a and Vivier, Baptiste and Michaud, Emma}
}
@article {7779,
	title = {First highlight of sound production in the glassy sweeper Pempheris schomburgkii (Pempheridae)},
	journal = {Marine Biology},
	volume = {168},
	year = {2021},
	month = {Jan-03-2021},
	issn = {0025-3162},
	doi = {10.1007/s00227-021-03829-8},
	url = {http://link.springer.com/10.1007/s00227-021-03829-8},
	author = {Fr{\'e}d{\'e}ric Bertucci and Parmentier, Eric and Hillion, Ana{\"\i}s and Cordonnier, S{\'e}bastien and Lecchini, David and Ren{\'e}-Trouillefou, Malika}
}
@article {8392,
	title = {Global systematic diversity, range distributions, conservation and taxonomic assessments of graylings (Teleostei: Salmonidae; Thymallus spp.)Abstract},
	journal = {Organisms Diversity \& Evolution},
	volume = {21},
	year = {2021},
	month = {Jan-03-2021},
	pages = {25 - 42},
	issn = {1439-6092},
	doi = {10.1007/s13127-020-00468-7},
	url = {http://link.springer.com/10.1007/s13127-020-00468-7},
	author = {Weiss, Steven J. and Gon{\c c}alves, Duarte V. and Secci-Petretto, Giulia and Englmaier, Gernot K. and Gomes-Dos-Santos, Andr{\'e} and Denys, Ga{\"e}l and Persat, Henri and Antonov, Alexander and Hahn, Christoph and Taylor, Eric B. and Froufe, Elsa}
}
@article {8147,
	title = {Impacts of climate change on the Bay of Seine ecosystem: Forcing a spatio-temporal trophic model with predictions from an ecological niche model},
	journal = {Fisheries Oceanography},
	volume = {30},
	year = {2021},
	month = {Jan-09-2021},
	pages = {471 - 489},
	issn = {1054-6006},
	doi = {10.1111/fog.v30.510.1111/fog.12531},
	url = {https://onlinelibrary.wiley.com/toc/13652419/30/5},
	author = {Bourdaud, Pierre and Ben Rais Lasram, Frida and Araignous, Emma and Champagnat, Juliette and Grusd, Samantha and Halouani, Ghassen and Hattab, Tarek and Leroy, Boris and Nogues, Quentin and Raoux, Aurore and Safi, Georges and Nathalie Niquil}
}
@article {8109,
	title = {Influence of infrastructure material composition and microtopography on marine biofilm growth and photobiology},
	journal = {Biofouling},
	year = {2021},
	month = {Apr-08-2022},
	pages = {1 - 17},
	issn = {0892-7014},
	doi = {10.1080/08927014.2021.1959918},
	url = {https://www.tandfonline.com/doi/full/10.1080/08927014.2021.1959918},
	author = {Vivier, Baptiste and Pascal Claquin and Lelong, Christophe and Lesage, Quentin and Peccate, Mathias and Hamel, Bastien and Georges, Marine and Bourguiba, Amel and Sebaibi, Nassim and Boutouil, Mohamed and Goux, Didier and Dauvin, Jean-Claude and Francis Orvain}
}
@article {9129,
	title = {Interactions between Filter-Feeding Bivalves and Toxic Diatoms: Influence on the Feeding Behavior of Crassostrea gigas and Pecten maximus and on Toxin Production by Pseudo-nitzschia},
	journal = {Toxins},
	volume = {13},
	year = {2021},
	month = {Jan-08-2021},
	pages = {577},
	doi = {10.3390/toxins13080577},
	url = {https://www.mdpi.com/2072-6651/13/8/577},
	author = {Sauvey, Aurore and Denis, Fran{\c c}oise and H{\'e}garet, H{\'e}l{\`e}ne and Le Roy, Bertrand and Lelong, Christophe and Jolly, Orianne and Pavie, Marie and Juliette Fauchot}
}
@article {8446,
	title = {Involvement of RFamide neuropeptides in polyp contraction of the adult scleractinian corals Euphyllia ancora and Stylophora pistillata},
	journal = {General and Comparative Endocrinology},
	volume = {314},
	year = {2021},
	month = {Jan-12-2021},
	pages = {113905},
	issn = {00166480},
	doi = {10.1016/j.ygcen.2021.113905},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0016648021001982},
	author = {Zhang, Yan and Shikina, Shinya and Ho, Yu-Ying and Chiu, Yi-Ling and I-Chen Yao, Jack and C{\'e}line Zatylny-Gaudin and Sylvie Dufour and Chang, Ching-Fong}
}
@article {8754,
	title = {La protection des milieux aquatiques. Vuln{\'e}rabilit{\'e} et sensibilit{\'e} fonctionnelle des communaut{\'e}s de poissons},
	journal = {Sciences Eaux \& Territoires},
	volume = {N{\textdegree} 37},
	year = {2021},
	month = {Jan-12-2022},
	pages = {76 - 81},
	abstract = {Les approches en {\'e}cologie fonctionnelle ouvrent aujourd{\textquoteright}hui de nouvelles perspectives dans le domaine du diagnostic {\'e}cologique. C{\textquoteright}est le cas par exemple du crit{\`e}re de la redondance fonctionnelle que les auteurs de cet article ont appliqu{\'e} aux communaut{\'e}s de poissons pour {\'e}valuer leur sensibilit{\'e} fonctionnelle {\`a} la perte d{\textquoteright}esp{\`e}ces, et au-del{\`a}, mesurer l{\textquoteright}influence d{\textquoteright}un d{\'e}clin potentiel de diversit{\'e} sur le fonctionnement de l{\textquoteright}{\'e}cosyst{\`e}me. L{\textquoteright}int{\'e}gration de ce type d{\textquoteright}indice, en compl{\'e}ment des crit{\`e}res habituels, est utile pour d{\'e}finir des plans de gestion ou des sites prioritaires {\`a} prot{\'e}ger face {\`a} des perturbations environnementales, en se concentrant sur les processus {\'e}cosyst{\'e}miques.},
	issn = {2109-3016},
	doi = {10.3917/set.037.0076},
	url = {https://www.cairn.info/revue-sciences-eaux-et-territoires-2021-3-page-76.htm?ref=doi},
	author = {Teichert, Nils and Lepage, Mario and Hette-Tronquart, Nicolas and Argillier, Christine}
}
@article {8445,
	title = {Marine Transcriptomic Analysis for the Identification of New Antimicrobial Peptides},
	journal = {Marine Drugs},
	volume = {19},
	year = {2021},
	month = {Jan-09-2021},
	pages = {490},
	doi = {10.3390/md19090490},
	url = {https://www.mdpi.com/1660-3397/19/9/490},
	author = {Houyvet, Baptiste and Bouchon-Navaro, Yolande and Bouchon, Claude and Corre, Erwan and C{\'e}line Zatylny-Gaudin}
}
@article {8837,
	title = {The Merits of Loop Analysis for the Qualitative Modeling of Social-Ecological Systems in Presence of Offshore Wind Farms},
	journal = {Frontiers in Ecology and Evolution},
	volume = {9},
	year = {2021},
	month = {May-02-2022},
	doi = {10.3389/fevo.2021.635798},
	url = {https://www.frontiersin.org/articles/10.3389/fevo.2021.635798/full},
	author = {Nathalie Niquil and Scotti, Marco and Fofack-Garcia, Rhoda and Haraldsson, Matilda and Thermes, Maud and Raoux, Aurore and Le Loc{\textquoteright}h, Francois and Maz{\'e}, Camille}
}
@article {8524,
	title = {A new species of freshwater pipefish (Teleostei: Syngnathidae: Coelonotus) from Papua New Guinea},
	journal = {Cybium},
	volume = {45},
	year = {2021},
	pages = {275-282},
	abstract = {A new species of Coelonotus, a freshwater pipefish, is described on the basis of six specimens from the Gavuvu river of West new Britain Island (Papua new Guinea). It differs from other Coelonotus species by a combination of morphomeristic values including: number of dorsal fin rays (45-47), number of subdorsal (4-5) and tail rings (35-37). the Folmer dna barcode fragment of the COI mitochondrial gene shows that this new species is indeed a different genetic lineage from other Coelonotus species of this area.},
	doi = {https://doi.org/10.26028/cybium/2021-454-003},
	author = {Vincent Ha{\"y} and Marion Mennesson and Philippe Keith and Clara Lord}
}
@article {9186,
	title = {A new species of Microphis (Teleostei: Syngnathidae) from Papua New Guinea. },
	journal = {Cybium},
	volume = {45},
	year = {2021},
	month = {11/2021},
	pages = {275-282},
	author = {Ha{\"y}, Vincent and Marion Mennesson and Philippe Keith and Clara Lord}
}
@article {8002,
	title = {North Atlantic warming over six decades drives decreases in krill abundance with no associated range shiftAbstract},
	journal = {Communications Biology},
	volume = {4},
	year = {2021},
	month = {Jan-12-2021},
	abstract = {In the North Atlantic, euphausiids (krill) form a major link between primary production and predators including commercially exploited fish. This basin is warming very rapidly, with species expected to shift northwards following their thermal tolerances. Here we show, however, that there has been a 50\% decline in surface krill abundance over the last 60 years that occurred in situ, with no associated range shift. While we relate these changes to the warming climate, our study is the first to document an in situ squeeze on living space within this system. The warmer isotherms are shifting measurably northwards but cooler isotherms have remained relatively static, stalled by the subpolar fronts in the NW Atlantic. Consequently the two temperatures defining the core of krill distribution (7{\textendash}13 {\textdegree}C) were 8{\textdegree} of latitude apart 60 years ago but are presently only 4{\textdegree} apart. Over the 60 year period the core latitudinal distribution of euphausiids has remained relatively stable so a {\textquoteleft}habitat squeeze{\textquoteright}, with loss of 4{\textdegree} of latitude in living space, could explain the decline in krill. This highlights that, as the temperature warms, not all species can track isotherms and shift northward at the same rate with both losers and winners emerging under the {\textquoteleft}Atlantification{\textquoteright} of the sub-Arctic.},
	doi = {10.1038/s42003-021-02159-1},
	url = {http://www.nature.com/articles/s42003-021-02159-1},
	author = {Martin Edwards and Pierre H{\'e}laou{\"e}t and Goberville, Eric and Lindley, Alistair and Tarling, Geraint A. and Burrows, Michael T. and Angus Atkinson}
}
@article {8059,
	title = {Pelagic habitats under the MSFD D1: scientific advice of policy relevance : recommendations to frame problems and solutions for the pelagic habitats{\textquoteright} assessment.},
	year = {2021},
	institution = {Publications Office of the European Union},
	abstract = {Pelagic habitats are a policy priority below Descriptor 1 (Biodiversity) of the Marine Strategy Framework Directive (MSFD). They are addressed under the D1C6 criterion, stating {\textquotedblleft}the condition of the habitat type, including its biotic and abiotic structure and its functions{\textellipsis}, is not adversely affected due to anthropogenic pressures{\textquotedblright}. The evaluation of pelagic habitats status is challenged by the functional and structural characteristics of pelagic habitat diversity and processes. To date, pelagic habitats assessments are lacking in common criteria and methodologies that characterize the habitat while accounting for the effects of anthropogenic pressures to achieve the Good Environmental Status (GES). It is therefore necessary to prioritise communication between scientific and policy communities and frame pelagic research to agree on common methods and approaches at regional or EU scale. This is key for achieving harmonised and comparable pelagic assessments for the MSFD. This report summarizes the outcomes on the assessment workflow of pelagic habitats of the JRC {\textquotedblleft}MSFD pelagic habitats{\textquotedblright} workshop (9th and 10th March 2021), and the need for coordinated evaluations of the scientific challenges of policy relevance. Recommendations on the MSFD implementation of D1C6, that were generated from the experts during the workshop, will be communicated to the MSFD policy groups and the EU Member States competent authorities to support future harmonised assessment of pelagic habitats.},
	doi = {10.2760/081368},
	url = {https://data.europa.eu/doi/10.2760/081368},
	author = {Magliozzi, Chiara and Druon, Jean-Noel and Palialexis, Andreas and Aguzzi, Laura and Alexande, Brittany and Antoniadis, Konstantinos and Artigas, Luis Felipe and Azzellino, Arianna and Bisinicu, Elena and Boicenco, Laura and Bojanic, Natalia and Borrello, Patrizia and Boschetti, Simona and Carmo, Vanda and Cervantes, Pablo and Coll, Marta and Curmi, Marta and Del Amo, Yolanda and Dutz, Joerg and Franc{\'e}, Janja and Garces, Esther and Gea, Guillermo and Giannakourou, Antonia and Goberville, Eric and Goffart, Anne and Gomes Pereira, Jose Nuno and Gonzalez-Quiros, Rafael and Gorokhova, Elena and Guglielmo, Letterio and Pierre H{\'e}laou{\"e}t and Henriques, Filipe and Heyden, Birgit and Jaanus, Andres and Jakobsen, Hans and Johansen, Marie and Jurgensone, Iveta and Korpinen, Samuli and Kremp, Anke and Kuosa, Harri and Labayle, Lucille and Lazar, Luminita and Abigail McQuatters-Gollop and Nincevic, Zivana and Pagou, Popi and Penna, Antonella and Pettersson, Karin and Ruiter, Hans and Skejic, Sanda and Spada, Emanuela and Spinu, Alina and Tew-Kai, Emilie and Totti, Cecilia and Tunesi, Leonardo and Vadrucci, Maria Rosaria and Valavanis, Vasilis and Varkitzi, Ioanna and Vasiliades, Lavrendios and Veldeki, Georgia and Vidjak, Olja and Vincent, Doroth{\'e}e and Zervoudaki, Soultana}
}
@article {8083,
	title = {Photoperiodic regulation of pituitary thyroid-stimulating hormone and brain deiodinase in Atlantic salmon},
	journal = {Molecular and Cellular Endocrinology},
	volume = {519},
	year = {2021},
	month = {Jan-01-2021},
	pages = {111056},
	issn = {03037207},
	doi = {10.1016/j.mce.2020.111056},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0303720720303580},
	author = {Irachi, Shotaro and Hall, Daniel J. and Fleming, Mitchell S. and Maugars, Gersende and Bj{\"o}rnsson, Bj{\"o}rn Thrandur and Sylvie Dufour and Uchida, Katsuhisa and McCormick, Stephen D.}
}
@article {8249,
	title = {Photosynthesis from stolen chloroplasts can support sea slug reproductive fitness},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	volume = {288},
	year = {2021},
	month = {May-09-2023},
	abstract = {Some sea slugs are able to steal functional chloroplasts (kleptoplasts) from their algal food sources, but the role and relevance of photosynthesis to the animal host remain controversial. While some researchers claim that kleptoplasts are slowly digestible {\textquoteleft}snacks{\textquoteright}, others advocate that they enhance the overall fitness of sea slugs much more profoundly. Our analysis shows light-dependent incorporation of\&nbsp;13C and\&nbsp;15N in the albumen gland and gonadal follicles of the sea slug\&nbsp;Elysia timida, representing translocation of photosynthates to kleptoplast-free reproductive organs. Long-chain polyunsaturated fatty acids with reported roles in reproduction were produced in the sea slug cells using labelled precursors translocated from the kleptoplasts. Finally, we report reduced fecundity of\&nbsp;E. timida\&nbsp;by limiting kleptoplast photosynthesis. The present study indicates that photosynthesis enhances the reproductive fitness of kleptoplast-bearing sea slugs, confirming the biological relevance of this remarkable association between a metazoan and an algal-derived organelle.},
	issn = {0962-8452},
	doi = {10.1098/rspb.2021.1779},
	url = {https://royalsocietypublishing.org/doi/10.1098/rspb.2021.1779},
	author = {Cartaxana, Paulo and Rey, Felisa and LeKieffre, Charlotte and Lopes, Diana and C{\'e}dric Hubas and Spangenberg, Jorge E. and Escrig, St{\'e}phane and Bruno Jesus and Calado, Gon{\c c}alo and Domingues, Ros{\'a}rio and K{\"u}hl, Michael and Calado, Ricardo and Meibom, Anders and Cruz, S{\'o}nia}
}
@article {8430,
	title = {Pituitary Hormones mRNA Abundance in the Mediterranean Sea Bass Dicentrarchus labrax: Seasonal Rhythms, Effects of Melatonin and Water Salinity},
	journal = {Frontiers in Physiology},
	volume = {12},
	year = {2021},
	month = {12/15/2021},
	pages = {774975},
	type = {Research article},
	abstract = {In fish, most hormonal productions of the pituitary gland display daily and/or seasonal<br>
rhythmic patterns under control by upstream regulators, including internal biological<br>
clocks. The pineal hormone melatonin, one main output of the clocks, acts at different<br>
levels of the neuroendocrine axis. Melatonin rhythmic production is synchronized mainly<br>
by photoperiod and temperature. Here we aimed at better understanding the role<br>
melatonin plays in regulating the pituitary hormonal productions in a species of scientific<br>
and economical interest, the euryhaline European sea bass Dicentrarchus labrax. We<br>
investigated the seasonal variations in mRNA abundance of pituitary hormones in two<br>
groups of fish raised one in sea water (SW fish), and one in brackish water (BW fish). The<br>
mRNA abundance of three melatonin receptors was also studied in the SW fish. Finally,<br>
we investigated the in vitro effects of melatonin or analogs on the mRNA abundance of<br>
pituitary hormones at two times of the year and after adaptation to different salinities.<br>
We found that (1) the reproductive hormones displayed similar mRNA seasonal profiles<br>
regardless of the fish origin, while (2) the other hormones exhibited different patterns<br>
in the SW vs. the BW fish. (3) The melatonin receptors mRNA abundance displayed<br>
seasonal variations in the SW fish. (4) Melatonin affected mRNA abundance of most<br>
of the pituitary hormones in vitro; (5) the responses to melatonin depended on its<br>
concentration, the month investigated and the salinity at which the fish were previously<br>
adapted. Our results suggest that the productions of the pituitary are a response to<br>
multiple factors from internal and external origin including melatonin. The variety of the<br>
responses described might reflect a high plasticity of the pituitary in a fish that faces<br>
multiple external conditions along its life characterized by marked daily and seasonal<br>
changes in photoperiod, temperature and salinity.},
	keywords = {annual variations, hormones, melatonin, photoperiod, pituitary, salinity, sea bass},
	doi = {10.3389/fphys.2021.774975},
	url = {https://www.frontiersin.org/articles/10.3389/fphys.2021.774975/full?\&utm_source=Email_to_authors_\&utm_medium=Email\&utm_content=T1_11.5e1_author\&utm_campaign=Email_publication\&field=\&journalName=Frontiers_in_Physiology\&id=774975},
	author = {Jack Falcon},
	editor = {Maria-Jesus Herrero and Laura-Gabriela Nisembaum}
}
@article {8389,
	title = {The rise and fall of the ancient northern pike master sex-determining gene},
	journal = {eLife},
	volume = {10},
	year = {2021},
	month = {Apr-01-2023},
	doi = {10.7554/eLife.62858},
	url = {https://elifesciences.org/articles/62858},
	author = {Pan, Qiaowei and Feron, Romain and Jouanno, Elodie and Darras, Hugo and Herpin, Amaury and Koop, Ben and Rondeau, Eric and Goetz, Frederick W and Larson, Wesley A and Bernatchez, Louis and Tringali, Mike and Curran, Stephen S and Saillant, Eric and Denys, Ga{\"e}l and von Hippel, Frank A and Chen, Songlin and L{\'o}pez, J Andr{\'e}s and Verreycken, Hugo and Ocalewicz, Konrad and Guyomard, Rene and Eche, Camille and Lluch, Jerome and Roques, Celine and Hu, Hongxia and Tabor, Roger and DeHaan, Patrick and Nichols, Krista M and Journot, Laurent and Parrinello, Hugues and Klopp, Christophe and Interesova, Elena A and Trifonov, Vladimir and Schartl, Manfred and Postlethwait, John and Guiguen, Yann}
}
@article {9067,
	title = {Sargassum Differentially Shapes the Microbiota Composition and Diversity at Coastal Tide Sites and Inland Storage Sites on Caribbean Islands},
	journal = {Frontiers in Microbiology},
	volume = {12},
	year = {2021},
	month = {May-10-2023},
	doi = {10.3389/fmicb.2021.701155},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2021.701155/full},
	author = {Herv{\'e}, Vincent and Lambourdi{\`e}re, Josie and Ren{\'e}-Trouillefou, Malika and Devault, Damien Alain and Pascal Jean Lopez}
}
@article {8503,
	title = {Sargassum Differentially Shapes the Microbiota Composition and Diversity at Coastal Tide Sites and Inland Storage Sites on Caribbean Islands},
	journal = {Front Microbiol},
	volume = {12},
	year = {2021},
	month = {2021},
	pages = {701155},
	abstract = {<p>Rafts of drifting pelagic that are circulating across the Atlantic Ocean are complex ecosystems composed of a large number of associated species. Upon massive stranding, they lead to various socio-environmental issues including the inflow of contaminants and human health concerns. In this study, we used metabarcoding approaches to examine the differences in both the eukaryotic- and prokaryotic-associated communities from present in two islands of the Lesser Antilles, namely Guadeloupe and Martinique. We detected significant differences in microbial community structure and composition between landing , the surrounding seawater, and from inland storage sites. In total we identified 22,214 prokaryotic and 17,679 eukaryotic OTUs. Among them, functional prediction analyses revealed a number of prokaryotes that might contribute to organic matter decomposition, nitrogen cycling and gas production, including sulfate-reducing bacteria at coastal landing sites, and methanogenic archaea at inland storage sites. We also found that Metazoan was the most abundant group in samples, with nematode clades that presented exclusive or specific richness and abundance patterns depending on their substrate. Together, these molecular inventories of the micro- and meiofauna communities provide baseline information for further characterization of trophic interactions, algal organic matter decomposition and nutrient transfers at coastal and inland storage sites.</p>
},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2021.701155},
	author = {Herv{\'e}, Vincent and Josie Lambourdi{\`e}re and Ren{\'e}-Trouillefou, Malika and Devault, Damien Alain and Pascal Jean Lopez}
}
@article {9176,
	title = {Short communication: Amphidromous goby postlarvae (penja) migration seasons and fisheries in West Sulawesi, Indonesia},
	journal = {Biodiversitas Journal of Biological Diversity},
	volume = {23},
	year = {2021},
	month = {Jan-12-2022},
	issn = {1412-033X},
	doi = {10.13057/biodiv/d230138},
	url = {https://smujo.id/biodiv/article/view/9789},
	author = {Nurjirana, Nurjirana and Burhanuddin, Andi I and Philippe Keith and Haris, Abdul and Afrisal, Muhammad}
}
@article {8453,
	title = {Small rodent communities (Muridae) in Gabonese savannas: species diversity and biogeographical affinitiesAbstract},
	journal = {Mammalia},
	volume = {85},
	year = {2021},
	month = {Jan-05-2021},
	pages = {256 - 268},
	issn = {0025-1461},
	doi = {10.1515/mammalia-2020-0079},
	url = {https://www.degruyter.com/document/doi/10.1515/mammalia-2020-0079/html},
	author = {Mboumba, Jean-Fran{\c c}ois and Herv{\'e}, Maxime R. and Guyot, V{\'e}ronique and Fr{\'e}d{\'e}ric Ysnel}
}
@article {7853,
	title = {Temporal Patterns and Intra- and Inter-Cellular Variability in Carbon and Nitrogen Assimilation by the Unicellular Cyanobacterium Cyanothece sp. ATCC 51142Data_Sheet_1.pdfData_Sheet_2.XLSX},
	journal = {Frontiers in Microbiology},
	volume = {12},
	year = {2021},
	month = {Apr-02-2021},
	doi = {10.3389/fmicb.2021.62091510.3389/fmicb.2021.620915.s00110.3389/fmicb.2021.620915.s002},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2021.620915/full},
	author = {Polerecky, Lubos and Masuda, Takako and Eichner, Meri and Rabouille, Sophie and Vancov{\'a}, Marie and Kienhuis, Michiel V. M. and Bern{\'a}t, Gabor and Bonomi-Barufi, Jose and Campbell, Douglas Andrew and Pascal Claquin and {\v C}erven{\'y}, Jan and Giordano, Mario and Kotabov{\'a}, Eva and Kromkamp, Jacco and Lombardi, Ana Teresa and Luke{\v s}, Martin and Pr{\'a}{\v s}il, Ondrej and Stephan, Susanne and Suggett, David and Zav{\v r}el, Tomas and Halsey, Kimberly H.}
}
@article {8078,
	title = {Towards a better understanding of the effects of self-shading on Fucus serratus populations},
	journal = {Peer Community In Ecology},
	year = {2021},
	month = {Feb-08-2021},
	doi = {10.24072/pci.ecology.100086},
	url = {https://ecology.peercommunityin.org/},
	author = {C{\'e}dric Hubas}
}
@article {7215,
	title = {Trophic niche of the invasive gregarious species Crepidula fornicata, in relation to ontogenic changes},
	journal = {bioRxiv},
	year = {2021},
	pages = {2020.07.30.229021},
	type = {ver. 4 peer-reviewed and recommended by Peer Community In Ecology},
	abstract = {Crepidula fornicata\&nbsp;is a common and widespread invasive gregarious species along the European coast. Among its life-history traits, well documented ontogenic changes in behavior (i.e., motile male to sessile female) suggest a potential shift in feeding strategy across its life stages. Considering the ecological significance of this species in colonized areas, understanding how conspecifics share the trophic resource is crucial. Using fatty acids (FA) and stable isotopes (SI) as complementary trophic markers, we conducted a field survey between late winter and spring to investigate the trophic niche of three ontogenic stages of\&nbsp;C. fornicata\&nbsp;that bear different sexual (male/female) and motility (motile/sessile) traits. Potential trophic sources were characterized by their pigment, FA and SI compositions and showed well discriminated compositions over the studied period. We showed that the biofilm covering\&nbsp;C. fornicata\&nbsp;shells harbored a higher biomass of primary producers (i.e., chlorophytes and diatoms) than the surrounding sediment. Over the studied period, we observed a covariation between the three ontogenic stages for both FA and SI compositions which suggest that the trophic niche of\&nbsp;C. fornicata\&nbsp;does not change significantly across its benthic life. During periods of low food availability, slipper limpets displayed an opportunistic suspension-feeding behaviour, relying on both fresh and detrital organic matter, likely coming from superficial sedimentary organic matter. However, during high food availability (i.e., spring phytoplankton bloom), all ontogenic stages largely benefited from this fresh supply of organic matter (pelagic diatoms in this case). The three ontogenic stages showed consistent differences in FA composition, and to a lesser extent in SI composition. These differences persist over time, as they originate from ontogenic physiological changes (differential growth rates, metabolic rate or gametogenesis) rather than diet discrepancies. This study revealed that multiple trophic markers allow high complementary to characterize organic matter as well as food partitioning between conspecific organisms.<br>
Recommended by PCI Ecology : https://ecology.peercommunityin.org/articles/rec?id=140},
	doi = {10.1101/2020.07.30.229021},
	url = {https://www.biorxiv.org/content/10.1101/2020.07.30.229021v1.abstract},
	author = {Androuin, Thibault and Stanislas Dubois and C{\'e}dric Hubas and Lefebvre, Gwendoline and Le Grand, Fabienne and Gauthier Schaal and Carlier, Antoine}
}
@article {8104,
	title = {Upstream/downstream food quality differences in a Caribbean Island River},
	journal = {Aquatic Ecology},
	year = {2021},
	month = {Oct-08-2021},
	issn = {1386-2588},
	doi = {10.1007/s10452-021-09887-w},
	url = {https://link.springer.com/10.1007/s10452-021-09887-w},
	author = {Frott{\'e}, Lou and Alexandre Bec and C{\'e}dric Hubas and Perri{\`e}re, Fanny and Cordonnier, S{\'e}bastien and Bezault, Etienne and Monti, Dominique}
}
@article {6975,
	title = {Advances in the use of Paris-Edinburgh presses for high pressure neutron scattering},
	journal = {Journal of Neutron Research},
	volume = {21},
	year = {2020},
	month = {May-01-2022},
	pages = {117 - 124},
	issn = {10238166},
	doi = {10.3233/JNR-190120},
	url = {https://content.iospress.com/articles/journal-of-neutron-research/jnr190120},
	author = {Klotz, S and Hansen, Th and Leli{\`e}vre-Berna, E and Amand, Louis and Maurice, J and Payre, C}
}
@article {6654,
	title = {Assessing the impact of toothed whale depredation on socio-ecosystems and fishery management in wide-ranging subantarctic fisheries},
	journal = {Reviews in Fish Biology and Fisheries},
	volume = {30},
	year = {2020},
	pages = {203-217},
	abstract = {Marine predators feeding on fisheries catches directly on the fishing gear, a behaviour termed {\textquotedblleft}depredation{\textquotedblright}, has emerged as a major human-wildlife conflict globally, often resulting in substantial socio-economic and ecological impacts. This study investigated the extent of this conflict in commercial Patagonian toothfish (Dissostichus eleginoides) fisheries across subantarctic waters where both killer whales (Orcinus orca) and sperm whales (Physeter macrocephalus) feed on toothfish caught on longline hooks. Using long-term datasets from six major fishing areas, from southern Chile to the Indian Ocean sector of the Southern Ocean, statistical models were developed to quantify the catch removals due to whale depredation interactions. The results indicated that these removals were large, totalling more than 6600 t of toothfish between 2009 and 2016 with an annual mean of 837 t [95\% CI 480{\textendash}1195 t], comprised of 317 t [232{\textendash}403 t] and 518 t [247{\textendash}790 t] removed by killer whales and sperm whales, respectively. Catch removals greatly varied between areas, with the largest estimates found at Crozet, where on average 279 t [179{\textendash}379 t] of toothfish per year, equivalent to 30\% [21{\textendash}37\%] of the total catches. Together, these findings provide metrics to assess the impacts of depredation interactions on the fishing industry, whale populations, fish stocks and associated ecosystems. With an estimated $15\&nbsp;M USD worth of fish depredated every year, this study highlights the large geographic scale and economic significance of the depredation issue and its potential to compromise the viability of some toothfish fisheries which are the primary socio-economic activity in subantarctic regions.},
	doi = {10.1007/s11160-020-09597-w},
	url = {https://link.springer.com/article/10.1007/s11160-020-09597-w},
	author = {Tixier, Paul and Burch, Paul and Massiot-Granier, F{\'e}lix and Ziegler, Philippe and Welsford, Dirk and Lea, Mary-Anne and Hindell, Mark A and Guinet, Christophe and Wotherspoon, Simon and Nicolas Gasco and Clara P{\'e}ron and Guy Duhamel and Arangio, Rhys and Tascheri, Renzo and Somhlaba, Sobahle and Arnould, John P. Y.}
}
@article {8551,
	title = {Behavioural inference from signal processing using animal-borne multi-sensor loggers: a novel solution to extend the knowledge of sea turtle ecology},
	journal = {Royal Society Open Science},
	volume = {7},
	year = {2020},
	month = {Jan-05-2020},
	pages = {200139},
	doi = {10.1098/rsos.200139},
	url = {https://royalsocietypublishing.org/doi/10.1098/rsos.200139},
	author = {Jeantet, Lor{\`e}ne and Planas-Bielsa, V{\'\i}ctor and Benhamou, Simon and Geiger, S{\'e}bastien and Martin, Jordan and Siegwalt, Flora and Lelong, Pierre and Gresser, Julie and Etienne, Denis and Hielard, Ga{\"e}lle and Arqu{\'e}, Alexandre and R{\'e}gis, Sidney and Lecerf, Nicolas and Frouin, C{\'e}dric and Benhalilou, Abdelwahab and Murgale, C{\'e}line and Maillet, Thomas and Andreani, Lucas and Campistron, Guilhem and Delvaux, H{\'e}l{\`e}ne and Guyon, Christelle and Richard, Sandrine and Lefebvre, Fabien and Aubert, Nathalie and Habold, Caroline and Le Maho, Yvon and Chevallier, Damien}
}
@article {7047,
	title = {Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo-Australian Archipelago through the iterative use of DNA-based species delimitation and specimen assignment methods},
	journal = {Evolutionary Applications},
	year = {2020},
	month = {Nov-02-2020},
	abstract = {DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA-based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo-Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA-based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA-based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo-Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.},
	keywords = {Coral Triangle, Cryptic diversity, DNA barcoding, reference library, taxonomic gap},
	issn = {1752-4571},
	doi = {10.1111/eva.12926},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12926},
	author = {Delrieu-Trottin, Erwan and Durand, Jean-Dominique and Limmon, Gino and Sukmono, Tedjo and Kadarusman and Sugeha, Hagi Yulia and Chen, Wei-Jen and Busson, Frederic and Borsa, Philippe and Dahruddin, Hadi and Sauri, Sopian and Fitriana, Yuli and Zein, Mochamad Syamsul Arifin and Hocd{\'e}, R{\'e}gis and Pouyaud, Laurent and Philippe Keith and Wowor, Daisy and Steinke, Dirk and Hanner, Robert and Hubert, Nicolas}
}
@article {7587,
	title = {Comparison of approaches for incorporating depredation on fisheries catches into Ecopath},
	journal = {ICES Journal of Marine Science},
	year = {2020},
	month = {Jan-11-2022},
	issn = {1054-3139},
	doi = {10.1093/icesjms/fsaa219},
	url = {https://academic.oup.com/icesjms/advance-article/doi/10.1093/icesjms/fsaa219/6000671},
	author = {Clavareau, Lyndsay and Marzloff, Martin P and Trenkel, Verena M and Bulman, Catherine M and Gourguet, Sophie and Le Gallic, Bertrand and Hernvann, Pierre-Yves and Clara P{\'e}ron and Nicolas Gasco and Faure, Johanna and Tixier, Paul},
	editor = {Northridge, Simon}
}
@article {7101,
	title = {A database of freshwater fish species of the Amazon Basin},
	journal = {Scientific data},
	volume = {7},
	year = {2020},
	pages = {1{\textendash}9},
	url = {https://www.nature.com/articles/s41597-020-0436-4},
	author = {J{\'e}z{\'e}quel, C{\'e}line and Tedesco, Pablo A and Bigorne, Remy and Maldonado-Ocampo, Javier A and Ortega, Hernan and Hidalgo, Max and Martens, Koen and Torrente-Vilara, Gislene and Zuanon, Jansen and Acosta, Astrid and others}
}
@article {7164,
	title = {Deciphering mollusc shell production: the roles of genetic mechanisms through to ecology, aquaculture and biomimetics.},
	journal = {Biol Rev Camb Philos Soc},
	year = {2020},
	month = {2020 Jul 31},
	abstract = {<p>Most molluscs possess shells, constructed from a vast array of microstructures and architectures. The fully formed shell is composed of calcite or aragonite. These CaCO crystals form complex biocomposites with proteins, which although typically less than 5\% of total shell mass, play significant roles in determining shell microstructure. Despite much research effort, large knowledge gaps remain in how molluscs construct and maintain their shells, and how they produce such a great diversity of forms. Here we synthesize results on how shell shape, microstructure, composition and organic content vary among, and within, species in response to numerous biotic and abiotic factors. At the local level, temperature, food supply and predation cues significantly affect shell morphology, whilst salinity has a much stronger influence across latitudes. Moreover, we emphasize how advances in genomic technologies [e.g. restriction site-associated DNA sequencing (RAD-Seq) and epigenetics] allow detailed examinations of whether morphological changes result from phenotypic plasticity or genetic adaptation, or a combination of these. RAD-Seq has already identified single nucleotide polymorphisms associated with temperature and aquaculture practices, whilst epigenetic processes have been shown significantly to modify shell construction to local conditions in, for example, Antarctica and New Zealand. We also synthesize results on the costs of shell construction and explore how these affect energetic trade-offs in animal metabolism. The cellular costs are still debated, with CaCO precipitation estimates ranging from 1-2 J/mg to 17-55 J/mg depending on experimental and environmental conditions. However, organic components are more expensive (~29 J/mg) and recent data indicate transmembrane calcium ion transporters can involve considerable costs. This review emphasizes the role that molecular analyses have played in demonstrating multiple evolutionary origins of biomineralization genes. Although these are characterized by lineage-specific proteins and unique combinations of co-opted genes, a small set of protein domains have been identified as a conserved biomineralization tool box. We further highlight the use of sequence data sets in providing candidate genes for in situ localization and protein function studies. The former has elucidated gene expression modularity in mantle tissue, improving understanding of the diversity of shell morphology synthesis. RNA interference (RNAi) and clustered regularly interspersed short palindromic repeats - CRISPR-associated protein 9 (CRISPR-Cas9) experiments have provided proof of concept for use in the functional investigation of mollusc gene sequences, showing for example that Pif (aragonite-binding) protein plays a significant role in structured nacre crystal growth and that the Lsdia1 gene sets shell chirality in Lymnaea stagnalis. Much research has focused on the impacts of ocean acidification on molluscs. Initial studies were predominantly pessimistic for future molluscan biodiversity. However, more sophisticated experiments incorporating selective breeding and multiple generations are identifying subtle effects and that variability within mollusc genomes has potential for adaption to future conditions. Furthermore, we highlight recent historical studies based on museum collections that demonstrate a greater resilience of molluscs to climate change compared with experimental data. The future of mollusc research lies not solely with ecological investigations into biodiversity, and this review synthesizes knowledge across disciplines to understand biomineralization. It spans research ranging from evolution and development, through predictions of biodiversity prospects and future-proofing of aquaculture to identifying new biomimetic opportunities and societal benefits from recycling shell products.</p>
},
	issn = {1469-185X},
	doi = {10.1111/brv.12640},
	author = {Clark, Melody S and Peck, Lloyd S and Arivalagan, Jaison and Backeljau, Thierry and Berland, Sophie and Cardoso, Joao C R and Caurcel, Carlos and Chapelle, Gauthier and De Noia, Michele and Dupont, Sam and Gharbi, Karim and Hoffman, Joseph I and Last, Kim S and Marie, Arul and Melzner, Frank and Michalek, Kati and Morris, James and Power, Deborah M and Ramesh, Kirti and Sanders, Trystan and Sillanp{\"a}{\"a}, Kirsikka and Sleight, Victoria A and Stewart-Sinclair, Phoebe J and Sundell, Kristina and Telesca, Luca and Vendrami, David L J and Ventura, Alexander and Wilding, Thomas A and Yarra, Tejaswi and Harper, Elizabeth M}
}
@article {7046,
	title = {Disentangling the taxonomy of the subfamily Rasborinae (Cypriniformes, Danionidae) in Sundaland using DNA barcodes},
	journal = {Scientific Reports},
	volume = {10},
	year = {2020},
	month = {Jan-12-2020},
	abstract = {iodiversity hotspots have provided useful geographic proxies for conservation efforts. Delineated from a few groups of animals and plants, biodiversity hotspots do not reflect the conservation status of freshwater fishes. With hundreds of new species described on a yearly basis, fishes constitute the most poorly known group of vertebrates. This situation urges for an acceleration of the fish species inventory through fast and reliable molecular tools such as DNA barcoding. The present study focuses on the freshwater fishes diversity in the Sundaland biodiversity hotspot in Southeast Asia. Recent studies evidenced large taxonomic gaps as well as unexpectedly high levels of cryptic diversity, particularly so in the islands of Java and Bali. The Cypriniformes genera Rasbora and Nemacheilus account for most of the endemic species in Java and Bali, however their taxonomy is plagued by confusion about species identity and distribution. This study examines the taxonomic status of the Rasbora and Nemacheilus species in Java, Bali and Lombok islands through DNA barcodes, with the objective to resolve taxonomic confusion and identify trends in genetic diversity that can be further used for conservation matters. Several species delimitation methods based on DNA sequences were used and confirmed the status of most species, however several cases of taxonomic confusion and two new taxa are detected. Mitochondrial sequences argue that most species range distributions currently reported in the literature are inflated due to erroneous population assignments to the species level, and further highlight the sensitive conservation status of most Rasbora and Nemacheilus species on the islands of Java, Bali and Lombok.},
	keywords = {Conservation genetics, Cryptic diversity, Population fragmentation, Southeast Asia, taxonomy},
	doi = {10.1038/s41598-020-59544-9},
	url = {http://www.nature.com/articles/s41598-020-59544-9},
	author = {Sholihah, Arni and Delrieu-Trottin, Erwan and Sukmono, Tedjo and Dahruddin, Hadi and Risdawati, Renny and Elvyra, Roza and Wibowo, Arif and Kustiati, Kustiati and Busson, Frederic and Sauri, Sopian and Nurhaman, Ujang and Dounias, Edmond and Zein, Muhamad Syamsul Arifin and Fitriana, Yuli and Utama, Ilham Vemendra and Muchlisin, Zainal Abidin and Agn{\`e}se, Jean-Fran{\c c}ois and Hanner, Robert and Wowor, Daisy and Steinke, Dirk and Philippe Keith and R{\"u}ber, Lukas and Hubert, Nicolas}
}
@article {6910,
	title = {Effect of Light Intensity and Light Quality on Diatom Behavioral and Physiological Photoprotection},
	journal = {Frontiers in Marine Science},
	volume = {7},
	year = {2020},
	pages = {203},
	abstract = {In this study, we investigated the different photoregulation responses of diatom dominated natural biofilms to different light intensities and wavelengths, over a tidal cycle in the laboratory. We compared the overall effect of light spectral quality from its light absorption (Qphar) dependent effect. Two different conditions were compared to study photoprotective strategies: sediment (migrational) and without sediment (non-migrational). Three different colors (blue, green, and red) and two light intensities (low light, LL at 210 μmol.photons.m<sup>{\textendash}2</sup>.s<sup>{\textendash}1</sup> and high light, HL at 800 μmol.photons.m<sup>{\textendash}2</sup>.s<sup>{\textendash}1</sup>) showed strong interactions in inducing behavioral and physiological photoprotection. Non-migrational biofilm non-photochemical quenching (NPQ) was much more reactive to blue HL than red HL while it did not differ in LL. We observed a biphasic NPQ response with a light threshold between 200 and 250 μmol.photons.m<sup>{\textendash}2</sup>.s<sup>{\textendash}1</sup> of Qphar that elicited the onset of physiological photoprotection. Similar HL differences were not observed in migrational biofilms due to active vertical migration movements that compensated light saturating effects. Our results showed that within migrational biofilms there was an interaction between light quality and light intensity on cell accumulation pattern at the sediment surface. This interaction led to inverse diatom accumulation patterns between blue and red light at the same intensity: LL (blue + 200.67\%, red + 123.96\%), HL (blue + 109.15\%, red + 150.34\%). These differences were largely related to the differential amount of light absorbed at different wavelengths and highlighted the importance of using wavelength standardized intensities. Different vertical migration patterns significantly affected the total pigment content measured at the surface, suggesting that cell could migrate downward more than 2 mm as a photoregulatory response. Colloidal carbohydrates patterns paralleled the vertical migration movements, highlighting their possible role in diatom motility. Our data strongly suggests a wavelength and Qphar dependent light stress threshold that triggers upward and downward movements to position microphytobenthic diatoms at their optimal depth.},
	issn = {2296-7745},
	doi = {10.3389/fmars.2020.00203},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2020.00203},
	author = {Prins, Antoine and Deleris, Paul and C{\'e}dric Hubas and Bruno Jesus}
}
@article {7539,
	title = {Exploring brain diversity in crustaceans: sensory systems of deep vent shrimpsAbstract},
	journal = {Neuroforum},
	year = {2020},
	month = {Nov-04-2021},
	issn = {0947-0875},
	doi = {10.1515/nf-2020-0009},
	url = {https://www.degruyter.com/view/journals/nf/ahead-of-print/article-10.1515-nf-2020-0009/article-10.1515-nf-2020-0009.xml},
	author = {Machon, Julia and Krieger, Jakob and Magali Zbinden and Juliette Ravaux and Harzsch, Steffen}
}
@article {7042,
	title = {Exploring community assembly among Javanese and Balinese freshwater shrimps (Atyidae, Palaemonidae) through DNA barcodes},
	journal = {Hydrobiologia},
	volume = {847},
	year = {2020},
	month = {Jan-01-2020},
	pages = {647 - 663},
	abstract = {Species proliferate through evolutionary mechanisms but coexist through ecological dynamics. As such, it might be expected that mechanisms of speciation and species maintenance jointly influence the settlement of ecological communities, a process called community assembly. Disentangling the relative contribution of evolutionary and ecological dynamics might be a difficult task, particularly so for the tropical biotas due to their extreme diversity and large knowledge gaps. Here, we explore genetic diversity and distribution of 23 freshwater shrimp species of the genera Caridina and Macrobrachium in Sundaland to examine patterns of species co-occurrence based on 1583 observations across 19 sites in Java and Bali islands. DNA-based species delimitation methods applied to 204 cytochrome oxidase I sequences detected 30 operational taxonomic units and a few cases of deep intraspecific divergence. Species co-occurrence and phylogenetic community structure show no departure from expectations under a random distribution of species in landscapes and support a lottery model of community assembly. Species age estimates expand beyond the geological settlement of Sundaland, suggesting that species proliferation and community assembly are driven by mechanisms acting at distinct spatial and temporal scales.},
	keywords = {Caridina, Dispersa, Lottery model, Macrobrachium, Phylogenetic community structure, Species delimitation},
	issn = {0018-8158},
	doi = {10.1007/s10750-019-04127-7},
	url = {http://link.springer.com/10.1007/s10750-019-04127-7},
	author = {Hernawati, Rena and Nurhaman, Ujang and Busson, Frederic and Suryobroto, Bambang and Hanner, Robert and Philippe Keith and Wowor, Daisy and Hubert, Nicolas}
}
@article {7533,
	title = {Exposure to Artificial Light at Night and the Consequences for Flora, Fauna, and Ecosystems},
	journal = {Frontiers in Neuroscience},
	volume = {14},
	year = {2020},
	month = {Apr-11-2021},
	doi = {10.3389/fnins.2020.602796},
	url = {https://www.frontiersin.org/articles/10.3389/fnins.2020.602796/full},
	author = {Falc{\'o}n, Jack and Torriglia, Alicia and Attia, Dina and Vi{\'e}not, Fran{\c c}oise and Gronfier, Claude and Behar-Cohen, Francine and Martinsons, Christophe and Hicks, David}
}
@article {6863,
	title = {The food source of Sargasso Sea leptocephali},
	journal = {Marine Biology},
	volume = {167},
	year = {2020},
	month = {Jan-05-2020},
	issn = {0025-3162},
	doi = {10.1007/s00227-020-3662-6},
	url = {http://link.springer.com/10.1007/s00227-020-3662-6},
	author = {Miller, Michael J. and Hanel, Reinhold and Eric Feunteun and Tsukamoto, Katsumi}
}
@article {7185,
	title = {Food sources, digestive efficiency and resource allocation in the sea cucumber Holothuria forskali (Echinodermata: Holothuroidea): Insights from pigments and fatty acids},
	journal = {Aquaculture Nutrition},
	volume = {26},
	year = {2020},
	month = {Apr-08-2022},
	pages = {1568-1583},
	abstract = {Various research projects in Europe and North Africa have recently intended to breed temperate holothurians to alleviate fishing pressure on natural populations. However, to date little is known about the nutritional requirements of East Atlantic and Mediterranean species. In this study, we propose a {\textquotedblleft}natural population{\textquotedblright}-oriented approach to characterize food sources, digestive efficiency and resources allocation based on the composition of pigments and fatty acids (FA) in gut contents and tis- sues (muscles, gonads and digestive tract walls) of wild individuals of the species Holothuria (Panningothuria) forskali (Delle Chiaje, 1823) sampled in Brittany (France). Our study reveals that neither green nor red algae enter the diet of H. forskali in spring and that the only fresh vegetal material found in gut contents is brown algae (very likely diatoms). The high nutritional quality of gut contents however contrasts with the detrital nature of the ingested food sources, suggesting that a trophic up- grading of organic matter occurs before digestion. In addition, unusual FA (i.e. only present in a few groups of living species) such as long-chain monounsaturated FA (especially the FA 23:1ω9) were found in large proportions in muscles and gonad and their effect on sea cucumber fitness needs further investigation.},
	keywords = {echinoderms, fatty acids, gut contents, Holothuria forskali, pigments, sea cucumbers},
	issn = {1353-5773},
	doi = {10.1111/anu.13103},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/anu.13103},
	author = {Frank David and C{\'e}dric Hubas and Laguerre, Hel{\`e}ne and Badou, Aicha and Herault, Gwen and Bordelet, Th{\'e}o and Ameziane, Nadia}
}
@article {7060,
	title = {Functional kleptoplasts intermediate incorporation of carbon and nitrogen in cells of the Sacoglossa sea slug Elysia viridis},
	journal = {Scientific Reports},
	volume = {10},
	year = {2020},
	month = {Jan-12-2020},
	abstract = {Some sacoglossan sea slugs incorporate intracellular functional algal chloroplasts, a process termed kleptoplasty. {\textquotedblleft}Stolen{\textquotedblright} chloroplasts (kleptoplasts) can remain photosynthetically active up to several months, contributing to animal nutrition. Whether this contribution occurs by means of translocation of photosynthesis-derived metabolites from functional kleptoplasts to the animal host or by simple digestion of such organelles remains controversial. Imaging of\&nbsp;13C and\&nbsp;15N assimilation over a 12-h incubation period of\&nbsp;Elysia viridis\&nbsp;sea slugs showed a light-dependent incorporation of carbon and nitrogen, observed first in digestive tubules and followed by a rapid accumulation into chloroplast-free organs. Furthermore, this work revealed the presence of\&nbsp;13C-labeled long-chain fatty acids (FA) typical of marine invertebrates, such as arachidonic (20:4n-6) and adrenic (22:4n-6) acids. The time frame and level of\&nbsp;13C- and\&nbsp;15N-labeling in chloroplast-free organs indicate that photosynthesis-derived primary metabolites were made available to the host through functional kleptoplasts. The presence of specific\&nbsp;13C-labeled long-chain FA, absent from\&nbsp;E. viridis\&nbsp;algal food, indicates animal based-elongation using kleptoplast-derived FA precursors. Finally, carbon and nitrogen were incorporated in organs and tissues involved in reproductive functions (albumin gland and gonadal follicles), implying a putative role of kleptoplast photosynthesis in the reproductive fitness of the animal host.},
	doi = {10.1038/s41598-020-66909-7},
	url = {http://www.nature.com/articles/s41598-020-66909-7},
	author = {Cruz, S{\'o}nia and LeKieffre, Charlotte and Cartaxana, Paulo and C{\'e}dric Hubas and Najet Thiney and Jakobsen, Sofie and Escrig, St{\'e}phane and Bruno Jesus and K{\"u}hl, Michael and Calado, Ricardo and Meibom, Anders}
}
@article {8285,
	title = {Giuris (Teleostei: Eleotridae) from Indonesia, with description of a new species},
	journal = {Cybium},
	volume = {44},
	year = {2020},
	pages = {331-349},
	author = {Philippe Keith and Marion Mennesson and Sauri, S and Fr{\'e}d{\'e}ric Busson and Delrieu-Trottin, Erwan and Limmon, G and Sukomono, T and Jiran and Risdawati, Renny and Dahruddin, Hadi and Hubert, Nicolas}
}
@article {8142,
	title = {The globally invasive small Indian mongoose Urva auropunctata is likely to spread with climate changeAbstract},
	journal = {Scientific Reports},
	volume = {10},
	year = {2020},
	month = {Jan-12-2020},
	doi = {10.1038/s41598-020-64502-6},
	url = {http://www.nature.com/articles/s41598-020-64502-6},
	author = {Louppe, Vivien and Leroy, Boris and Herrel, Anthony and Veron, G{\'e}raldine}
}
@article {8548,
	title = {High fidelity of sea turtles to their foraging grounds revealed by satellite tracking and capture-mark-recapture: New insights for the establishment of key marine conservation areas},
	journal = {Biological Conservation},
	volume = {250},
	year = {2020},
	month = {Jan-10-2020},
	pages = {108742},
	issn = {00063207},
	doi = {10.1016/j.biocon.2020.108742},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0006320720308004},
	author = {Siegwalt, Flora and Benhamou, Simon and Girondot, Marc and Jeantet, Lor{\`e}ne and Martin, Jordan and Bonola, Marc and Lelong, Pierre and Grand, Cl{\'e}ment and Chambault, Philippine and Benhalilou, Abdelwahab and Murgale, C{\'e}line and Maillet, Thomas and Andreani, Lucas and Campistron, Guilhem and Jacaria, Fran{\c c}ois and Hielard, Ga{\"e}lle and Arqu{\'e}, Alexandre and Etienne, Denis and Gresser, Julie and R{\'e}gis, Sidney and Lecerf, Nicolas and Frouin, C{\'e}dric and Lefebvre, Fabien and Aubert, Nathalie and Vedie, Fabien and Barnerias, Cyrille and Thieulle, Laurent and Guimera, Christelle and Bouaziz, Myriam and Pinson, Adrien and Flora, Fr{\'e}d{\'e}ric and George, Francis and Eggenspieler, Joffrey and Woignier, Thierry and All{\'e}nou, Jean-Pierre and Louis-Jean, Laurent and Chanteur, B{\'e}n{\'e}dicte and B{\'e}ranger, Christelle and Crillon, Jessica and Brador, Aude and Habold, Caroline and Le Maho, Yvon and Robin, Jean-Patrice and Chevallier, Damien}
}
@article {7469,
	title = {Highly variable taxa-specific coral bleaching responses to thermal stresses},
	journal = {Marine Ecology Progress Series},
	volume = {648},
	year = {2020},
	month = {27-08-2020},
	pages = {135 - 151},
	abstract = {Complex histories of chronic and acute sea surface temperature (SST) stresses are expected to trigger taxon- and location-specific responses that will ultimately lead to novel coral communities. The 2016 El Ni{\~n}o-Southern Oscillation provided an opportunity to examine largescale and recent environmental histories on emerging patterns in 226 coral communities distributed across 12 countries from East Africa to Fiji. Six main coral communities were identified that largely varied across a gradient of Acropora to massive Porites dominance. Bleaching intensity was taxon-specific and was associated with complex interactions among the 20 environmental variables that we examined. Coral community structure was better aligned with the historical temperature patterns between 1985 and 2015 than the 2016 extreme temperature event. Additionally, bleaching responses observed during 2016 differed from historical reports during past warm years. Consequently, coral communities present in 2016 are likely to have been reorganized by both long-term community change and acclimation mechanisms. For example, less disturbed sites with cooler baseline temperatures, higher mean historical SST background variability, and infrequent extreme warm temperature stresses were associated with Acropora-dominated communities, while more disturbed sites with lower historical SST background variability and frequent acute warm stress were dominated by stress-resistant massive Porites corals. Overall, the combination of taxon-specific responses, community-level reorganization over time, geographic variation, and multiple environmental stressors suggest complex responses and a diversity of future coral communities that can help contextualize management priorities and activities.},
	keywords = {acclimation, Adaptation, Climate Change, community structure, Geography, Stress responses},
	issn = {0171-8630},
	doi = {10.3354/meps13402},
	url = {https://www.int-res.com/abstracts/meps/v648/p135-151/},
	author = {McClanahan, T.R. and Darling, E.S. and Maina, J.M. and Muthiga, NA and D{\textquoteright}agata, S. and Leblond, J. and Arthur, R. and Jupiter, S.D. and Wilson, S.K. and Mangubhai, S. and Ussi, A.M. and Mireille M.M. Guillaume and Humphries, A.T. and Patankar, V. and Shedrawi, G. and Pagu, J. and Grimsditch, G.}
}
@article {7105,
	title = {How good is the evidence that light at night can affect human health?},
	journal = {Graefe{\textquoteright}s Archive for Clinical and Experimental Ophthalmology},
	volume = {258},
	year = {2020},
	month = {Jan-02-2020},
	pages = {231 - 232},
	issn = {0721-832X},
	doi = {10.1007/s00417-019-04579-6},
	url = {http://link.springer.com/10.1007/s00417-019-04579-6},
	author = {Hicks, David and Attia, Dina and Behar-Cohen, Francine and Carr{\'e}, Samuel and Enouf, Olivier and Jack Falcon and Gronfier, Claude and Martinsons, Christophe and Metlaine, Arnaud and Tahkamo, Leena and Torriglia, Alicia and Fran{\c c}oiseVi{\'e}not}
}
@article {7089,
	title = {How to model social-ecological systems? {\textendash} A case study on the effects of a future offshore wind farm on the local society and ecosystem, and whether social compensation matters},
	journal = {Marine Policy},
	volume = {119},
	year = {2020},
	abstract = {Models of social-ecological systems (SES) are acknowledged as an important tool to understand human-nature relations. However, many SES models fail to integrate adequate information from both the human and ecological subsystems. With an example model of a future Offshore Wind Farm development and its effects on both the ecosystem and local human population, we illustrate a method facilitating a {\textquotedblleft}balanced{\textquotedblright} SES model, in terms of including information from both subsystems. We use qualitative mathematical modeling, which allows to quickly analyze the structure and dynamics of a system without including quantitative data, and therefore to compare alternative system structures based on different understandings of how the system works. By including similar number of system variables in the two subsystems, we balanced the complexity between them. Our analyses show that this complexity is important in order to predict indirect and sometimes counterintuitive effects. We also highlight some conceptually important questions concerning social compensations during developmental projects in general, and wind farms in particular. Our results suggest that the more project holders get involved in various manner in the local socio-ecological system, the more society will benefit as a whole. Increased involvement through e.g. new projects or job-opportunities around the windfarm has the capacity to offset the negative effects of the windfarm on the local community. These benefits are enhanced when there is an overall acceptance and appropriation of the project. We suggest this method as a tool to support the decision-making process and to facilitate discussions between stakeholders, especially among local communities. {\textcopyright} The Authors},
	keywords = {Acceptance, comparative study, Complexity, Decision making, development project, Eastern English channel, environmental impact assessment, future prospect, local participation, Network, numerical model, offshore structure, participatory approach, Perception, Qualitative modeling, quantitative analysis, Renewable energy, social impact assessment, stakeholder, wind farm},
	issn = {0308597X (ISSN)},
	doi = {10.1016/j.marpol.2020.104031},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85085318224\&doi=10.1016\%2fj.marpol.2020.104031\&partnerID=40\&md5=9e69340af6d591878af0f943cd4bc347},
	author = {Haraldsson, M. and Raoux, A. and Riera, F. and Hay, J. and Dambacher, J.M. and Nathalie Niquil}
}
@article {7035,
	title = {Identification and structural characterization of the factors involved in vitellogenesis and its regulation in the African Osteoglossiforme of aquacultural interest Heterotis niloticus (Cuvier, 1829)},
	journal = {General and Comparative Endocrinology},
	year = {2020},
	month = {Jan-06-2020},
	pages = {113532},
	issn = {00166480},
	doi = {10.1016/j.ygcen.2020.113532},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0016648020302859},
	author = {Daniel Koua, N{\textquoteright}Zi and Jesus Nu{\~n}ez-Rodriguez and Orjuela, Julie and C{\'e}line Zatylny-Gaudin and Dubos, Marie-Pierre and Bernay, Beno{\^\i}t and Pontin, Julien and Corre, Erwan and Henry, Jo{\"e}l}
}
@article {7656,
	title = {In-Depth In Silico Search for Cuttlefish Antimicrobial Peptides Following Bacterial Challenge of Haemocytes},
	journal = {Marine Drugs},
	volume = {18},
	year = {2020},
	month = {Jan-09-2020},
	pages = {439},
	doi = {10.3390/md18090439},
	url = {https://www.mdpi.com/1660-3397/18/9/439},
	author = {Benoist, Louis and Houyvet, Baptiste and Henry, Jo{\"e}l and Corre, Erwan and Zanuttini, Bruno and C{\'e}line Zatylny-Gaudin}
}
@article {6961,
	title = {Influence of larval and juvenile life history on age at first maturity in two tropical amphidromous fish species},
	journal = {Ecology of Freshwater Fish},
	volume = {29},
	year = {2020},
	month = {Feb-01-2022},
	pages = {63 - 73},
	issn = {0906-6691},
	doi = {10.1111/eff.v29.110.1111/eff.12488},
	url = {https://onlinelibrary.wiley.com/toc/16000633/29/1},
	author = {Lagarde, Rapha{\"e}l and Teichert, Nils and Grondin, Henri and Hue, Thomas and Gaudin, Philippe and Ponton, Dominique}
}
@article {6916,
	title = {An integrated investigation of the effects of ocean acidification on adult abalone (Haliotis tuberculata)},
	journal = {ICES Journal of Marine Science},
	volume = {77},
	year = {2020},
	month = {Sep-01-2020},
	pages = {757 - 772},
	type = {research article},
	abstract = {Ocean acidification (OA) and its subsequent changes in seawater carbonate chemistry are threatening the survival of calcifying organisms.Due to their use of calcium carbonate to build their shells, marine molluscs are particularly vulnerable. This study investigated the effect of CO2-induced OA on adult European abalone (Haliotis tuberculata) using a multi-parameter approach. Biological (survival, growth), physiological (pHT of haemolymph, phagocytosis, metabolism, gene expression), and structural responses (shell strength, nano-indentation measurements,Scanning electron microscopy imaging of microstructure) were evaluated throughout a 5-month exposure to ambient (8.0) and low (7.7) pH conditions. During the first 2 months, the haemolymph pH was reduced, indicating that abalone do not compensate for the pH decrease of their internal fluid. Overall metabolism and immune status were not affected, suggesting that abalone maintain their vital functions when facing OA. However, after 4 months of exposure, adverse effects on shell growth, calcification, microstructure, and resistance were highlighted, whereas the haemolymph pH was compensated. Significant reduction in shell mechanical properties was revealed at pH 7.7, suggesting that OA altered the biomineral architecture leading to a more fragile shell. It is concluded that under lower pH, abalone metabolism is maintained at a cost to growth and shell integrity. This may impact both abalone ecology and aquaculture.},
	keywords = {Abalone, calcification, Gene Expression, Growth, mechanical properties, Ocean acidification, Physiology, shell microstructure},
	issn = {1054-3139},
	doi = {10.1093/icesjms/fsz257},
	url = {https://academic.oup.com/icesjms/article/77/2/757/5699268},
	author = {Avignon, Sol{\`e}ne and St{\'e}phanie Auzoux-Bordenave and Martin, Sophie and Dubois, Philippe and Badou, Aicha and Coheleach, Manon and Richard, Nicolas and Di Giglio, Sarah and Malet, Lo{\"\i}c and Servili, Arianna and Gaillard, Fanny and Huchette, Sylvain and Roussel, Sabine}
}
@article {7122,
	title = {Laminariales Host Does Impact Lipid Temperature Trajectories of the Fungal Endophyte Paradendryphiella salina (Sutherland.)},
	journal = {Marine Drugs},
	volume = {18},
	year = {2020},
	pages = {379},
	abstract = {Kelps are colonized by a wide range of microbial symbionts. Among them, endophytic fungi remain poorly studied, but recent studies evidenced yet their high diversity and their central role in algal defense against various pathogens. Thus, studying the metabolic expressions of kelp endophytes under different conditions is important to have a better understanding of their impacts on host performance. In this context, fatty acid composition is essential to a given algae fitness and of interest to food web studies either to measure its nutritional quality or to infer about its contribution to consumers diets. In the present study,\&nbsp;Paradendryphiella salina, a fungal endophyte was isolated from\&nbsp;Saccharina latissima\&nbsp;(L.) and\&nbsp;Laminaria digitata\&nbsp;(Hudson.) and its fatty acid composition was assessed at increasing salinity and temperature conditions. Results showed that fungal composition in terms of fatty acids displayed algal-dependent trajectories in response to temperature increase. This highlights that C18 unsaturated fatty acids are key components in the host-dependant acclimation of\&nbsp;P. salina\&nbsp;to salinity and temperature changes},
	keywords = {fatty acids, fungal endophytes, laminariales, Paradendryphiella salina},
	doi = {10.3390/md18080379},
	url = {https://www.mdpi.com/1660-3397/18/8/379},
	author = {Vallet, Marine and Tarik Meziane and Najet Thiney and Prado, Soizic and C{\'e}dric Hubas}
}
@article {7470,
	title = {Large geographic variability in the resistance of corals to thermal stress},
	journal = {Global Ecology and Biogeography},
	year = {2020},
	month = {May-10-2020},
	abstract = {<strong>Aim</strong>: Predictions for the future of coral reefs are largely based on thermal exposure and poorly account for potential geographic variation in biological sensitivity to thermal stress. Without accounting for complex sensitivity responses, simple climate exposure models and associated predictions may lead to poor estimates of future coral survival and lead to policies that fail to identify and implement the most appropriate interventions. To begin filling this gap, we evaluated a number of attributes of coral taxa and communities that are predicted to influence coral resistance to thermal stress over a large geographic range.<br>
<strong>Location</strong>:\&nbsp;Western Indo-Pacific and Central Indo-Pacific Ocean Realms.<br>
<strong>Major taxa studied</strong>:\&nbsp;Zooxanthellate Scleractinia {\textendash} hard corals.<br>
<strong>Methods</strong>:\&nbsp;We evaluated the geographic variability of coral resistance to thermal stress as the ratio of thermal exposure and sensitivity in 12 countries during the 2016 global-bleaching event. Thermal exposure was estimated by two metrics: (a) historical excess summer heat (cumulative thermal anomaly, CTA), and (b) a multivariate index of sea-surface temperature (SST), light, and water flow (climate exposure, CE). Sensitivity was estimated for 226 sites using coordinated bleaching observations and underwater surveys of coral communities. We then evaluated coral resistance to thermal stress using 48 generalized linear mixed models (GLMMs) to compare the potential influences of geography, historical SST variation, coral cover and coral richness.<br>
<strong>Results</strong>:\&nbsp;Geographic faunal provinces and ecoregions were the strongest predictors of coral resistance to thermal stress, with sites in the Australian, Indonesian and Fiji-Caroline Islands coral provinces having higher resistance to thermal stress than Africa-India and Japan-Vietnam provinces. Ecoregions also showed strong gradients in resistance with highest resistance to thermal stress in the western Pacific and Coral Triangle and lower resistance in the surrounding ecoregions. A more detailed evaluation of Coral Triangle and non-Coral Triangle sites found higher resistance to thermal stress within the Coral Triangle, associated with\&nbsp;c.\&nbsp;2.5 times more recent historical thermal anomalies and more centralized, warmer, and cool-water skew SST distributions, than in non-Coral Triangle sites. Our findings identify the importance of environmental history and geographic context in future predictions of bleaching, and identify some potential drivers of coral resistance to thermal stress.<br>
<strong>Main conclusions</strong>:\&nbsp;Simple threshold models of heat stress and coral acclimation are commonly used to predict the future of coral reefs. Here and elsewhere we show that large-scale responses of coral communities to heat stress are geographically variable and associated with differential environmental stresses and histories.},
	issn = {1466-822X},
	doi = {10.1111/geb.13191},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/geb.13191},
	author = {McClanahan, Timothy R. and Maina, Joseph M. and Darling, Emily S. and Mireille M.M. Guillaume and Muthiga, Nyawira A. and D{\textquoteright}agata, Stephanie and Leblond, Julien and Arthur, Rohan and Jupiter, Stacy D. and Wilson, Shaun K. and Mangubhai, Sangeeta and Ussi, Ali M. and Humphries, Austin T. and Patankar, Vardhan and Shedrawi, George and Julius, Pagu and Ndagala, January and Grimsditch, Gabriel}
}
@article {8136,
	title = {A macroscopic and stereological imaging dataset of Pleuronectes platessa ovariesAbstract},
	journal = {Scientific Data},
	volume = {7},
	year = {2020},
	month = {Jan-12-2020},
	doi = {10.1038/s41597-020-0505-8},
	url = {http://www.nature.com/articles/s41597-020-0505-8},
	author = {Sauger, Carine and Quinquis, J{\'e}r{\^o}me and Kellner, Kristell and Clothilde Heude-Berthelin and Lepoittevin, M{\'e}lanie and Elie, Nicolas and Dubroca, Laurent}
}
@article {6482,
	title = {Modelling European small pelagic fish distribution: Methodological insights},
	journal = {Ecological Modelling},
	volume = {416},
	year = {2020},
	month = {Jan-01-2020},
	pages = {108902},
	abstract = {The distribution of marine organisms is strongly influenced by climatic gradients worldwide. The ecological niche (sensu Hutchinson) of a species, i.e. the combination of environmental tolerances and resources required by an organism, interacts with the environment to determine its geographical range. This duality between niche and distribution allows climate change biologists to model potential species{\textquoteright} distributions from past to future conditions. While species distribution models (SDMs) have been intensively used over the last years, no consensual framework to parametrise, calibrate and evaluate models has emerged. Here, to model the contemporary (1990{\textendash}2017) spatial distribution of seven highly harvested European small pelagic fish species, we implemented a comprehensive and replicable numerical procedure based on 8 SDMs (7 from the Biomod2 framework plus the NPPEN model). This procedure considers critical issues in species distribution modelling such as sampling bias, pseudo-absence selection, model evaluation and uncertainty quantification respectively through (i) an environmental filtration of observation data, (ii) a convex hull based pseudo-absence selection, (iii) a multi-criteria evaluation of model outputs and (iv) an ensemble modelling approach. By mitigating environmental sampling bias in observation data and by identifying the most ecologically relevant predictors, our framework helps to improve the modelling of fish species{\textquoteright} environmental suitability. Not only average temperature, but also temperature variability appears as major factors driving small pelagic fish distribution, and areas of highest environmental suitability were found along the north-western Mediterranean coasts, the Bay of Biscay and the North Sea. We demonstrate in this study that the use of appropriate data pre-processing techniques, an often-overlooked step in modelling, increase model predictive performance, strengthening our confidence in the reliability of predictions.},
	keywords = {Convex hull, Pseudo-absence, Sampling bias, Small pelagic fish, species distribution models, uncertainty},
	issn = {03043800},
	doi = {10.1016/j.ecolmodel.2019.108902},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0304380019304107},
	author = {Schickele, Alexandre and Leroy, Boris and Gr{\'e}gory Beaugrand and Goberville, Eric and Hattab, Tarek and Patrice Francour and Virginie Raybaud}
}
@article {8523,
	title = {Needlepoint non-destructive internal sampling for precious fish specimens},
	journal = {Cybium},
	volume = {44},
	year = {2020},
	pages = {73-79},
	abstract = {In this paper, we describe a new non-damaging internal tissue sampling method for preserved collection of teleostean specimens. It was tested on freshwater pipefish, as external tissue sampling is made difficult by the lack of scales, the lack of pelvic fins, the atrophy of pectoral and anal fins. The internal tissue is detached by scratching the inside of the urogenital papilla with a fine metallic probe. 95\% ethanol is injected using a fine syringe, and then sucked back into the syringe with the detached tissue. this protocol has been tested on 6 specimens from 5 species of pipefish. For each specimen DNA was extracted from the internal tissue, a caudal fin clip, and when possible, eggs sampled from the male brooding pouch. Partial Cytochrome c oxydase I (COI) was amplified and sequenced. For each specimen, the 582 bp long sequences obtained from the internal tissue, the fin clip and the eggs were identical. These results validate this non-damaging internal tissue sampling method, which leaves absolutely no trace on the specimen. Although this method was developed on pipefish, it could be applied to other teleostean, even precious museum collection specimens such as type specimens. the aim of this paper, using the example of freshwater pipefish, is to present this method, which aims at preserving precious collection specimens while still valorising them.},
	doi = {https://doi.org/10.26028/cybium/2020-441-010},
	author = {Vincent Ha{\"y} and Marion Mennesson and Agn{\`e}s Dettai and C{\'e}line Bonillo and Philippe Keith and Clara Lord}
}
@article {7216,
	title = {Novel α-Hydroxy γ-Butenolides of Kelp Endophytes Disrupt Bacterial Cell-to-Cell Signaling},
	journal = {Frontiers in Marine Science},
	volume = {7},
	year = {2020},
	month = {Jun-07-2022},
	doi = {10.3389/fmars.2020.0060110.3389/fmars.2020.00601.s001},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2020.00601/full},
	author = {Vallet, Marine and Chong, Yee-Meng and Tourneroche, Anne and Genta-Jouve, Gregory and C{\'e}dric Hubas and Lami, Rapha{\"e}l and Gachon, Claire M. M. and Klochkova, Tatyana and Chan, Kok-Gan and Prado, Soizic}
}
@article {6915,
	title = {Ocean acidification impacts growth and shell mineralization in juvenile abalone (Haliotis tuberculata)},
	journal = {Marine Biology},
	volume = {167},
	year = {2020},
	month = {Jan-01-2020},
	type = {research article},
	abstract = {Ocean acidification is a major global driver that leads to substantial changes in seawater carbonate chemistry, with potentially serious consequences for calcifying organisms. Marine shelled molluscs are ecologically and economically important species, providing essential ecosystem services and food sources for other species. Due to their physiological characteristics and their use of calcium carbonate (CaCO3) to build their shells, molluscs are among the most vulnerable invertebrates with regard to ocean acidification, with early developmental stages being particularly sensitive to pH changes. This study investigated the effects of CO2-induced ocean acidification on juveniles of the European abalone Haliotis tuberculata, a commercially important gastropod species. Six-month-old juvenile abalones were cultured for 3 months at four pH levels (8.1, 7.8, 7.7, 7.6) representing current and predicted near-future conditions. Survival, growth, shell microstructure, thickness and strength were compared across the four pH treatments. After three months of exposure, significant reductions in juvenile shell length, weight and strength were revealed in the pH 7.6 treatment. SEM observations also revealed modified texture and porosity of the shell mineral layers as well as alterations of the periostracum at pH 7.6 which was the only treatment with an aragonite saturation state below 1. It is concluded that low pH induces both general effects on growth mechanisms and corrosion of deposited shell in H. tuberculata.<br>
This will impact both the ecological role of this species and the costs of its aquaculture.},
	keywords = {Abalone, Growth, Juvenile, Ocean acidification, Shell mineralization},
	issn = {0025-3162},
	doi = {10.1007/s00227-019-3623-0},
	url = {http://link.springer.com/10.1007/s00227-019-3623-0},
	author = {St{\'e}phanie Auzoux-Bordenave and Wessel, Nathalie and Badou, Aicha and Martin, Sophie and M{\textquoteright}Zoudi, Saloua and Avignon, Sol{\`e}ne and Roussel, Sabine and Huchette, Sylvain and Dubois, Philippe}
}
@article {7655,
	title = {-Omic Analysis of the Sepia officinalis White Body: New Insights into Multifunctionality and Haematopoiesis Regulation},
	journal = {Journal of Proteome Research},
	volume = {19},
	year = {2020},
	month = {Jul-08-2020},
	pages = {3072 - 3087},
	issn = {1535-3893},
	doi = {10.1021/acs.jproteome.0c0010010.1021/acs.jproteome.0c00100.s00110.1021/acs.jproteome.0c00100.s002},
	url = {https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00100},
	author = {Benoist, Louis and Corre, Erwan and Bernay, Beno{\^\i}t and Henry, Jo{\"e}l and C{\'e}line Zatylny-Gaudin}
}
@article {8141,
	title = {An open-source framework to model present and future marine species distributions at local scale},
	journal = {Ecological Informatics},
	volume = {59},
	year = {2020},
	month = {Jan-09-2020},
	pages = {101130},
	issn = {15749541},
	doi = {10.1016/j.ecoinf.2020.101130},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1574954120300807},
	author = {Ben Rais Lasram, Frida and Hattab, Tarek and Nogues, Quentin and Beaugrand, Gr{\'e}gory and Dauvin, Jean Claude and Halouani, Ghassen and Le Loc{\textquoteright}h, Francois and Nathalie Niquil and Leroy, Boris}
}
@article {7092,
	title = {An open-source framework to model present and future marine species distributions at local scale},
	journal = {Ecological Informatics},
	volume = {59},
	year = {2020},
	abstract = {Species Distribution Models (SDMs) are useful tools to project potential future species distributions under climate change scenarios. Despite the ability to run SDMs in recent and reliable tools, there are some misuses and proxies that are widely practiced and rarely addressed together, particularly when dealing with marine species. In this paper, we propose an open-source framework that includes (i) a procedure for homogenizing occurrence data to reduce the influence of sampling bias, (ii) a procedure for generating pseudo-absences, (iii) a hierarchical-filter approach, (iv) full incorporation of the third dimension by considering climatic variables at multiple depths and (v) building of maps that predict current and potential future ranges of marine species. This framework is available for non-modeller ecologists interested in investigating future species ranges with a user-friendly script. We investigated the robustness of the framework by applying it to marine species of the Eastern English Channel. Projections were built for the middle and the end of this century under RCP2.6 and RCP8.5 scenarios. {\textcopyright} 2020 Elsevier B.V.},
	keywords = {Climate Change, ecological modeling, English Channel, filter, future prospect, hierarchical system, marine ecosystem, sampling, scenario analysis, species diversity},
	issn = {15749541},
	doi = {10.1016/j.ecoinf.2020.101130},
	url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85086876945\&doi=10.1016\%2fj.ecoinf.2020.101130\&partnerID=40\&md5=0a5c308eac10a69880027d5de2e6fe98},
	author = {Ben Rais Lasram, F. and Hattab, T. and Nogues, Quentin and Beaugrand, G. and Dauvin, J.C. and Halouani, G. and Le Loc{\textquoteright}h, F. and Nathalie Niquil and Leroy, B.}
}
@article {7398,
	title = {Physical properties of epilithic river biofilm as a new lead to perform pollution bioassessments in overseas territories},
	journal = {Scientific Reports},
	volume = {10},
	year = {2020},
	month = {Jan-12-2020},
	abstract = {Chlordecone (CLD) levels measured in the rivers of the French West Indies were among the highest values detected worldwide in freshwater ecosystems, and its contamination is recognised as a severe health, environmental, agricultural, economic, and social issue. In these tropical volcanic islands, rivers show strong originalities as simplified food webs, or numerous amphidromous migrating species, making the bioindication of contaminations a difficult issue. The objective of this study was to search for biological responses to CLD pollution in a spatially fixed and long-lasting component of the rivers in the West Indies: the epilithic biofilm. Physical properties were investigated through complementary analyses: friction, viscosity as well as surface adhesion were analyzed and coupled with measures of biofilm carbon content and exopolymeric substance (EPS) production. Our results have pointed out a mesoscale chemical and physical reactivity of the biofilm that can be correlated with CLD contamination. We were able to demonstrate that epilithic biofilm physical properties can effectively be used to infer freshwater environmental quality of French Antilles rivers. The friction coefficient is reactive to contamination and well correlated to carbon content and EPS production. Monitoring biofilm physical properties could offer many advantages to potential users in terms of effectiveness and ease of use, rather than more complex or time-consuming analyses.},
	doi = {10.1038/s41598-020-73948-7},
	url = {http://www.nature.com/articles/s41598-020-73948-7},
	author = {Monti, Dominique and C{\'e}dric Hubas and Louren{\c c}o, Xavier and Begarin, Farid and Haouis{\'e}e, Alexandre and Romana, Laurence and Lefran{\c c}ois, Estelle and Jestin, Alexandra and Budzinski, H{\'e}l{\`e}ne and Tapie, Nathalie and Risser, Th{\'e}o and Mansot, Jean-Louis and Philippe Keith and Gros, Olivier and Pascal Jean Lopez and Lauga, B{\'e}atrice}
}
@article {7545,
	title = {Public Perceptions of Mangrove Forests Matter for Their Conservation},
	journal = {Frontiers in Marine Science},
	volume = {7},
	year = {2020},
	month = {Jul-11-2021},
	abstract = {Iconic species and landscapes attract public attention to help reverse the degradation of ecosystems and their biodiversity (Thompson and Rog, 2019); sharing their images on social media can act as a powerful way to influence perceptions and drive positive actions by the public (Wu et al., 2018). Social media platforms such as Twitter, Facebook and Instagram have been used to great effect to communicate the urgency required to halt and reverse tropical forest loss (Lamb et al., 2005) and the plight of coral reefs (Curnock et al., 2019). Ecosystems such as seagrass meadows, mudflats, and mangrove forests receive substantially less media exposure (Duarte et al., 2008). Yet these under-recognized ecosystems are hugely important for local and global societies, providing benefits such as shoreline protection (Barbier, 2016), fisheries (Carrasquilla-Henao and Juanes, 2017), carbon capture and storage (Duarte et al., 2013), alongside supporting rich marine and terrestrial biodiversity (Sievers et al., 2019;\&nbsp;Thompson and Rog, 2019) (Figure 1). Apart from these important ecosystem functions, goods and services, mangrove forests are home to a huge diversity of organisms with ecologically and evolutionarily unique adaptations to life in the intertidal zone, including vivipary and salt tolerance in trees, air-breathing in crabs and amphibious behavior in fish (mudskippers); this makes mangrove forests a dynamic and fascinating evolutionary laboratory.},
	doi = {10.3389/fmars.2020.60365110.3389/fmars.2020.603651.s001},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2020.603651/full},
	author = {Dahdouh-Guebas, Farid and Ajonina, Gordon N. and Amir, A. Aldrie and Andradi-Brown, Dominic A. and Aziz, Irfan and Balke, Thorsten and Barbier, Edward B. and Cannicci, Stefano and Cragg, Simon M. and Cunha-Lignon, Mar{\'\i}lia and Curnick, David J. and Duarte, Carlos M. and Duke, Norman C. and Endsor, Charlie and Fratini, Sara and Feller, Ilka C. and Fromard, Fran{\c c}ois and Hug{\'e}, Jean and Huxham, Mark and Kairo, James G. and Kajita, Tadashi and Kathiresan, Kandasamy and Koedam, Nico and Lee, Shing Yip and Lin, Hsing-Juh and Mackenzie, Jock R. and Mangora, Mwita M. and Marchand, Cyril and Tarik Meziane and Minchinton, Todd E. and Pettorelli, Nathalie and Polan{\'\i}a, Jaime and Polgar, Gianluca and Poti, Meenakshi and Primavera, Jurgenne and Quarto, Alfredo and Rog, Stefanie M. and Satyanarayana, Behara and Schaeffer-Novelli, Yara and Spalding, Mark and Van der Stocken, Tom and Wodehouse, Dominic and Yong, Jean W. H. and Zimmer, Martin and Friess, Daniel A.}
}
@article {7088,
	title = {Quantitative food web modeling unravels the importance of the microphytobenthos-meiofauna pathway for a high trophic transfer by meiofauna in soft-bottom intertidal food webs.},
	journal = {Ecological Modelling},
	volume = {430},
	year = {2020},
	abstract = {Meiofauna are known to have an important role on many ecological processes, although, their role in food web dynamics is often poorly understood, partially as they have been an overlooked and under sampled organism group. Here, we used quantitative food web modeling to evaluate the trophic relationship between meiofauna and their food sources and how meiofauna can mediate the carbon flow to higher trophic levels in five contrasting soft-bottom intertidal habitats (including seagrass beds, mudflats and sandflats). Carbon flow networks were constructed using the linear inverse model-Markov chain Monte Carlo technique, with increased resolution of the meiofauna compartments (i.e. biomass and feeding ecology of the different trophic groups of meiofauna) compared to most previous modeling studies. These models highlighted that the flows between the highly productive microphytobenthos and the meiofauna compartments play an important role in transferring carbon to the higher trophic levels, typically more efficiently so than macrofauna. The pathway from microphytobenthos to meiofauna represented the largest flow in all habitats and resulted in high production of meiofauna independent of habitat. All trophic groups of meiofauna, except for selective deposit feeders, had a very high dependency on microphytobenthos. Selective deposit feeders relied instead on a wider range of food sources, with varying contributions of bacteria, microphytobenthos and sediment organic matter. Ecological network analyses (e.g. cycling, throughput and ascendency) of the modeled systems highlighted the close positive relationship between the food web efficiency and the assimilation of high-quality food sources by primary consumers, e.g. meiofauna and macrofauna. Large proportions of these flows can be attributed to trophic groups of meiofauna. The sensitivity of the network properties to the representation of meiofauna in the models leads to recommending a greater attention in ecological data monitoring and integrating meiofauna into food web models. {\textcopyright} 2020 Elsevier B.V.},
	keywords = {Carbon, Carbon flow networks, deposit feeder, Deposits, Ecological network analysis, Ecological process, Ecosystems, Feeding, Feeding ecology, food web, Food web model, intertidal community, intertidal habitats, Inverse problems, linear inverse model, Linear inverse models, Markov chain Monte Carlo techniques, Markov chains, Meiofauna, Microphytobenthos, Monte Carlo methods, Phytobenthos, quantitative analysis, Sediment organic matters, soft-bottom environment, stable isotope mixing models, trophic level, Trophic relationships, Trophic structure},
	issn = {03043800 (ISSN)},
	doi = {10.1016/j.ecolmodel.2020.109129},
	author = {van der Heijden, L.H. and Nathalie Niquil and Haraldsson, M. and Asmus, R.M. and Pacella, S.R. and Graeve, M. and Rzeznik-Orignac, J. and Asmus, H. and Saint-B{\'e}at, B. and Lebreton, B.}
}
@article {6865,
	title = {Relationship between bacterial compartment and particulate organic matter (POM) in coastal systems: An assessment using fatty acids and stable isotopes},
	journal = {Estuarine, Coastal and Shelf Science},
	volume = {239},
	year = {2020},
	month = {Jan-07-2020},
	pages = {106720},
	issn = {02727714},
	doi = {10.1016/j.ecss.2020.106720},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0272771419301593},
	author = {Li{\'e}nart, Camilla and Savoye, Nicolas and Conan, Pascal and David, Val{\'e}rie and Barbier, Pierrick and Bichon, Sabrina and Charlier, Karine and Costes, Laurence and Derriennic, Herv{\'e} and Ferreira, Sophie and Gueux, Aurore and C{\'e}dric Hubas and Maria, Eric and Tarik Meziane}
}
@article {8393,
	title = {Revision of Phoxinus in France with the description of two new species (Teleostei, Leuciscidae)},
	journal = {Cybium},
	volume = {44},
	year = {2020},
	pages = {205-237},
	abstract = {French minnows of the genus Phoxinus are revised based on molecular data (COI and 12S rDNA markers), morphological characters and nuptial colouration patterns. The results delineate six groups of populations, which are recognised as species. Phoxinus phoxinus is found in eastern France in the lower and middle Rhine and Seine drainages. Phoxinus bigerri occurs in the Adour drainage and populations from the Lake Geneva basin and the upper Rhine drainage are identified as Phoxinus csikii. Phoxinus dragarum, new species, from the Garonne drainage, is distinguished by its unique nuptial colour pattern (green stripe in Z3 reaching up to the anal fin base and Z4 greenish yellow in male; Z4 green-ochre and black line below in Z5 reaching from the pectoral fin bases to the anal fin base in female), and by an incomplete lateral line generally reaching to a point in front of the anal fin base or just shortly beyond the origin of the last anal fin ray. Phoxinus fayollarum, new species, from the Loire drainage, is distinguished by its unique nuptial colour pattern (green bars in Z3 and Z4, Z4 bright yellow, and belly red in male; green stripe in Z3, Z4 yellow-pinkish, and red spots at the pectoral, pelvic and anal fin base in female). Minnows of the Rh{\^o}ne drainage are identified as Phoxinus septimaniae. We consider Pisciculus varius and Phoxynus montanus as nomen oblitum and Phoxinus septimaniae as nomen protectum, and Leuciscus obtusus as incertae sedis within Leuciscidae.},
	author = {Denys, Ga{\"e}l and Dettai, Agn{\`e}s and Persat, Henri and Daszkiewicz, Piotr and Hautecoeur, M{\'e}lyne and Philippe Keith}
}
@article {Niquil202020190326,
	title = {Shifting levels of ecological network{\textquoteright}s analysis reveals different system properties},
	journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
	volume = {375},
	number = {1796},
	year = {2020},
	note = {cited By 0},
	pages = {20190326},
	publisher = {NLM (Medline)},
	abstract = {Network analyses applied to models of complex systems generally contain at least three levels of analyses. Whole-network metrics summarize general organizational features (properties or relationships) of the entire network, while node-level metrics summarize similar organization features but consider individual nodes. The network- and node-level metrics build upon the primary pairwise relationships in the model. As with many analyses, sometimes there are interesting differences at one level that disappear in the summary at another level of analysis. We illustrate this phenomenon with ecosystem network models, where nodes are trophic compartments and pairwise relationships are flows of organic carbon, such as when a predator eats a prey. For this demonstration, we analysed a time-series of 16 models of a lake planktonic food web that describes carbon exchanges within an autumn cyanobacteria bloom and compared the ecological conclusions drawn from the three levels of analysis based on inter-time-step comparisons. A general pattern in our analyses was that the closer the levels are in hierarchy (node versus network, or flow versus node level), the more they tend to align in their conclusions. Our analyses suggest that selecting the appropriate level of analysis, and above all regularly using multiple levels, may be a critical analytical decision. This article is part of the theme issue {\textquoteright}Unifying the essential concepts of biological networks: biological insights and philosophical foundations{\textquoteright}.},
	issn = {14712970},
	doi = {10.1098/rstb.2019.0326},
	url = {https://royalsocietypublishing.org/doi/abs/10.1098/rstb.2019.0326},
	author = {Nathalie Niquil and Haraldsson, M. and Sime-Ngando, T. and Huneman, P. and Borrett, S.R.}
}
@article {7990,
	title = {A spatial food web model to investigate potential spillover effects of a fishery closure in an offshore wind farm},
	journal = {Journal of Marine Systems},
	volume = {212},
	year = {2020},
	month = {Jan-12-2020},
	pages = {103434},
	issn = {09247963},
	doi = {10.1016/j.jmarsys.2020.103434},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0924796320301305},
	author = {Halouani, Ghassen and Villanueva, Ching-Maria and Raoux, Aurore and Dauvin, Jean Claude and Ben Rais Lasram, Frida and Foucher, Eric and Le Loc{\textquoteright}h, Francois and Safi, Georges and Araignous, Emma and Jean-Paul Robin and Nathalie Niquil}
}
@article {7038,
	title = {A standardized, innovative method to characterize the structure of aquatic protein hydrolysates},
	journal = {Heliyon},
	volume = {6},
	year = {2020},
	month = {Jan-06-2020},
	pages = {e04170},
	issn = {24058440},
	doi = {10.1016/j.heliyon.2020.e04170},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2405844020310148},
	author = {Leduc, Alexandre and Fournier, Vincent and Henry, Jo{\"e}l}
}
@article {7988,
	title = {Stock assessment and management of cephalopods: advances and challenges for short-lived fishery resourcesAbstract},
	journal = {ICES Journal of Marine Science},
	year = {2020},
	month = {Mar-05-2020},
	issn = {1054-3139},
	doi = {10.1093/icesjms/fsaa038},
	url = {https://academic.oup.com/icesjms/advance-article/doi/10.1093/icesjms/fsaa038/5828442},
	author = {Arkhipkin, Alexander I and Hendrickson, Lisa C and Pay{\'a}, Ignacio and Pierce, Graham J and Roa-Ureta, Ruben H and Jean-Paul Robin and Winter, Andreas},
	editor = {Browman, Howard}
}
@article {7100,
	title = {Unmasking continental natal homing in goliath catfish from the upper Amazon},
	journal = {Freshwater Biology},
	volume = {65},
	year = {2020},
	month = {Jul-02-2020},
	pages = {325 - 336},
	issn = {0046-5070},
	doi = {10.1111/fwb.v65.210.1111/fwb.13427},
	url = {https://onlinelibrary.wiley.com/toc/13652427/65/2},
	author = {Hauser, Marilia and Duponchelle, Fabrice and Hermann, Theodore W. and Limburg, Karin E. and Castello, Leandro and Stewart, Donald J. and Torrente-Vilara, Gislene and Garc{\'\i}a-Vasquez, Aurea and Garc{\'\i}a-D{\'a}vila, Carmen and Marc Pouilly and Pecheyran, Christophe and Ponzevera, Emmanuel and Renno, Jean-Fran{\c c}ois and Moret, Arthur S. and Doria, Carolina R. C.}
}
@article {7272,
	title = {Unravelling the changes during induced vitellogenesis in female European eel through RNA-Seq: What happens to the liver?},
	journal = {PLOS ONE},
	volume = {15},
	year = {2020},
	month = {Jan-08-2021},
	pages = {e0236438},
	doi = {10.1371/journal.pone.023643810},
	url = {https://dx.plos.org/10.1371/journal.pone.0236438},
	author = {Bertolini, Francesca and J{\o}rgensen, Michelle Grace Pinto and Henkel, Christiaan and Sylvie Dufour and Tomkiewicz, Jonna}
}
@article {6911,
	title = {An Untargeted Metabolomic Approach for Microphytobenthic Biofilms in Intertidal Mudflats},
	journal = {Frontiers in Marine Science},
	volume = {7},
	year = {2020},
	pages = {250},
	abstract = {Microphytobenthic (MPB) biofilms in intertidal muddy sediments play important ecological functions in coastal ecosystems. These biofilms are mainly composed of epipelic diatoms but also prokaryotes, with a dominance of bacteria, which excrete diverse extracellular polymeric substances (EPS) according to their environment. While numerous studies have investigated the main components of these EPS matrices via traditional colorimetric assays, their fine composition, notably in specialized metabolites, is still largely unknown. A better chemical characterization of these MPB biofilms is necessary, especially regarding the numerous functions their chemical components play for microorganisms (e.g., motility, cell protection, defense mechanisms, and chemical communication), but also for coastal systems (e.g., primary production, sediment stabilization, larval settlement of some invertebrates with high economical value). An alternative approach to traditional analyses is the use of untargeted metabolomic techniques, which have not yet been applied to such MPB biofilms. The objectives of the present study were to (a) propose a protocol for metabolic fingerprinting by LC-MS and GC-MS for metabolites analysis in polar and non-polar fractions in MPB biofilms extracted from mudflat sediment and to (b) apply this protocol to a case study: the effect of light exposure on the metabolomic fingerprint of the MPB biofilm community. We compared three extraction methods using different mixes of solvents and selected a methanol/chloroform mix (1:1), which gave better results for both techniques and fractions. We then applied the selected protocol to our case study using a short-term light exposure experiment in aquaria (7 days). The present study is the first using a detailed untargeted metabolomic approach on MPB biofilms from mudflat sediment and will provide a solid baseline for further work in this area.},
	issn = {2296-7745},
	doi = {10.3389/fmars.2020.00250},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2020.00250},
	author = {Gaubert-Boussarie, Julie and Prado, Soizic and C{\'e}dric Hubas}
}
@proceedings {8401,
	title = {Upstream as a sanctuary for the French populations of catalan chub Squalius laietanus (Teleostei , Leuciscidae) threatened by the allochtonous European chub S. cephalus},
	year = {2020},
	abstract = {In the Pyr{\'e}n{\'e}es-Orientales department (France), three Mediterranean catchments (Agly, T{\^e}t and Tech) are subject to high variations in water levels during Cevenol-type events. In order to fight against the effects of these floods, dams and wiers were built along these rivers with consequences on aquatic fauna, eliminating the ecological continuum. The chub Squalius is a potamodromous fish occurring from the salmonids stream to close to the estuaries. Moreover, whereas the European chub S. cephalus was thought to be represented by a single species in France, another species, endemic to Catalonia, was described: the Catalan chub S. laietanus. However, S. cephalus was also introduced in the catchments of this area with possibly threats of hybridization. Samples from eight populations of Squalius spp coming from these rivers were genetically identified using a DNA Barcoding approach with a mitochondrial (COI) and a nuclear (RAG1) markers. Our results confirm the presence of both species in the three drainages as well as their hybridization, threatening S. laietanus by hybridization as in 70\% of Mediterrannean endemic species. There is also a downstream-upstream gradient in the presence of S. cephalus in the T{\^e}t and Tech catchments. S. laietanus seems less impacted by S. cephalus in headwaters than downstream. One of the explanations would be the numerous weirs between these areas. If the negative impacts of the absence of ecological continuum on the ichthyofauna are known and cannot be denied, these weirs might form in this case a barrier against the presence of S. cephalus in headwaters. As a consequence, S. laietanus has been evaluated as EN in the last French UICN Red List published in 2019. While the ecological parameters still need to be examined, our study brings additional information for better suited conservation actions regarding the ecological continuum.},
	author = {Rose, Morgane and Dettai, Agn{\`e}s and Lef{\`e}bvre, St{\'e}phane and Blanc, Laurence and Poulet, Nicolas and Baudier, Olivier and Hautecoeur, M{\'e}lyne and Denys, Ga{\"e}l}
}
@article {7480,
	title = {What evidence exists on the impacts of chemicals arising from human activity on tropical reef-building corals? A systematic map protocol},
	journal = {Environmental Evidence},
	volume = {9},
	year = {2020},
	month = {Aug-03-2020},
	abstract = {<strong>Background:</strong> Tropical coral reefs cover ca. 0.1\% of the Earth{\textquoteright}s surface but host an outstanding biodiversity and provide important ecosystem services to millions of people living nearby. However, they are currently threatened by both local (e.g. nutrient enrichment and chemical pollution of coastal reefs, arising from poor land management, agriculture and industry) and global stressors (mainly seawater warming and acidification, i.e. climate change). Global and local stressors interact together in different ways, but the presence of one stressor often reduces the tolerance to additional stress. While global stressors cannot be halted by local actions, local stressors can be reduced through ecosystem management, therefore minimizing the impact of climate change on reefs. To inform decision-makers, we propose here to systematically map the evidence of impacts of chemicals arising from anthropogenic activities on tropical reef-building corals, which are the main engineer species of reef ecosystems. We aim to identify the combinations of chemical and coral responses that have attracted the most attention and for which evidence can be further summarized in a systematic review that will give practical information to decision-makers.<br>
<strong>Methods:</strong> The systematic map will follow the Collaboration for Environmental Evidence Guidelines and Standards for Evidence Synthesis in Environmental Management. We will search the relevant literature using English terms combined in a tested search string in two publication databases (Web Of Science Core Collection and Scopus). The search string will combine terms describing the population (tropical reef-building corals) and the exposure (chemicals). We will supplement this literature with some more obtained through search engines, specialist websites, and through a call to local stakeholders. Titles, abstracts, and full-texts will then be successively screened using pre-defined eligibility criteria. A list of pre-defined variables will then be extracted from full-texts. Finally, a database of all studies included in the map with coded metadata will be produced. The evidence will be described in a map report with text, figures and tables, and a matrix showing the distribution and frequency of included study into types of exposure and types of outcomes will be computed to identify potential knowledge gaps and knowledge clusters.},
	keywords = {Contamination, Hermatypic, Nutrients, pollution, Scleractinian},
	doi = {10.1186/s13750-020-00203-x},
	url = {https://environmentalevidencejournal.biomedcentral.com/articles/10.1186/s13750-020-00203-x},
	author = {Ou{\'e}draogo, Dakis-Yaoba and Sordello, Romain and Brugneaux, S. and Burga, K. and Calvayrac, C. and Castelin, Magalie and Domart-Coulon, Isabelle and Ferrier-Pages, C and Mireille M.M. Guillaume and H{\'e}douin, L. and Joannot, P. and Perceval, O. and Reyjol, Yorick}
}
@article {6879,
	title = {Are shallow-water shrimps proxies for hydrothermal-vent shrimps to assess the impact of deep-sea mining?},
	journal = {Marine Environmental Research},
	volume = {151},
	year = {2019},
	month = {Jan-10-2019},
	pages = {104771},
	issn = {01411136},
	doi = {10.1016/j.marenvres.2019.104771},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0141113619303216},
	author = {Mestre, N.C. and Auguste, M. and de S{\'a}, L.C. and Fonseca, T.G. and Cardoso, C. and Brown, A. and Barthelemy, D. and Charlemagne, N. and Hauton, C. and Machon, J. and Juliette Ravaux and Bruce Shillito and Thatje, S. and Bebianno, M.J.}
}
@article {6876,
	title = {Assessing a species thermal tolerance through a multiparameter approach: the case study of the deep-sea hydrothermal vent shrimp Rimicaris exoculata},
	journal = {Cell Stress and Chaperones},
	volume = {24},
	year = {2019},
	month = {Jan-05-2019},
	pages = {647 - 659},
	issn = {1355-8145},
	doi = {10.1007/s12192-019-01003-0},
	url = {http://link.springer.com/10.1007/s12192-019-01003-0},
	author = {Juliette Ravaux and L{\'e}ger, Nelly and Hamel, G{\'e}rard and Bruce Shillito}
}
@article {7110,
	title = {AVIS et RAPPORT de l{\textquoteright}Anses relatif aux effets sur la sant{\'e} humaine et sur l{\textquoteright}environnement (faune et flore)  des syst{\`e}mes utilisant des diodes {\'e}lectroluninescentes (LED)},
	year = {2019},
	institution = {ANSES},
	address = {Maisons-Alfort},
	keywords = {Fauna, Flora, health, LED, Light-at-night, pollution},
	issn = {Saisine n{\textdegree} {\guillemotleft} 2014-SA-0253 {\guillemotright}},
	url = {https://www.anses.fr/fr/search/site/LED?iso1=fr\&iso2=en},
	author = {Attia, Dina and Behard-Cohen Francine and Carr{\'e}, Samuel and Enouf, Olivier and Jack Falcon and Gronfier, Claude and Hicks, David and Martinsons, Christophe and Metlaine, Arnaud and Tahkamo, Leena and Torriglia, Alicia and Vi{\'e}not, Fran{\c c}oise}
}
@article {6077,
	title = {Bacterial{\textendash}Fungal Interactions in the Kelp Endomicrobiota Drive Autoinducer-2 Quorum Sensing},
	journal = {Frontiers in Microbiology},
	volume = {10},
	year = {2019},
	pages = {1693},
	abstract = {<p>Brown macroalgae are an essential component of temperate coastal ecosystems and a growing economic sector. They harbor diverse microbial communities that regulate algal development and health. This algal holobiont is dynamic and achieves equilibrium via a complex network of microbial and host interactions. We now report that bacterial and fungal endophytes associated with four brown algae (Ascophyllum nodosum, Pelvetia canaliculata, Laminaria digitata, and Saccharina latissima) produce metabolites that interfere with bacterial autoinducer-2 quorum sensing, a signaling system implicated in virulence and host colonization. Additionally, we performed co-culture experiments combined to a metabolomic approach and demonstrated that microbial interactions influence production of metabolites, including metabolites involved in quorum sensing. Collectively, the data highlight autoinducer-2 quorum sensing as a key metabolite in the complex network of interactions within the algal holobiont.</p>
},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2019.01693},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2019.01693},
	author = {Tourneroche, Anne and Lami, Rapha{\"e}l and C{\'e}dric Hubas and Blanchet, Elodie and Vallet, Marine and Escoubeyrou, Karine and Paris, Alain and Prado, Soizic}
}
@article {5597,
	title = {Behavior of Antimicrobial Peptide K4 in a Marine Environment.},
	journal = {Probiotics Antimicrob Proteins},
	volume = {11},
	year = {2019},
	pages = {676-686.},
	abstract = {<p>K4 is a de novo peptide with antibacterial activity on human pathogens. It has a short sequence (14 amino acids), with a cationic N-terminal moiety and an amphipathic ɑ-helix structure. The present paper demonstrates its activity on Vibrio bacteria in a marine environment. It was found non-toxic on marine organisms including Artemia salina, Dicentrarchus labrax, and Magallana gigas at different developmental stages, but influenced the growth of unicellular organisms like microalgae, depending on the algal strain and on K4 concentration. Furthermore, an original approach coupling liquid chromatography (RP-HPLC) and mass spectrometry (MS/MS) allowed us to monitor the degradation time course of the peptide for the first time in conditions close to a hatchery environment, i.e., in the presence of oyster spat. We detected truncated forms over time, and the full K4 was gradually no longer found in these filter-feeder oysters. Finally, using an automated optical density meter, we monitored the growth of several aquatic bacteria identified as pathogenic on animals. K4 had a bactericidal effect on Aeromonas salmonicida and Vibrio splendidus LGP32 at concentrations below 45\&nbsp;μg\&nbsp;mL-1. Our results show that K4 could be an environment-friendly alternative to antibiotics, non-toxic to several marine organisms. The use of K4 would be particularly useful to decrease the bacterial load associated with food intake in the early developmental stages of marine animals reared in hatcheries</p>
},
	doi = {10.1007/s12602-018-9454-3},
	author = {Houyvet, Baptiste and Leduc, Alexandre and Cornet, Val{\'e}rie and Pontin, Julien and Bernay, Beno{\^\i}t and Jo{\"e}l Henry and Vetois, Emilie and C{\'e}line Zatylny-Gaudin}
}
@article {6933,
	title = {Biochemical composition and energy content of size-fractionated zooplankton east of the Kerguelen Islands},
	journal = {Polar Biology},
	volume = {42},
	year = {2019},
	month = {Jan-03-2019},
	pages = {603 - 617},
	issn = {0722-4060},
	doi = {10.1007/s00300-019-02458-8},
	url = {http://link.springer.com/10.1007/s00300-019-02458-8},
	author = {Harmelin-Vivien, Mireille and Bӑnaru, Daniela and Charlotte R. Dromard and Ourgaud, M{\'e}lanie and Carlotti, Fran{\c c}ois}
}
@article {6741,
	title = {Changes in marine phytoplankton diversity: Assessment under the Marine Strategy Framework Directive},
	journal = {Ecological Indicators},
	volume = {102},
	year = {2019},
	pages = {265 - 277},
	abstract = {The Marine Strategy Framework Directive requires EU Member States to assess the Good Environmental Status (GES) of their marine waters in a coherent and strategic manner. For the regional assessment of biodiversity, the OSPAR Intersessional Coordination Group of Biodiversity Assessment and Monitoring (ICG-COBAM) provides substantial advice. Through expert working groups, phytoplankton indicators are currently being developed to measure the state and the change in pelagic diversity, to quantify food web dynamics and to measure the extent of eutrophication impacts. We developed a multi-metric indicator that is compliant with the common OSPAR indicator {\textquotedblleft}Changes in plankton diversity{\textquotedblright} (PH3). The aim was to describe the structure of the phytoplankton community (alpha diversity) and to detect significant temporal changes (beta diversity) to evaluate the health of pelagic habitats. In this pilot study, we used three coastal time-series in the Western Channel and the north of the Bay of Biscay (North Atlantic, France) to test the efficiency and the performance of several existing diversity indices. We validated two alpha diversity indices, namely the Menhinick Index (D) and the Hulburt Index (δ), based on their complementary ecological information, their strong relationship with habitat characteristics, and their relative ease of interpretation for stakeholders. Temporal shifts or rate of change in community structure were detected by the Local Contributions to Beta Diversity index (LCBD; a beta diversity measure). For the years where significantly high LCBD values were found, the Importance Value Index (IVI) was calculated to potentially identify the taxa (genus) responsible for the {\textquotedblleft}unusual{\textquotedblright} community structure. For example, at the Ouest Loscolo site in 2008, an elevated LCBD (0.45) coincided with a high dominance value (Hulburt{\textquoteright}s Index) caused by the occurrence of a monospecific bloom of Leptocylindrus spp. (IVI = 73\%) in July (2.22 {\texttimes} 106 cells L-1) and October (8 {\texttimes} 106 cells L-1). In this way, PH3 informs on different aspects of phytoplankton diversity from a community to a genus level. At the current stage of development, however, PH3 acts as a {\textquotedblleft}surveillance{\textquotedblright} rather than an operational indicator since the relationship to GES is not directly tracked. In the future, by additional testing of PH3 and extending the geographical scope, the robustness of the assessment could be further determined across the OSPAR Maritime Area.},
	keywords = {community composition, Good environmental status, Indicators, Marine policy, MSFD, OSPAR, Pelagic habitat, Plankton},
	issn = {1470-160X},
	doi = {https://doi.org/10.1016/j.ecolind.2019.02.009},
	url = {http://www.sciencedirect.com/science/article/pii/S1470160X19301190},
	author = {Rombouts, I. and Nathalie Simon and Anais Aubert and T. Cariou and Eric Feunteun and Laurent Guerin and M. Hoebeke and A. McQuatters-Gollop and F. Rigaut-Jalabert and Luis Felipe Artigas}
}
@article {7104,
	title = {Commercial traceability of Arapaima spp. fisheries in the Amazon basin: can biogeochemical tags be useful?},
	year = {2019},
	author = {Santos, Roberto and Hauser, Marilia and Duponchelle, Fabrice and Carvajal, Fernando and Pecheyran, Christophe and B{\'e}rail, Sylvain and Marc Pouilly and Pereira, Luciana}
}
@article {6014,
	title = {Contrasting biodiversity of eel larvae across the central Indian Ocean subtropical gyre},
	journal = {Deep Sea Research Part II: Tropical Studies in Oceanography},
	volume = {161},
	year = {2019},
	pages = {120{\textendash}131},
	abstract = {The unique semi-enclosed Indian Ocean basin includes large Mascarene\&nbsp;Plateau\&nbsp;banks, offshore\&nbsp;coral-reef\&nbsp;islands, seasonal equatorial current jets, and cross-basin westward South Equatorial Current (SEC) flow, making it interesting for studying long larval-duration eel larvae (leptocephali) and regional eel biodiversity. Three surveys for\&nbsp;leptocephali\&nbsp;(in 2003, 2006, 2010) included sampling west of the Mascarene Plateau (west), a major survey and other stations off Sumatra and Java (east), and 2 cross-basin transects across the SEC. The highest numbers of leptocephali species were observed along Sumatra (2003: ~143 species; 2006: 72 species) and south of Java (2010: 69), with intermediate numbers being collected in the western Indian Ocean (2006: 71; 2010: 53) compared to low numbers in the hydrographically variable offshore zones (2006, 2010: 3{\textendash}27). The larger\&nbsp;continental shelf\&nbsp;areas along Sumatra including the Mentawai Islands provide more coral reef and other habitats for species such as congrid, muraenid, ophichthid, and chlopsid eels compared to the Mascarene Plateau banks. Some larvae in these areas get transported offshore, but the majority of offshore larvae were of Nemichthyidae and Serrivomeridae mesopelagic eels that were spawning across the basin. Habitat differences between the southern Mascarene Plateau and Sumatra and southern Indonesia along the edge of the high biodiversity Coral Triangle likely explain the higher biodiversity of eel larvae observed along the western side of the basin, which for the Congridae and Ophichthidae included more species than observed previously within the central Indonesian Seas. In addition to local spawning, seasonal currents likely transport larger larvae towards Sumatra from the north or west and larvae may enter the basin from the Indonesian\&nbsp;Throughflow\&nbsp;in the east, but it is unknown if equatorial jets or the SEC can transport larvae across the whole basin.},
	doi = {doi.org/10.1016/j.dsr2.2018.02.012},
	url = {https://www.sciencedirect.com/science/article/pii/S0967064517304393},
	author = {Miller, Michael J and Wouthuyzen, Sam and Eric Feunteun and Aoyama, Jun and Watanabe, Shun and Syahailatua, Augy and Kuroki, Mari and Robinet, Tony and Hagihara, Seishi and Otake, Tsuguo and others}
}
@article {6688,
	title = {Correlations between broad-scale taxonomic and genetic differentiations suggest a dominant imprint of historical processes on beta diversities},
	journal = {Journal of Biogeography},
	volume = {46},
	year = {2019},
	month = {Jan-05-2020},
	pages = {1083 - 1095},
	issn = {0305-0270},
	doi = {10.1111/jbi.2019.46.issue-510.1111/jbi.13559},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jbi.13559},
	author = {Robuchon, Marine and Leroy, Boris and J{\'e}z{\'e}quel, C{\'e}line and Hugueny, Bernard}
}
@article {7106,
	title = {Correspondence: An appraisal of the effects on human health and the environment of using light-emitting diodes},
	journal = {Lighting Research \& Technology},
	volume = {51},
	year = {2019},
	month = {Jan-12-2019},
	pages = {1275 - 1276},
	issn = {1477-1535},
	doi = {10.1177/1477153519891878},
	url = {http://journals.sagepub.com/doi/10.1177/1477153519891878},
	author = {Martinsons, Christophe and Attia, Dina and Behar-Cohen, Francine and Carr{\'e}, Samuel and Enouf, Olivier and Jack Falcon and Gronfier, Claude and Hicks, David and Metlaine, Arnaud and Tahkamo, Leena and Torriglia, Alicia and Vi{\'e}not, Fran{\c c}oise}
}
@article {6693,
	title = {Current and future climatic regions favourable for a globally introduced wild carnivore, the raccoon Procyon lotor},
	journal = {Scientific Reports},
	volume = {9},
	year = {2019},
	month = {Jan-12-2019},
	doi = {10.1038/s41598-019-45713-y},
	url = {https://www.nature.com/articles/s41598-019-45713-y},
	author = {Louppe, Vivien and Leroy, Boris and Herrel, Anthony and Veron, G{\'e}raldine}
}
@article {6737,
	title = {Distribution of anguillid leptocephali and possible spawning areas in the South Pacific Ocean},
	journal = {Progress in Oceanography},
	volume = {180},
	year = {2019},
	pages = {102234},
	abstract = {Seven South Pacific anguillid eel species live from New Guinea to French Polynesia, but their spawning areas and life histories are mostly unknown despite previous sampling surveys. A July{\textendash}October 2016 research cruise was conducted to study the spawning areas and times, and larval distributions of South Pacific anguillid eels, which included a short 155{\textdegree}E station-line northeast of New Guinea and five long transects (5{\textendash}25{\textdegree}S, 160{\textdegree}E{\textendash}140{\textdegree}W) crossing the South Equatorial (SEC) and other currents. This survey collected nearly 4000 anguilliform leptocephali at 179 stations using an Isaacs-Kidd Midwater Trawl accompanied by 104 CTD casts. Based on morphometric observations and DNA sequencing, 74 anguillid leptocephali were collected, which in the southern areas included 29 larvae of six species: Anguilla bicolor pacifica, A. marmorata, A. australis, A. reinhardtii, A. megastoma,and A. obscura (all anguillid species of the region were caught except A. dieffenbachii). Small A. australis (9.0{\textendash}16.8\&nbsp;mm) and A. reinhardtii (12.4, 12.5\&nbsp;mm) leptocephali were collected south of the Solomon Islands, other A. australis (10.8{\textendash}12.0\&nbsp;mm) larvae were caught northwest of Fiji along with an A. obscura (20.0\&nbsp;mm) larva, and an A. marmorata (7.8\&nbsp;mm) larva was collected near Samoa. Considering collection sites, larval ages from otolith analysis, and westward SEC drift, multiple spawning locations occurred from south of the Solomon Islands and the Fiji area (16{\textendash}20\&nbsp;days old larvae) to near Samoa (19\&nbsp;days old larva) during June and July in areas where high-salinity Subtropical Underwater (STUW, 150\&nbsp;m depth) and the warm, low-salinity surface Fresh Pool were present. Five long hydrographic sections showed the strong Fresh Pool in the west and the STUW formation area in the east.},
	keywords = {Early life history, Freshwater eels, Migration, otolith, South Pacific, Spawning},
	issn = {0079-6611},
	doi = {https://doi.org/10.1016/j.pocean.2019.102234},
	url = {http://www.sciencedirect.com/science/article/pii/S0079661119304148},
	author = {Mari Kuroki and Michael J. Miller and Eric Feunteun and Pierre Sasal and Timothy Pikering and Yu-San Han and Elisabeth Faliex and Anthony Acou and Aur{\'e}lie Dessier and Robert Schabetsberger and Shun Watanabe and Tatsuya Kawakami and Hiroaki Onda and Takatoshi Higuchi and Aya Takeuchi and Madoka Shimizu and Chinthaka A. Hewavitharane and Seishi Hagihara and Terumasa Taka and Shingo Kimura and Noritaka Mochioka and Tsuguo Otake and Katsumi Tsukamoto}
}
@proceedings {6079,
	title = {Ecoregionalisation and conservation of benthic communities in the French exclusive economic zone of Kerguelen},
	volume = {1},
	year = {2019},
	month = {11/06/2019},
	pages = {pp 413},
	publisher = {Australian Antarctic Division},
	edition = {Australian Antarctic Division, Kingston, Tasmania, Australia},
	address = {Kingston, Tasmania, Australia},
	abstract = {<p>The deep-sea benthic ecosystems of the French Kerguelen exclusive economic zone remain poorly understood. To address benthic conservation issues, the authors recently contributed expert knowledge to guide the recent extension of the Marine Reserve of the {\textquoteleft}Terres australes fran{\c c}aises{\textquoteright}. In this new study, we propose a benthic ecoregionalisation of the northern Kerguelen Plateau based on a measurable and repeatable methodology that relies on the generalised dissimilarity modelling technique. Data of macro-epibenthic invertebrate species from the POKER 2 (2010) fish stock assessment survey have been used to compute the models. Our results allow us (i) to characterise and map benthic landscape units based on assemblages of marine invertebrates pooled by taxa and life-history traits, (ii) to highlight the environmental drivers of the spatial distribution of benthic assemblages, (iii) to assess the relevance of the CCAMLR{\textquoteright}s vulnerable marine ecosystems bioindicator taxa, and (iv) to assess the effectiveness of {\textquoteleft}strictly protected areas{\textquoteright} of the new Marine Reserve for the conservation of deep-sea benthic ecosystems.</p>
},
	keywords = {benthic ecosystems, benthos, deep-sea, ecoregionalisation, kerguelen, poker},
	url = {http://heardisland.antarctica.gov.au/__data/assets/pdf_file/0009/229158/34-Martin-FullMS.pdf},
	author = {Martin, Alexis},
	editor = {Trouslard, Emmanuelle and Hautecoeur, M{\'e}lyne and Blettery, Jonathan and Moreau, Camille and Sauc{\`e}de, Thomas and Ameziane, Nadia and Guy Duhamel and Eleaume, Marc}
}
@article {8554,
	title = {Fine scale geographic residence and annual primary production drive body condition of wild immature green turtles ( <i>Chelonia mydas</i>               ) in Martinique Island (Lesser Antilles)},
	journal = {Biology Open},
	year = {2019},
	month = {Jan-01-2019},
	doi = {10.1242/bio.048058},
	url = {https://journals.biologists.com/bio/article/doi/10.1242/bio.048058/266150/Fine-scale-geographic-residence-and-annual-primary},
	author = {Bonola, Marc and Girondot, Marc and Robin, Jean-Patrice and Martin, Jordan and Siegwalt, Flora and Jeantet, Lor{\`e}ne and Lelong, Pierre and Grand, Cl{\'e}ment and Chambault, Philippine and Etienne, Denis and Gresser, Julie and Hielard, Ga{\"e}lle and Alexandre, Arqu{\'e} and R{\'e}gis, Sidney and Nicolas, Lecerf and Frouin, C{\'e}dric and Lefebvre, Fabien and Sutter, Emmanuel and Vedie, Fabien and Barnerias, Cyrille and Laurent, Thieulle and Bordes, Robinson and Guimera, Christelle and Aubert, Nathalie and Bouaziz, Myriam and Pinson, Adrien and Fr{\'e}d{\'e}ric, Flora and Matthieu, Duru and Benhalilou, Abdelwahab and C{\'e}line, Murgale and Maillet, Thomas and Andreani, Lucas and Campistron, Guilhem and Sikora, Maxym and Rateau, Fabian and Francis, George and Joffrey, Eggenspieler and Woignier, Thierry and All{\'e}nou, Jean-Pierre and Louis-Jean, Laurent and Chanteur, B{\'e}n{\'e}dicte and B{\'e}ranger, Christelle and Crillon, Jessica and Brador, Aude and Habold, Caroline and Le Maho, Yvon and Chevallier, Damien}
}
@article {5844,
	title = {Functional traits unravel temporal changes in fish biomass production on artificial reefs},
	journal = {Marine Environmental Research},
	volume = {145},
	year = {2019},
	pages = {137-146},
	abstract = {<p>Artificial reefs (ARs) are deployed worldwide as they are expected to support fisheries management. While the underlying mechanisms remain widely debated, production was recently determined as the most probable cause of increases in fish biomass. Changes in fish biomass in a temperate AR system were investigated from December 2008 to November 2015 by considering seven distinct functional groups, and isotopic functional indices were used to identify how these changes may have affected organic matter (OM) fluxes. Contrasting patterns of change were observed between functional trophic groups, highlighting that combining the biomass of all species present in a community is inappropriate for assessing AR-induced effects. Benthic sedentary species predominated (\&gt;75\% of the total biomass) through massive production, with a 68-fold increase in mean biomass over the study period. Mobile species tended to vary seasonally, suggesting only a slight influence of AR. Zooplanktivores biomass decreased over the 6-year period, as a possible result of changes in environmental conditions. Isotopic indices helped to reveal both the community maturation and the importance of local OM sources not only in supporting fish biomass production but also in attracting pelagic species. Our results corroborate that production and attraction are two extremes of a range of contrasting patterns and highlight the importance of considering the specific responses of functional components of fish communities to accurately describe changes in AR functioning. Functional attributes such as trophic traits, habitat use and dispersal abilities must not be overlooked as they modulate fish species responses to the deployment of man-made rocky substrates.</p>
},
	keywords = {Artificial reefs, Fish biomass production, Isotopic functional indices, Mediterranean sea},
	issn = {0141-1136},
	doi = {https://doi.org/10.1016/j.marenvres.2019.02.018},
	url = {http://www.sciencedirect.com/science/article/pii/S0141113618307979},
	author = {Cresson, Pierre and Le Direach, Laurence and Rouanet, Elodie and Goberville, Eric and Astruch, Patrick and Ourgaud, M{\'e}lanie and Mireille Harmelin-Vivien}
}
@article {6694,
	title = {Global biogeographical regions of freshwater fish species},
	journal = {Journal of Biogeography},
	volume = {46},
	year = {2019},
	month = {Jun-11-2019},
	pages = {2407 - 2419},
	issn = {0305-0270},
	doi = {10.1111/jbi.13674},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jbi.13674},
	author = {Leroy, Boris and Dias, Murilo S. and Giraud, Emilien and Hugueny, Bernard and J{\'e}z{\'e}quel, C{\'e}line and Leprieur, Fabien and Oberdorff, Thierry and Pablo Tedesco}
}
@article {6047,
	title = {The global geography of fish diadromy modes},
	journal = {Global Ecology and Biogeography},
	year = {2019},
	abstract = {<p class="rtejustify"><strong>Aim:</strong> Geographical gradients in resource production are likely to translate into macroecological patterns in the biodiversity of migratory organisms, but few studies have addressed this question at a global scale. Here, we tested a hypothesis based on uncoupled latitudinal gradients in marine and freshwater primary productivities aimed at explaining where (e.g., at which latitude) and at which stage of the life cycle (larvae, amphidromy; juvenile, catadromy; or adult, anadromy) migration from ocean to freshwater occurs (diadromy).</p>

<p class="rtejustify"><strong>Location: </strong>Global.</p>

<p class="rtejustify"><strong>Time period:</strong> Current.</p>

<p class="rtejustify"><strong>Major taxa studied: </strong>Fishes.</p>

<p class="rtejustify"><strong>Methods:</strong> We modelled, using multinomial regressions, the proportion of catadromous, anadromous and amphidromous species in 994 river basins as a function of freshwater and marine net primary productivities (NPP; in milligrams of carbon per square metre per day) and additional biotic and abiotic variables. Using data extracted from the Global Biodiversity Information Facility (GBIF) database, we tested whether diadromous, catadromous and amphidromous species differed with respect to the NPP of their marine and freshwater occurrences.</p>

<p class="rtejustify"><strong>Results: </strong>Among diadromous species, anadromous species are present in higher proportions when conditions for growth are more favourable in the sea (higher productivity, higher temperature and lower number of competitors) than in freshwaters. The model reconstructs the latitudinal pattern observed in the proportion of anadromous species, including an asymmetry between the Northern and Southern Hemispheres. According to GBIF occurrences, the ratio of marine over freshwater productivity is higher for anadromous species compared with catadromous and amphidromous species.</p>

<p class="rtejustify"><strong>Main conclusions:</strong> Our results support the hypothesis stating that migration between ocean and freshwater occurs by choosing the biome that optimizes pre-reproductive growth and is one more example of the importance of primary productivity in shaping large-scale community patterns. This result suggests that some diadromous fish populations and species may suffer from anticipated climate change if interbiome productivity gradients are affected.</p>
},
	keywords = {amphidromy, anadromy, Biogeography, catadromy, dispersal, GBIF database, Last Glacial Maximum, latitudinal gradient, Migration, Species richness},
	doi = {DOI: 10.1111/geb.12931},
	author = {Chalant, Ana{\"\i}s and J{\'e}z{\'e}quel, C{\'e}line and Philippe Keith and Bernard Hugueny}
}
@conference {6682,
	title = {Important readjustments in the biomass and distribution of groundfish species in the northern part of the Kerguelen Plateau and Skiff Bank.},
	booktitle = {The Kerguelen Plateau: marine ecosystem and fisheries},
	year = {2019},
	pages = {135-184},
	publisher = {Australian Antarctic Division},
	organization = {Australian Antarctic Division},
	edition = {Welsford, D., J. Dell and G. Duhamel (Eds)},
	address = { Kingston, Tasmania, Australia.},
	isbn = {978-1-876934-30-9},
	url = {http://heardisland.antarctica.gov.au},
	author = {Guy Duhamel and Clara P{\'e}ron and Sin{\`e}gre, Romain and Charlotte Chazeau and Nicolas Gasco and M{\'e}lyne Hautecoeur and Martin, Alexis and Durand, Isabelle and Causse, Romain}
}
@article {6888,
	title = {Is It First the Egg or the Shrimp? {\textendash} Diversity and Variation in Microbial Communities Colonizing Broods of the Vent Shrimp Rimicaris exoculata During Embryonic Development},
	journal = {Frontiers in Microbiology},
	volume = {10},
	year = {2019},
	month = {May-04-2020},
	doi = {10.3389/fmicb.2019.00808},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2019.00808/full},
	author = {Methou, Pierre and Hern{\'a}ndez-{\'A}vila, Ivan and Aube, Johanne and Cueff-Gauchard, Val{\'e}rie and Gayet, Nicolas and Amand, Louis and Bruce Shillito and Pradillon, Florence and Cambon-Bonavita, Marie-Anne}
}
@article {5971,
	title = {The long time adaptation of coelacanths to moderate deep water: reviewing the evidences},
	journal = {Bulletin of Kitakyushu Museum of Natural History and Human History. Series A: Natural History},
	volume = {17},
	year = {2019},
	pages = {29-35},
	author = {Cupello, C and Cl{\'e}ment, Ga{\"e}l and Fran{\c c}ois J Meunier and Herbin, Marc and Yoshikata Yabumoto and Brito, Paulo M.}
}
@article {8402,
	title = {Minnow, Minnow, new and old, who is the fairest of them all: the taxonomical review of the French minnows Phoxinus spp. (Actinopterygii, Leuciscidae)},
	journal = {Frontiers in Marine Science},
	volume = {6},
	year = {2019},
	month = {Jan-01-2019},
	doi = {10.3389/conf.fmars.2019.07.00102},
	url = {http://www.frontiersin.org/Community/AbstractDetails.aspx?ABS_DOI=10.3389\%2fconf.fmars.2019.07.00102},
	author = {Denys, Ga{\"e}l and Dettai, Agn{\`e}s and Persat, Henri and Hautecoeur, M{\'e}lyne and Philippe Keith}
}
@article {6816,
	title = {Neuroanatomy of a hydrothermal vent shrimp provides insights into the evolution of crustacean integrative brain centers},
	journal = {eLife},
	volume = {8},
	year = {2019},
	month = {Jun-08-2019},
	abstract = {Alvinocaridid shrimps are emblematic representatives of the deep hydrothermal vent<br />
fauna at the Mid-Atlantic Ridge. They are adapted to a mostly aphotic habitat with extreme<br />
physicochemical conditions in the vicinity of the hydrothermal fluid emissions. Here, we<br />
investigated the brain architecture of the vent shrimp Rimicaris exoculata to understand possible<br />
adaptations of its nervous system to the hydrothermal sensory landscape. Its brain is modified from<br />
the crustacean brain ground pattern by featuring relatively small visual and olfactory neuropils that<br />
contrast with well-developed higher integrative centers, the hemiellipsoid bodies. We propose that<br />
these structures in vent shrimps may fulfill functions in addition to higher order sensory processing<br />
and suggest a role in place memory. Our study promotes vent shrimps as fascinating models to<br />
gain insights into sensory adaptations to peculiar environmental conditions, and the evolutionary<br />
transformation of specific brain areas in Crustacea.},
	doi = {10.7554/eLife.47550.001},
	url = {https://elifesciences.org/articles/47550},
	author = {Machon, Julia and Krieger, Jakob and Meth, Rebecca and Magali Zbinden and Juliette Ravaux and Montagn{\'e}, Nicolas and Chertemps, Thomas and Harzsch, Steffen}
}
@article {Meddeb201967,
	title = {A new type of plankton food web functioning in coastal waters revealed by coupling Monte Carlo Markov chain linear inverse method and ecological network analysis},
	journal = {Ecological Indicators},
	volume = {104},
	year = {2019},
	note = {cited By 0},
	pages = {67-85},
	publisher = {Elsevier B.V.},
	abstract = {Plankton food webs (PFW) typology is based on different categories of functioning, according to the dominant processes and the role played by heterotrophic bacteria, small vs large phytoplankton, and small vs large zooplankton. Investigating the structure and the function of planktonic food webs in two SW Mediterranean waters (inshore and marine sites) at four seasons, using inverse (LIM-MCMC) and ecological network (ENA) analyses, we identified a new type of food web, called the {\textquotedblleft}bacterial multivorous food web{\textquotedblright}. This food web adds to the conventional trophic continuum as previously reported. The {\textquotedblleft}bacterial multivorous food web{\textquotedblright} present in winter showed the lowest primary production among seasons, but highest bacterial production. Several food web ratios characterized this new typology e.g. picophytoplankton net primary production to total primary production varied from 0.20 to 0.28; bacterial to primary production ratio is higher than values reported in global scale (≅1); bacterial net production to the potential protozoan prey net production was high (\&gt;0.2). In this special food web, carbon was mostly recycled, with a moderate fraction channeled to deep waters, which lead to a higher retention of carbon inside the ecosystem. This winter PFW also seemed to be the most organized, specialized, stable and mature, as related to common interpretations of ENA. The spring was characterized by herbivorous food web, with highest activity coinciding with low stability. Although less usual, the herbivorous pathway was also observed during summer, in inshore waters. The autumn food webs, which functioned as multivorous or microbial food webs, appeared to be stable and mature. Finally, our study demonstrates the usefulness of food web models derived ratios combined with ecological network analysis indices to conduct evaluation of the structure and functioning of ecosystems and potentially to support management decisions in marine environment. {\textcopyright} 2019},
	keywords = {Bacteria (microorganisms), bacterium, Carbon, Chemical contamination, coastal water, Coastal waters, ecological modeling, Ecology, ecosystem function, Ecosystems, Electric network analysis, Food microbiology, food web, Food web model, Food webs, inverse analysis, Inverse problems, Markov chain, Markov processes, Mediterranean sea, Monte Carlo analysis, Monte Carlo methods, net primary production, network analysis, Phytoplankton, picoplankton, Plankton, Protozoa, protozoan, Seasonal variation, trophic status, Trophic structure},
	issn = {1470160X},
	doi = {10.1016/j.ecolind.2019.04.077},
	url = {https://www.sciencedirect.com/science/article/abs/pii/S1470160X19303243},
	author = {Meddeb, M. and Nathalie Niquil and Grami, B. and Mejri, K. and Haraldsson, M. and Chaalali, A. and Pringault, O. and Hlaili, A.S.}
}
@article {8555,
	title = {Population recovery changes population composition at a major southern Caribbean juvenile developmental habitat for the green turtle, Chelonia mydasAbstract},
	journal = {Scientific Reports},
	volume = {9},
	year = {2019},
	month = {Jan-12-2019},
	doi = {10.1038/s41598-019-50753-5},
	url = {http://www.nature.com/articles/s41598-019-50753-5},
	author = {van der Zee, Jurjan P. and Christianen, Marjolijn J. A. and Nava, Mabel and Velez-Zuazo, Ximena and Hao, Wensi and B{\'e}rub{\'e}, Martine and van Lavieren, Hanneke and Hiwat, Michael and Berzins, Rachel and Chevalier, Johan and Chevallier, Damien and Lankester, Marie-Cl{\'e}lia and Bjorndal, Karen A. and Bolten, Alan B. and Becking, Leontine E. and Palsb{\o}ll, Per J.}
}
@article {7043,
	title = {Preliminary note on the morphological characters of <i>penja</i>               (amphidromous goby postlarvae) in West Sulawesi and Gorontalo Bay},
	journal = {IOP Conference Series: Earth and Environmental Science},
	volume = {370},
	year = {2019},
	month = {Jan-11-2019},
	pages = {012007},
	abstract = {Penjais the local name for the postlarvae of fish belonging to the Gobioidei, whose appearance at certain times is an amphidromous migration process from the sea to rivers. This group of fish is generally referred to as amphidromous gobies. This study aimed toreveal some facts related to the species diversity of penja based on morphological characteristics. The study was  conducted  from  October  2017  to  March  2019  in  West  Sulawesi  and  Gorontalo  Bay, Indonesia.  Amphidromous  goby  samples  at  the penja(postlarval) stage  were  obtained  from fishermen{\textquoteright}s  catches  and from  traditional markets  in  each  location.  The  samples  obtained  were measured  and  described  based  on  morphological  differences.  The  total  length  of  the  sampled penja ranged  from  18  mm  to  58  mm.  All  penja  were  identified  as  belonging  to  one  of  two families, the Gobiidae and Eleotridae. Although the species obtained from the waters of West Sulawesi  and  Gorontalo  Bay  were  similar,  there  were  variations  in  species  composition (relative  abundance)  based  on  observed  morphology  of penja postlarvae  from  these  two locations.},
	doi = {10.1088/1755-1315/370/1/012007},
	url = {https://iopscience.iop.org/article/10.1088/1755-1315/370/1/012007},
	author = {Nurjirana and Haris, A and Sahami, F M and Philippe Keith and Burhanuddin, A I}
}
@article {6960,
	title = {Reproductive biology of a small amphidromous shrimp Atyoida serrata on Reunion Island, south-west Indian Ocean},
	journal = {Limnologica},
	volume = {76},
	year = {2019},
	month = {Jan-05-2019},
	pages = {41 - 47},
	issn = {00759511},
	doi = {10.1016/j.limno.2019.03.005},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0075951118301579},
	author = {Hoarau, Pierre E and Courtecuisse, Emilie and Treilhes, Camille RM and Lagarde, Rapha{\"e}l and Teichert, Nils and Valade, Pierre B}
}
@article {7041,
	title = {Revisiting species boundaries and distribution ranges of Nemacheilus spp. (Cypriniformes: Nemacheilidae) and Rasbora spp. (Cypriniformes: Cyprinidae) in Java, Bali and Lombok through DNA barcodes: implications for conservation in a biodiversity hotspot},
	journal = {Conservation Genetics},
	volume = {20},
	year = {2019},
	month = {Jan-06-2019},
	pages = {517 - 529},
	abstract = {Biodiversity hotspots have provided useful geographic proxies for conservation efforts. Delineated from a few groups of
animals and plants, biodiversity hotspots do not reflect the conservation status of freshwater fishes. With hundreds of new
species described on a yearly basis, fishes constitute the most poorly known group of vertebrates. This situation urges for an
acceleration of the fish species inventory through fast and reliable molecular tools such as DNA barcoding. The present study
focuses on the freshwater fishes diversity in the Sundaland biodiversity hotspot in Southeast Asia. Recent studies evidenced
large taxonomic gaps as well as unexpectedly high levels of cryptic diversity, particularly so in the islands of Java and Bali.
The Cypriniformes genera Rasbora and Nemacheilus account for most of the endemic species in Java and Bali, however their
taxonomy is plagued by confusion about species identity and distribution. This study examines the taxonomic status of the
Rasbora and Nemacheilus species in Java, Bali and Lombok islands through DNA barcodes, with the objective to resolve
taxonomic confusion and identify trends in genetic diversity that can be further used for conservation matters. Several species
delimitation methods based on DNA sequences were used and confirmed the status of most species, however several cases
of taxonomic confusion and two new taxa are detected. Mitochondrial sequences argue that most species range distributions
currently reported in the literature are inflated due to erroneous population assignments to the species level, and further
highlight the sensitive conservation status of most Rasbora and Nemacheilus species on the islands of Java, Bali and Lombok.},
	keywords = {Conservation genetics, Cryptic diversity, Population fragmentation, Southeast Asia, taxonomy},
	issn = {1566-0621},
	doi = {10.1007/s10592-019-01152-w},
	url = {http://link.springer.com/10.1007/s10592-019-01152-w},
	author = {Hubert, Nicolas and Lumbantobing, Daniel and Sholihah, Arni and Dahruddin, Hadi and Delrieu-Trottin, Erwan and Busson, Frederic and Sauri, Sopian and Hadiaty, Renny and Philippe Keith}
}
@article {7036,
	title = {Shedding light on the migratory patterns of the Amazonian goliath catfish, <i>Brachyplatystoma platynemum</i>               , using otolith <sup>87</sup>               Sr/ <sup>86</sup>               Sr analyses},
	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
	volume = {29},
	year = {2019},
	month = {Aug-03-2020},
	pages = {397 - 408},
	issn = {1052-7613},
	doi = {10.1002/aqc.v29.310.1002/aqc.3046},
	url = {https://onlinelibrary.wiley.com/toc/10990755/29/3},
	author = {Hauser, Marilia and Doria, Carolina R.C. and Santos, Roberto V. and Garc{\'\i}a-Vasquez, Aurea and Marc Pouilly and Pecheyran, Christophe and Ponzevera, Emmanuel and Torrente-Vilara, Gislene and B{\'e}rail, Sylvain and Panfili, Jacques and Darnaude, Audrey and Renno, Jean-Fran{\c c}ois and Garc{\'\i}a-D{\'a}vila, Carmen and Jesus Nu{\~n}ez-Rodriguez and Ferraton, Franck and Vargas, Gladys and Duponchelle, Fabrice}
}
@article {7103,
	title = {Shedding light on the migratory patterns of the Amazonian goliath catfish, Brachyplatystoma platynemum, using otolith 87Sr/86Sr analyses},
	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
	volume = {29},
	year = {2019},
	pages = {397{\textendash}408},
	doi = {doi.org/10.1002/aqc.3046},
	url = {https://onlinelibrary.wiley.com/doi/full/10.1002/aqc.3046},
	author = {Hauser, Marilia and Doria, Carolina RC and Santos, Roberto V and Garc{\'\i}a-Vasquez, Aurea and Marc Pouilly and Pecheyran, Christophe and Ponzevera, Emmanuel and Torrente-Vilara, Gislene and B{\'e}rail, Sylvain and Panfili, Jacques and others}
}
@article {6662,
	title = {Temperature patterns and mechanisms influencing coral bleaching during the 2016 El Ni{\~n}o},
	journal = {Nature Climate Change},
	volume = {9},
	year = {2019},
	pages = {845-851},
	abstract = {Under extreme heat stress, corals expel their symbiotic algae and colour (that is, {\textquoteleft}bleaching{\textquoteright}), which often leads to widespread mortality. Predicting the large-scale environmental conditions that reinforce or mitigate coral bleaching remains unresolved and limits strategic conservation actions1,2. Here we assessed coral bleaching at 226 sites and 26 environmental variables that represent different mechanisms of stress responses from East Africa to Fiji through a coordinated effort to evaluate the coral response to the 2014{\textendash}2016 El Ni{\~n}o/Southern Oscillation thermal anomaly. We applied common time-series methods to study the temporal patterning of acute thermal stress and evaluated the effectiveness of conventional and new sea surface temperature metrics and mechanisms in predicting bleaching severity. The best models indicated the importance of peak hot temperatures, the duration of cool temperatures and temperature bimodality, which explained 50\% of the variance, compared to the common degree-heating week temperature index that explained only 9\%. Our findings suggest that the threshold concept as a mechanism to explain bleaching alone was not as powerful as the multidimensional interactions of stresses, which include the duration and temporal patterning of hot and cold temperature extremes relative to average local conditions. {\textcopyright} 2019, The Author(s), under exclusive licence to Springer Nature Limited.},
	keywords = {Algae, Anthozoa},
	issn = {1758678X},
	doi = {10.1038/s41558-019-0576-8},
	url = {https://www.nature.com/articles/s41558-019-0576-8},
	author = {McClanahan, T.R. and Darling, E.S. and Maina, J.M. and Muthiga, N.A. and D{\textquoteright}agata, S. and Jupiter, S.D. and Arthur, R. and Wilson, S.K. and Mangubhai, S. and Nand, Y. and Ussi, A.M. and Humphries, A.T. and Patankar, V.J. and Mireille M.M. Guillaume and Philippe Keith and Shedrawi, G. and Julius, P. and Grimsditch, G. and Ndagala, J. and Leblond, J.}
}
@article {Arroyo20191543,
	title = {Towards coherent GES assessments at sub-regional level: Signs of fisheries expansion processes in the Bay of Biscay using an OSPAR food web indicator, the mean trophic level},
	journal = {ICES Journal of Marine Science},
	volume = {76},
	number = {6},
	year = {2019},
	note = {cited By 1},
	pages = {1543-1553},
	publisher = {Oxford University Press},
	abstract = {Using the Bay of Biscay (BoB) as a case study, we conducted a transnational assessment of the mean trophic level (MTL, Ospar FW4) indicator at sub-regional level, over the last three decades. Our results confirm the apparent recovery of BoB{\textquoteright}s bentho-demersal system, as shown by trends in the MTL indicator based on survey data. However, they also point at a concomitant "fishing through" process where the apparent stability revealed by the MTL indicator based on landed catch data may be masking the expansion of demersal fisheries to deeper waters, and an over-exploitation of resources (particularly abundant pelagic species). Moreover, they show how the combined examination of independent surveys and fishery landings allows the identification of ecological trends in ecosystem studies. In addition, our results confirm that analysing MTL at various threshold levels helps discerning the causality of trends in this indicator, especially if analyses for pelagic and demersal species are run independently. Further studies, at smaller (i.e. local) spatial scales, need to be conducted to ascertain our results and suggest appropriate management strategies aimed at regulating fisheries expansions in the area. {\textcopyright} 2019 International Council for the Exploration of the Sea 2019. All rights reserved.},
	keywords = {Atlantic Ocean, Bay of Biscay, catch statistics, demersal fishery, food web, pelagic fishery, range expansion, trophic level, trophic status},
	issn = {10543139},
	doi = {10.1093/icesjms/fsz023},
	url = {https://academic.oup.com/icesjms/article-abstract/76/6/1543/5369193},
	author = {Arroyo, N.-L. and Safi, Georges and Vouriot, P. and L{\'o}pez-L{\'o}pez, L. and Nathalie Niquil and Le Loc{\textquoteright}h, Francois and Hattab, Tarek and Preciado, I and Coll, M.}
}
@article {Safi2019116,
	title = {Vitamine ENA: A framework for the development of ecosystem-based indicators for decision makers},
	journal = {Ocean and Coastal Management},
	volume = {174},
	year = {2019},
	note = {cited By 5},
	pages = {116-130},
	publisher = {Elsevier Ltd},
	abstract = {The Water Framework Directive (article 2, paragraph 21) as well as the Marine Strategy Framework Directive (MSFD, Descriptor 4) stress the need for assessing the quality of the structure and the functioning of ecosystems. The MSFD also underlines the urgent need for development, testing, and validation of ecosystem state indicators. Holistic function-based criteria and indicators as provided by Ecological Network Analysis (ENA) could be used to define and assess the {\textquoteleft}Good Environmental Status{\textquoteright} of marine ecosystems. This approach also feeds Ecosystem Based Management (EBM). ENA generally analyses the fluxes{\textquoteright} quality of a single medium such as here the carbon fluxes in a food web and produces a number of useful metrics that indicate, inter alia, the total carbon flow through the system, the quality of the functioning of the system or the trophic efficiency of system. A short list of indices [i.e. Detritivory over Herbivory ratio (D/H), Connectance Index (CI), Transfer Efficiency (TE) over trophic levels, System Omnivory Index (SOI), Finn{\textquoteright}s Cycling Index (FCI), relative Redundancy (R/DC), Average Mutual Information (AMI) and Interaction Strength (IS)] is proposed for practical use. This paper presents a first framework for OSPAR Regional Sea Convention food web indicators based on ENA. These are presented here focusing on their applicability and what is needed for implementation, illustrating their potential use by case studies. {\textcopyright} 2019 Elsevier Ltd},
	keywords = {Average mutual information, Carbon, Carbon flux, Criteria and indicators, Decision making, Ecological network analysis, ecosystem function, ecosystem management, ecosystem structure, Ecosystem-based management, Ecosystems, Efficiency, environmental indicator, Environmental management, Environmental regulations, food web, Good environmental status, holistic approach, Interaction strength, marine ecosystem, Marine pollution, Marine strategy framework directives, Water conservation, Water Framework Directives},
	issn = {09645691},
	doi = {10.1016/j.ocecoaman.2019.03.005},
	url = {https://www.sciencedirect.com/science/article/abs/pii/S096456911830591X},
	author = {Safi, Georges and Giebels, D. and Arroyo, N.-L. and Heymans, J.J. and Preciado, I and Raoux, Aurore and Sch{\"u}ckel, U. and Samuele Tecchio and de Jonge, V.N. and Nathalie Niquil}
}
@article {5630,
	title = {Age and growth of the Amazonian migratory catfish Brachyplatystoma rousseauxii in the Madeira River basin before the construction of dams},
	journal = {Neotropical Ichthyology},
	volume = {16},
	year = {2018},
	pages = {e170130, 2018},
	abstract = {<p class="rtejustify">The goliath catfish <em>Brachyplatystoma rousseauxii</em> has crucial economical and ecological functions in the Amazon basin. Although its life history characteristics have been studied in the Amazon, there is little information in the Madeira River basin, which holds genetically distinct populations and where dams were recently built. Using fish collected in Bolivia, Brazil and Peru, this study provides a validation of growth rings deposition and details the growth patterns of <em>B. rousseauxii</em> in the Madeira before the dams{\textquoteright} construction. Age structure and growth parameters were determined from 497 otolith readings. The species exhibits two growth rings per year and sampled fish were between 0 and 16 years old. In the Brazilian portion of the basin, mainly young individuals below 5 years old were found, whereas older fish (\&gt; 5 years) were caught only in the Bolivian and Peruvian stretches, indicating that after migrating upstream to reproduce, adults remain in the headwaters of the Madeira River. Comparing with previous publications, <em>B. rousseauxii</em> had a slower growth and 20 cm lower maximum standard length in the Madeira River than in the Amazon River. This study provides a baseline for future evaluation of changes in population dynamics of the species following dams closure.</p>

<p class="rtejustify">Palabras clave:\&nbsp;Amazon; Biannual rings; Goliath catfish; Life cycle; Otolith</p>
},
	doi = {10.1590/1982-0224-20170130},
	author = {Hauser, Marilia and Doria, C R C and Melo, L and Santos, A and Ayala, D and Nogueira, L and Amadio, S. A. and Fabr{\'e}, N and Torrente-Vilara, Gislene and Garc{\'\i}a V{\'a}squez, A and Renno, Jean-Francois and Carvajal-Vallejos, F M and Alonso, J-C and N{\'u}{\~n}ez-Rodr{\'\i}guez, Jes{\'u}s and Fabrice Duponchelle}
}
@article {5282,
	title = {Aquatic urban ecology at the scale of a capital: community structure and interactions in street gutters.},
	journal = {ISME J.},
	volume = {12},
	year = {2018},
	month = {09/2017},
	pages = {253{\textendash}266},
	abstract = {<p>In most cities, streets are designed for collecting and transporting dirt, litter, debris, storm water and other wastes as a municipal sanitation system. Microbial mats can develop on street surfaces and form microbial communities that have never been described. Here, we performed the first molecular inventory of the street gutter-associated eukaryotes across the entire French capital of Paris and the non-potable waters sources. We found that the 5782 OTUs (operational taxonomic units) present in the street gutters which are dominated by diatoms (photoautotrophs), fungi (heterotrophs), Alveolata and Rhizaria, includes parasites, consumers of phototrophs and epibionts that may regulate the dynamics of gutter mat microbial communities. Network analyses demonstrated that street microbiome present many species restricted to gutters, and an overlapping composition between the water sources used for street cleaning (for example, intra-urban aquatic networks and the associated rivers) and the gutters. We propose that street gutters, which can cover a significant surface area of cities worldwide, potentially have important ecological roles in the remediation of pollutants or downstream wastewater treatments, might also be a niche for growth and dissemination of putative parasite and pathogens.The ISME Journal advance online publication, 13 October 2017; doi:10.1038/ismej.2017.166.</p>
},
	doi = {10.1038/ismej.2017.166},
	url = {https://www.nature.com/articles/ismej2017166},
	author = {Herv{\'e}, Vincent and Leroy, Boris and Da Silva Pires, Albert and Pascal Jean Lopez}
}
@article {5531,
	title = {Biofilm monitoring as a tool to assess the efficiency of artificial reefs as substrates: Toward 3D printed reefs},
	journal = {Ecological Engineering},
	volume = {120},
	year = {2018},
	pages = {230 - 237},
	abstract = {<p class="rtejustify">Habitat destruction is one of the main causes of the decline of biodiversity and of fishery resources in the marine environment. An artificial reef (AR) could be a tool for protecting or restoring these habitats and their declining biodiversity, and also help to enhance sustainable fisheries. The goal is to design non-polluting structures that best mimic the complexity of natural habitats in order to improve their service to the community. To date, the assessment of reef performance has been mostly focused on fish assemblages and species of ecological and/or socio-economic interest, and has disregarded the biofilm communities that determine the first level of an AR{\textquoteright}s trophic network. In this work, we used biofilm formation to compare the quality of substrates used as building parts for an AR, in order to optimize an eco-friendly material that will be used to design a new generation of \{ARs\} produced by giant 3D printers. The structure of the photosynthetic communities has been identified using pigment biomarkers and their production of exudates has been analysed. These polymeric substances were quantified in terms of total sugar and protein concentrations. They were further analysed in terms of amino acid content. We found no significant differences between the micro-algae communities developed on the different substrates. These photosynthetic communities were mainly composed of diatoms, prasinophytes, haptophytes, and dinoflagellates. However, we showed that the material for \{ARs\} is crucial for biofilm development, especially with regard to its secretions of sugar. The choice of an appropriate substrate for \{AR\} construction is thus of particular importance since biofilm secretions determine the organic substrate on which sessile macro-organisms will settle.</p>
},
	keywords = {Artificial reef substrates},
	issn = {0925-8574},
	doi = {https://doi.org/10.1016/j.ecoleng.2018.06.005},
	url = {https://www.sciencedirect.com/science/article/pii/S0925857418302167},
	author = {Elisabeth Riera and Lamy, Dominique and Christophe Goulard and Francour, P and C{\'e}dric Hubas}
}
@article {6078,
	title = {Chemically-Mediated Interactions Between Macroalgae, Their Fungal Endophytes, and Protistan Pathogens},
	journal = {Frontiers in Microbiology},
	volume = {9},
	year = {2018},
	pages = {3161},
	abstract = {<p>Filamentous fungi asymptomatically colonise the inner tissues of macroalgae, yet their ecological roles remain largely underexplored. Here, we tested if metabolites produced by fungal endophytes might protect their host against a phylogenetically broad spectrum of protistan pathogens. Accordingly, the cultivable fungal endophytes of four brown algal species were isolated and identified based on LSU and SSU sequencing. The fungal metabolomes were tested for their ability to reduce the infection by protistan pathogens in the algal model Ectocarpus siliculosus. The most active metabolomes effective against the oomycetes Eurychasma dicksonii and Anisolpidium ectocarpii, and the phytomixid Maullinia ectocarpii were further characterized chemically. Several pyrenocines isolated from Phaeosphaeria sp. AN596H efficiently inhibited the infection by all abovementioned pathogens. Strikingly, these compounds also inhibited the infection of nori (Pyropia yezoensis) against its two most devastating oomycete pathogens, Olpidiopsis pyropiae and Pythium porphyrae. We thus demonstrate that fungal endophytes associated with brown algae produce bioactive metabolites which might confer protection against pathogen infection. These results highlight the potential of metabolites to finely-tune the outcome of molecular interactions between algae, their endophytes and protistan pathogens. This also provide proof-of-concept towards the applicability of such metabolites in marine aquaculture to control otherwise untreatable diseases.</p>
},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2018.03161},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.03161},
	author = {Vallet, Marine and Strittmatter, Martina and Mur{\'u}a, Pedro and Lacoste, Sandrine and Dupont, Jo{\"e}lle and C{\'e}dric Hubas and Genta-Jouve, Gregory and Claire M. M. Gachon and Kim, Gwang Hoon and Prado, Soizic}
}
@article {8568,
	title = {Combined use of two supervised learning algorithms to model sea turtle behaviours from tri-axial acceleration data},
	journal = {Journal of Experimental Biology},
	year = {2018},
	month = {Jan-01-2018},
	issn = {0022-0949},
	doi = {10.1242/jeb.177378},
	url = {https://journals.biologists.com/jeb/article/doi/10.1242/jeb.177378/262989/Combined-use-of-two-supervised-learning-algorithms},
	author = {Jeantet, L. and Dell{\textquoteright}Amico, F. and Forin-Wiart, M. A. and Coutant, M. and Bonola, M. and Etienne, D. and Gresser, J. and Regis, S. and Lecerf, N. and Lefebvre, F. and de Thoisy, B. and Le Maho, Y. and Brucker, M. and Ch{\^a}telain, N. and Laesser, R. and Crenner, F. and Handrich, Y. and Wilson, R. and Chevallier, D.}
}
@article {8557,
	title = {Connecting paths between juvenile and adult habitats in the Atlantic green turtle using genetics and satellite tracking},
	journal = {Ecology and Evolution},
	volume = {8},
	year = {2018},
	month = {Jan-12-2018},
	pages = {12790 - 12802},
	issn = {2045-7758},
	doi = {10.1002/ece3.2018.8.issue-2410.1002/ece3.4708},
	url = {https://onlinelibrary.wiley.com/toc/20457758/8/24},
	author = {Chambault, Philippine and de Thoisy, Beno{\^\i}t and Huguin, Ma{\"\i}lis and Martin, Jordan and Bonola, Marc and Etienne, Denis and Gresser, Julie and Hielard, Ga{\"e}lle and Mailles, Julien and Vedie, Fabien and Barnerias, Cyrille and Sutter, Emmanuel and Guillemot, Blandine and Dumont-Dayot, {\'E}milie and R{\'e}gis, Sidney and Lecerf, Nicolas and Lefebvre, Fabien and Frouin, C{\'e}dric and Aubert, Nathalie and Guimera, Christelle and Bordes, Robinson and Thieulle, Laurent and Duru, Matthieu and Bouaziz, Myriam and Pinson, Adrien and Flora, Fr{\'e}d{\'e}ric and Queneherve, Patrick and Woignier, Thierry and Allenou, Jean-Pierre and Cimiterra, Nicolas and Benhalilou, Abdelwahab and Murgale, C{\'e}line and Maillet, Thomas and Rangon, Luc and Chanteux, No{\'e}mie and Chanteur, B{\'e}n{\'e}dicte and B{\'e}ranger, Christelle and Le Maho, Yvon and Petit, Odile and Chevallier, Damien}
}
@article {5440,
	title = {Crustacean cardioactive peptides: Expression, localization, structure, and a possible involvement in regulation of egg-laying in the cuttlefish Sepia officinalis.},
	journal = {Gen. Comp. Endocrinol.},
	volume = {1},
	year = {2018},
	pages = {67-79},
	abstract = {<p class="rtejustify">The cuttlefish (<em>Sepia officinalis</em>) is a cephalopod mollusk distributed on the western European coast, in the West African Ocean and in the Mediterranean Sea. On the Normandy coast (France), cuttlefish is a target species of professional fishermen, so its reproduction strategy is of particular interest in the context of stock management. Egg-laying, which is coastal, is controlled by several types of regulators among which neuropeptides. The cuttlefish neuropeptidome was recently identified by\&nbsp;Zatylny-Gaudin\&nbsp;<em>et al. </em>(2016). Among the 38 neuropeptide families identified, some were significantly overexpressed in egg-laying females as compared to mature males. This study is focused on crustacean cardioactive peptides (CCAPs), a highly expressed neuropeptide family strongly suspected of being involved in the control of egg-laying. We investigated the functional and structural characterization and tissue mapping of CCAPs, as well as the expression patterns of their receptors. CCAPs appeared to be involved in oocyte transport through the oviduct and in mechanical secretion of capsular products. Immunocytochemistry revealed that the neuropeptides were localized throughout the central nervous system (CNS) and in the nerve endings of the glands involved in egg-capsule synthesis and secretion, i.e. the oviduct gland and the main nidamental glands. The CCAP receptor was expressed in these glands and in the subesophageal mass of the CNS. Multiple sequence alignments revealed a high level of conservation of CCAP protein precursors in <em>Sepia officinalis</em> and Loligo pealei, two cephalopod decapods. Primary sequences of CCAPs from the two species were fully conserved, and cryptic peptides detected in the nerve endings were also partially conserved, suggesting biological activity that remains unknown for the time being.</p>
},
	doi = {10.1016/j.ygcen.2017.12.009},
	author = {Endress, Maxime and C{\'e}line Zatylny-Gaudin and Corre, Erwan and Le Corguill{\'e}, Gildas and Benoist, Louis and Leprince, J{\'e}r{\^o}me and Lefranc, Benjamin and Bernay, Beno{\^\i}t and Leduc, Alexandre and Rangama, Jimmy and Anne-Gaelle Lafont and Bondon, Arnaud and Jo{\"e}l Henry}
}
@article {8113,
	title = {Cryptic frenulates are the dominant chemosymbiotrophic fauna at Arctic and high latitude Atlantic cold seeps},
	journal = {PLOS ONE},
	volume = {13},
	year = {2018},
	month = {Apr-12-2020},
	pages = {e0209273},
	doi = {10.1371/journal.pone.0209273},
	url = {https://dx.plos.org/10.1371/journal.pone.0209273},
	author = {Sen, Arunima and Duperron, S{\'e}bastien and Hourdez, St{\'e}phane and Piquet, B{\'e}r{\'e}nice and L{\'e}ger, Nelly and Gebruk, Andrey and Le Port, Anne-Sophie and Svenning, Mette Marianne and Andersen, Ann C.},
	editor = {Kiel, Steffen}
}
@article {5596,
	title = {Design of antimicrobial peptides from a cuttlefish database.},
	journal = {Amino acids},
	year = {2018},
	abstract = {<p>No antimicrobial peptide has been identified in cephalopods to date. Annotation of transcriptomes or genomes using basic local alignment Search Tool failed to yield any from sequence identities. Therefore, we searched for antimicrobial sequences in the cuttlefish (Sepia officinalis) database by in silico analysis of a transcriptomic database. Using an original approach based on the analysis of cysteine-free antimicrobial peptides selected from our Antimicrobial Peptide Database (APD3), the online prediction tool of the Collection of Anti-Microbial Peptides (CAMPR3), and a homemade software program, we identified potential antibacterial sequences. Nine peptides less than 25 amino acids long were synthesized. The hydrophobic content of all nine of them ranged from 30 to 70\%, and they could form alpha-helices. Three peptides possessed similarities with piscidins, one with BMAP-27, and five were totally new. Their antibacterial activity was evaluated on eight bacteria including the aquatic pathogens Vibrio alginolyticus, Aeromonas salmonicida, or human pathogens such as Salmonella typhimurium, Listeria monocytogenes, or Staphylococcus aureus. Despite the prediction of an antimicrobial potential for eight of the peptides, only two-GR21\&nbsp;and KT19-inhibited more than one bacterial strain with minimal inhibitory concentrations below 25\&nbsp;{\textmu}M. Some sequences like VA20\&nbsp;and FK19\&nbsp;were hemolytic, while GR21\&nbsp;induced less than 10\% of hemolysis on human blood cells at a concentration of 200\&nbsp;{\textmu}M. GR21\&nbsp;was the only peptide derived from a precursor with a signal peptide, suggesting a real role in cuttlefish immune defense.</p>
},
	doi = {10.1007/s00726-018-2633-4},
	author = {Houyvet, Baptiste and Zanuttini, B and Corre, Erwan and Le Corguill{\'e}, Gildas and Jo{\"e}l Henry and C{\'e}line Zatylny-Gaudin}
}
@article {5025,
	title = {Diel Rhythm Does Not Shape the Vertical Distribution of Bacterial and Archaeal 16S rRNA Transcript Diversity in Intertidal Sediments: a Mesocosm Study},
	journal = {Microbial Ecology},
	volume = {75},
	year = {2018},
	month = {Aug},
	pages = {364-374.},
	abstract = {<p class="rtejustify">In intertidal sediments, circadian oscillations (i.e., tidal and diel rhythms) and/or depth may affect prokaryotic activity. However, it is difficult to distinguish the effect of each single force on active community changes in these natural and complex intertidal ecosystems. Therefore, we developed a tidal mesocosm to control the tidal rhythm and test whether diel fluctuation or sediment depth influence active prokaryotes in the top 10\&nbsp;cm of sediment. Day- and nighttime emersions were compared as they are expected to display contrasting conditions through microphytobenthic activity in five different sediment layers. A multiple factor analysis revealed that bacterial and archaeal 16S ribosomal RNA (rRNA) transcript diversity assessed by pyrosequencing was similar between day and night emersions. Potentially active benthic Bacteria were highly diverse and influenced by chlorophyll a and phosphate concentrations. While in oxic and suboxic sediments, Thaumarchaeota Marine Group I (MGI) was the most active archaeal phylum, suggesting the importance of the nitrogen cycle in muddy sediments, in anoxic sediments, the mysterious archaeal C3 group dominated the community. This work highlighted that active prokaryotes organize themselves vertically within sediments independently of diel fluctuations suggesting adaptation to physicochemical-specific conditions associated with sediment depth.</p>
},
	issn = {1432-184X},
	doi = {10.1007/s00248-017-1048-1},
	url = {https://doi.org/10.1007/s00248-017-1048-1},
	author = {Lavergne, C. and Hugoni, M. and C{\'e}dric Hubas and Debroas, D. and Christine Dupuy and Agogu{\'e}, H.}
}
@article {5499,
	title = {Dietary aquaculture by-product hydrolysates: impact on the transcriptomic response of the intestinal mucosa of European seabass (Dicentrarchus labrax) fed low fish meal diets},
	journal = {BMC Genomics},
	volume = {19},
	year = {2018},
	abstract = {<p class="rtejustify">Aquaculture production is expected to double by 2030, and demands for aquafeeds and raw materials are expected to increase accordingly. Sustainable growth of aquaculture will require the development of highly nutritive and functional raw materials to efficiently replace fish meal. Enzymatic hydrolysis of marine and aquaculture raw materials could bring new functionalities to finished products. The aim of this study was to determine the zootechnical and transcriptomic performances of protein hydrolysates of different origins (tilapia, shrimp, and a combination of the two) in European seabass (Dicentrarchux labrax) fed a low fish meal diet (5\%), for 65\&nbsp;days.</p>

<p><strong>Results</strong></p>

<p class="rtejustify">Results were compared to a positive control fed with 20\% of fish meal. Growth performances, anterior intestine histological organization and transcriptomic responses were monitored and analyzed. Dietary inclusion of protein hydrolysates in the low fish meal diet restored similar growth performances to those of the positive control. Inclusion of dietary shrimp hydrolysate resulted in larger villi and more goblet cells, even better than the positive control. Transcriptomic analysis of the anterior intestine showed that dietary hydrolysate inclusion restored a pattern of intestinal gene expression very close to the pattern of the positive control. However, as compared to the low fish meal diet and depending on their origin, the different hydrolysates did not modulate metabolic pathways in the same way. Dietary shrimp hydrolysate inclusion modulated more metabolic pathways related to immunity, while nutritional metabolism was more impacted by dietary tilapia hydrolysate. Interestingly, the combination of the two hydrolysates enhanced the benefits of hydrolysate inclusion in diets: more genes and metabolic pathways were regulated by the combined hydrolysates than by each hydrolysate tested independently.</p>

<p><strong>Conclusions</strong></p>

<p class="rtejustify">Protein hydrolysates manufactured from aquaculture by-products are promising candidates to help replace fish meal in aquaculture feeds without disrupting animal metabolism and performances.</p>
},
	keywords = {Aquaculture, Aquafeed, By-products, European seabass, Fishmeal replacement, Hydrolysate, Illumina RNA-sequencing, Intestinal organization, Metabolic pathways},
	doi = {doi.org/10.1186/s12864-018-4780-0},
	author = {Leduc, Alexandre and C{\'e}line Zatylny-Gaudin and Robert, Marie and Corre, Erwan and Le Corguill{\'e}, Gildas and Castel, H{\'e}l{\`e}ne and Lefevre-Scelles, Antoine and Fournier, Vincent and Gisbert, Enric and Andree, Karl B. and Jo{\"e}l Henry}
}
@article {5363,
	title = {Differences in home-range sizes of a bird species in its original, refuge and substitution habitats: challenges to conservation in anthropogenic habitats},
	journal = {Biodiversity and Conservation},
	volume = {27},
	year = {2018},
	pages = {719-732},
	abstract = {<p>In the current context of the anthropocene, the original habitats of many species have been modified or destroyed. Animals may be forced to move from their original habitats, either to refuge habitats that are suboptimal natural habitats, or to substitution habitats that are anthropogenic. The quality of refuge habitats may be lower than that of the original ones, whereas substitution habitats may be of a similar or even better quality. Here, we test this hypothesis empirically, using the example of coastal populations of the bluethroat, Luscinina svecica namnetum. In a radio-tracking survey, we compared the home-range sizes (considered here a proxy of habitat quality) of the breeding males in their original (coastal saltmarshes), refuge (inland reedbeds) and substitution (coastal salinas) habitats. We found that home ranges are up to 15 times larger in the substitution habitat than in the original one, and intermediate in the refuge habitat, suggesting that substitution habitats have the lowest quality and original habitats the highest. To date, most studies and<br />
conservation programs related to this species have focused on its substitution habitats. This result challenges the interest of focusing on anthropogenic habitats when studying and conserving such a species, because such habitats may only be low-quality substitutes.</p>
},
	doi = {doi.org/10.1007/s10531-017-1460-3},
	author = {Laurent Godet and Cl{\'e}ment Harmange and Matthieu Marquet and Emmanuel Joyeux and J{\'e}r{\^o}me Fournier}
}
@article {6930,
	title = {Different transfer pathways of an organochlorine pesticide across marine tropical food webs assessed with stable isotope analysis},
	journal = {PLOS ONE},
	volume = {13},
	year = {2018},
	month = {Jan-02-2018},
	pages = {e0191335},
	doi = {10.1371/journal.pone.019133510.1371/journal.pone.0191335.g00110.1371/journal.pone.0191335.t00110.1371/journal.pone.0191335.t00210.1371/journal.pone.0191335.s001},
	url = {https://dx.plos.org/10.1371/journal.pone.0191335},
	author = {Charlotte R. Dromard and Bouchon-Navaro, Yolande and Cordonnier, S{\'e}bastien and Gu{\'e}n{\'e}, Mathilde and Harmelin-Vivien, Mireille and Bouchon, Claude}
}
@article {6744,
	title = {Dynamics of particulate organic matter composition in coastal systems: Forcing of spatio-temporal variability at multi-systems scale},
	journal = {Progress in Oceanography},
	volume = {162},
	year = {2018},
	month = {Jan-03-2018},
	pages = {271 - 289},
	issn = {00796611},
	doi = {10.1016/j.pocean.2018.02.026},
	url = {https://www.sciencedirect.com/science/article/abs/pii/S0079661117302100},
	author = {Li{\'e}nart, Camilla and Savoye, Nicolas and David, Val{\'e}rie and Ramond, Pierre and Rodriguez Tress, Paco and Hanquiez, Vincent and Marieu, Vincent and Aubert, Fabien and Aubin, S{\'e}bastien and Bichon, Sabrina and Boinet, Christophe and Bourasseau, Line and Bozec, Yann and Br{\'e}ret, Martine and Elsa Breton and Caparros, Jocelyne and Cariou, Thierry and Claquin, Pascal and Conan, Pascal and Corre, Anne-Marie and Costes, Laurence and Muriel Crouvoisier and Del Amo, Yolanda and Derriennic, Herv{\'e} and Dindinaud, Fran{\c c}ois and Duran, Robert and Durozier, Ma{\"\i}a and Devesa, J{\'e}r{\'e}my and Ferreira, Sophie and Eric Feunteun and Garcia, Nicole and Geslin, Sandrine and Emilie Grossteffan and Gueux, Aurore and Guillaudeau, Julien and Guillou, Ga{\"e}l and Jolly, Orianne and Lachauss{\'e}e, Nicolas and Lafont, Michel and Lagadec, V{\'e}ronique and Lamoureux, J{\'e}zabel and Lauga, B{\'e}atrice and Lebreton, Beno{\^\i}t and Lecuyer, Eric and Lehodey, Jean-Paul and Leroux, C{\'e}dric and St{\'e}phane L{\textquoteright}Helguen and Mac{\'e}, Eric and Maria, Eric and Mousseau, Laure and Antoine Nowaczyk and Pineau, Philippe and Petit, Franck and Pujo-Pay, Mireille and Raimbault, Patrick and Rimmelin-Maury, Peggy and Rouaud, Vanessa and Sauriau, Pierre-Guy and Sultan, Emmanuelle and Susperregui, Nicolas}
}
@article {5619,
	title = {Effect of CO2{\textendash}induced ocean acidification on the early development and shell mineralization of the European abalone (Haliotis tuberculata)},
	journal = {Journal of Experimental Marine Biology and Ecology},
	volume = {508},
	year = {2018},
	pages = {52 - 63},
	abstract = {<p>Ocean acidification is a major global stressor that leads to substantial changes in seawater carbonate chemistry, with potentially significant consequences for calcifying organisms. Marine shelled mollusks are ecologically and economically important species providing essential ecosystem services and food sources for other species. Because they use calcium carbonate (CaCO3) to produce their shells, mollusks are among the most vulnerable invertebrates to ocean acidification, with early developmental stages being particularly sensitive to pH changes. This study investigated the effects of CO2-induced ocean acidification on larval development of the European abalone Haliotis tuberculata, a commercially important gastropod species. Abalone larvae were exposed to a range of reduced pHs (8.0, 7.7 and 7.6) over the course of their development cycle, from early-hatched trochophore to pre-metamorphic veliger. Biological responses were evaluated by measuring the survival rate, morphology and development, growth rate and shell calcification. Larval survival was significantly lower in acidified conditions than in control conditions. Similarly, larval size was consistently smaller under low pH conditions. Larval development was also affected, with evidence of a developmental delay and an increase in the proportion of malformed or unshelled larvae. In shelled larvae, the intensity of birefringence decreased under low pH conditions, suggesting a reduction in shell mineralization. Since these biological effects were observed for pH values expected by 2100, ocean acidification may have potentially negative consequences for larval recruitment and persistence of abalone populations in the near future.</p>
},
	keywords = {Abalone, larval development, Ocean acidification, Shell mineralization},
	issn = {0022-0981},
	doi = {https://doi.org/10.1016/j.jembe.2018.08.005},
	url = {http://www.sciencedirect.com/science/article/pii/S0022098117304070},
	author = {Nathalie Wessel and Sophie Martin and Badou, Aicha and Philippe Dubois and Sylvain Huchette and Vivien Julia and Flavia Nunes and Ewan Harney and Christine Paillard and St{\'e}phanie Auzoux-Bordenave}
}
@inbook {5441,
	title = {Egg-Laying in the cuttlefish Sepia officinalis},
	booktitle = {Biological Resources of Water},
	year = {2018},
	issn = {978-1-78923-081-9},
	doi = {DOI: 10.5772/intechopen.71915},
	author = {C{\'e}line Zatylny-Gaudin and Jo{\"e}l Henry}
}
@article {5439,
	title = {Identification of a moronecidin-like antimicrobial peptide in the venomous fish Pterois volitans: Functional and structural study of pteroicidin-α.},
	journal = {Fish and shellfish Immunology},
	year = {2018},
	pages = {318-324},
	abstract = {<p>The present study characterizes for the first time an antimicrobial peptide in lionfish (Pterois volitans), a venomous fish. Using a peptidomic approach, we identified a mature piscidin in lionfish and called it pteroicidin-α. We detected an amidated form (pteroicidin-α- CONH2) and a non-amidated form (pteroicidin-α-COOH), and then performed their functional and structural study. Interestingly, the two peptides displayed different antibacterial and hemolytic activity levels. Pteroicidin-α-CONH2\&nbsp;was bactericidal on human pathogens like Staphylococcus aureus or Escherichia coli, as well as on the fish pathogen Aeromonas salmonicida, while pteroicidin-α-COOH only inhibited their growth. Furthermore, the two peptides induced hemolysis of red blood cells from different vertebrates, namely humans, sea bass and lesser-spotted dogfish. Hemolysis occurred with low concentrations of pteroicidin-α-CONH2, indicating greater toxicity of the amidated form. Circular dichroism analysis showed that both peptides adopted a helical conformation, yet with a greater α-helix content in pteroicidin-α-CONH2. Overall, these results suggest that amidation strongly influences pteroicidin-α by modifying its structure and its physico-chemical characteristics and by increasing its hemolytic activity</p>
},
	author = {Houyvet, Baptiste and Yolande Bouchon-Navaro and Bouchon, Claude and Goux, Didier and Bernay, Beno{\^\i}t and Corre, Erwan and C{\'e}line Zatylny-Gaudin}
}
@article {8567,
	title = {Identification of marine key areas across the Caribbean to ensure the conservation of the critically endangered hawksbill turtle},
	journal = {Biological Conservation},
	volume = {223},
	year = {2018},
	month = {Jan-07-2018},
	pages = {170 - 180},
	issn = {00063207},
	doi = {10.1016/j.biocon.2018.05.002},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0006320718301423},
	author = {Nivi{\`e}re, Manon and Chambault, Philippine and P{\'e}rez, Thierry and Etienne, Denis and Bonola, Marc and Martin, Jordan and Barnerias, Cyrille and Vedie, Fabien and Mailles, Julien and Dumont-Dayot, {\'E}milie and Gresser, Julie and Hielard, Ga{\"e}lle and R{\'e}gis, Sidney and Lecerf, Nicolas and Thieulle, Laurent and Duru, Matthieu and Lefebvre, Fabien and Milet, Guillaume and Guillemot, Blandine and Bildan, Bernard and de Montgolfier, Benjamin and Benhalilou, Abdelwahab and Murgale, C{\'e}line and Maillet, Thomas and Queneherve, Patrick and Woignier, Thierry and Safi, Morjane and Le Maho, Yvon and Petit, Odile and Chevallier, Damien}
}
@article {5364,
	title = {Latitudinal Patterns in European Seagrass Carbon Reserves: Influence of Seasonal Fluctuations versus Short-Term Stress and Disturbance Events},
	journal = {Frontiers in Plant Science},
	volume = {9},
	year = {2018},
	abstract = {<p>Seagrass meadows form highly productive and valuable ecosystems in the marine environment. Throughout the year, seagrass meadows are exposed to abiotic and biotic variations linked to (i) seasonal fluctuations, (ii) short-term stress events such as, e.g., local nutrient enrichment, and (iii) small-scale disturbances such as, e.g., biomass removal by grazing. We hypothesized that short-term stress events and smallscale disturbances may affect seagrass chance for survival in temperate latitudes. To test this hypothesis we focused on seagrass carbon reserves in the form of starch stored seasonally in rhizomes, as these have been defined as a good indicator for winter survival. Twelve Zostera noltei meadows were monitored along a latitudinal<br />
gradient in Western Europe to firstly assess the seasonal change of their rhizomal starch content. Secondly, we tested the effects of nutrient enrichment and/or biomass removal on the corresponding starch content by using a short-term manipulative field experiment at a single latitude in the Netherlands. At the end of the growing season, we observed a weak but significant linear increase of starch content along the latitudinal gradient from south to north. This agrees with the contention that such reserves are essential for regrowth after winter, which is more severe in the north. In addition, we also observed a weak but significant positive relationship between starch content at the beginning of the growing season and past winter temperatures. This implies a lower regrowth potential after severe winters, due to diminished starch content at the beginning of the growing season. Short-term stress and disturbances<br />
may intensify these patterns, because our manipulative experiments show that when nutrient enrichment and biomass loss co-occurred at the end of the growing season, Z. noltei starch content declined. In temperate zones, the capacity of seagrasses to accumulate carbon reserves is expected to determine carbon-based regrowth after winter. Therefore, processes affecting those reserves might affect seagrass resilience. With increasing human pressure on coastal systems, short- and small-scale stress events are expected to become more frequent, threatening the resilience of seagrass ecosystems, particularly at higher latitudes, where populations tend to have an annual cycle highly dependent on their storage capacity.</p>
},
	doi = {doi: 10.3389/fpls.2018.00088},
	author = {L.M. Soissons and E.P. Haanstra and M.M. van Katwijk and R. Asmus and I. Auby and L. Barill{\'e} and F.G. Brun and P.G. Cardoso and Nicolas Desroy and J{\'e}r{\^o}me Fournier and F. Ganthy and J.M. Garmendia and Laurent Godet and T.F. Grilo and P. Kadel and B. Ondiviela and G. Peralta and A. Puente and M. Recio and L. Rigouin and M. Valle and P.M.J. Herman and T.J. Bouma}
}
@article {5611,
	title = {Marine sublittoral benthos fails to track temperature in response to climate change in a biogeographical transition zone},
	journal = {ICES Journal of Marine Science},
	year = {2018},
	abstract = {<p>Species ranges are shifting globally to track temperature changes in response to climate warming, with substantial variability among taxa. In<br />
the English Channel, a biogeographical transition zone between the cold temperate and warm temperate provinces of the North-East Atlantic, distribution shifts have been relatively well documented for plankton, fish and intertidal benthic organisms, but little information is available on sublittoral benthos. Following a description of the magnitude of the sea bottom temperature (SBT) rise, the changes in the distribution and occupancy of 65 benthic invertebrate species were analysed by comparing data collected throughout the English Channel at more<br />
than 200 stations sampled during a cool period in the 1960s{\textendash}1970s and at present in 2012{\textendash}2014. A non-uniform rise in SBT for the last three<br />
decades was observed at the regional scale, varying from 0.07 to 0.54C per decade. This rise differs from that reported for sea surface temperature<br />
(SST) in stratified areas suggesting that SBT should be used rather than SST to analyse responses of subtidal organisms to climate change. Despite shifts in both minimum and maximum sea bottom isotherms (2.5 and 3.2 km.year1, respectively), the distribution centroid shift of most species remained \&lt;1.0 km.year1, regardless of the average temperatures they usually experience. Conversely, decreases were observed in the occurrence of most cold-water species and increases were found in the occurrence of most warm-water species. These results suggest that ongoing climate change could lead to a decrease in benthic biodiversity at range limits, especially where connection routes are lacking for new migrants.</p>
},
	doi = {doi:10.1093/icesjms/fsy095},
	author = {Fran{\c c}ois Gaudin and Nicolas Desroy and Stanislas Dubois and Caroline Broudin and Louis Cabioch and J{\'e}r{\^o}me Fournier and Franck Gentil and Jacques Grall and C{\'e}line Houbin and Patrick Le Mao and Eric Thi{\'e}baut}
}
@article {7037,
	title = {Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms},
	journal = {PLOS ONE},
	volume = {13},
	year = {2018},
	month = {Dec-09-2018},
	pages = {e0202976},
	doi = {10.1371/journal.pone.0202976},
	url = {https://dx.plos.org/10.1371/journal.pone.0202976},
	author = {Mariac, C. and Vigouroux, Y. and Duponchelle, F. and Garc{\'\i}a-D{\'a}vila, C and Jesus Nu{\~n}ez-Rodriguez and Desmarais, E. and Renno, J.F.},
	editor = {Hajibabaei, Mehrdad}
}
@article {5418,
	title = {Microbial parasites make cyanobacteria blooms less of a trophic dead-end than commonly assumed},
	journal = {The ISME Journal},
	volume = {12},
	year = {2018},
	pages = {1008-1020},
	abstract = {<p class="rtejustify">Les parasites sont pr{\'e}sents dans tous les {\'e}cosyst{\`e}mes et peuvent {\^e}tre {\`a} l{\textquoteright}origine de changements dans la structure et le fonctionnement des r{\'e}seaux trophiques. Cependant, {\`a} ce jour, nos connaissances concernant les effets des parasites sur la dynamique des r{\'e}seaux trophiques restent limit{\'e}es. Dans cette {\'e}tude, nous analysons le r{\^o}le de parasites microbiens (virus de bact{\'e}ries, phytoplancton et cyanobact{\'e}ries, et des chitrides parasites des cyanobact{\'e}ries) sur le transfert d{\textquoteright}{\'e}nergie et le fonctionnement du r{\'e}seau trophique au cours d{\textquoteright}un bloom de cyanobact{\'e}rie {\`a} l{\textquoteright}aide d{\textquoteright}un mod{\`e}le d{\textquoteright}Analyse Inverse Lin{\'e}aire. Cette mod{\'e}lisation a permis de mettre en {\'e}vidence l{\textquoteright}importance du broutage sur les bact{\'e}ries h{\'e}t{\'e}rotrophes {\`a} travers la voie microbienne (DOC -\&gt; bact{\'e}ries -\&gt; consommateurs), ainsi que la d{\'e}pendance des consommateurs vis {\`a} vis des bact{\'e}ries notamment pendant les blooms de cyanobact{\'e}ries. Au fur et {\`a} mesure que les bact{\'e}ries deviennent la principale source d{\textquoteright}{\'e}nergie des consommateurs, le syst{\`e}me adopte une structure plus complexe, en r{\'e}seau, s{\textquoteright}accompagnant d{\textquoteright}une augmentation de l{\textquoteright}omnivorie du syst{\`e}me. Cette derni{\`e}re pourrait {\^e}tre {\`a} l{\textquoteright}origine d{\textquoteright}une augmentation de la capacit{\'e} du syst{\`e}me {\`a} r{\'e}sister {\`a} l{\textquoteright}efflorescence des cyanobact{\'e}ries. Finalement, nous avons {\'e}galement mis en {\'e}vidence les effets de la destruction des cellules h{\^o}tes des cyanobact{\'e}ries par les chitrides sur la dynamique du r{\'e}seau trophique. En effet, cette derni{\`e}re faciliterait le broutage des cyanobact{\'e}ries et offrirait des voies alternatives aux consommateurs, ce qui augmenteraient la stabilit{\'e} du syst{\`e}me.</p>

<p class="rtejustify">\&nbsp;</p>

<p class="rtejustify">Parasites exist in every ecosystem and can have large influence on food-web structure and function, yet, we know little about parasites{\textquoteright} effect on food-web dynamics. Here we investigate the role of microbial parasitism (viruses of bacteria, phytoplankton and cyanobacteria, and parasitic chytrids on cyanobacteria) on the dynamics of trophic pathways and food-web functioning during a cyanobacteria bloom, using linear inverse food-web modeling parameterized with a 2-month long dataset (biomasses, infection parameters, etc.). We show the importance of grazing on heterotrophic bacteria (the microbial pathway: DOC -\&gt; bacteria -\&gt; consumer) and how consumers depended on bacteria during peak-cyanobacteria bloom, which abundance was partly driven by the viral activity. As bacteria become the main energy pathway to the consumers, the system takes a more web-like structure through increased omnivory, and may thereby facilitate the system{\textquoteright}s persistence to the cyanobacteria outbreak. We also showed how the killing of cyanobacteria host-cells by chytrids had important impact on the food-web dynamics by facilitating grazing on the cyanobacteria, and by offering alternative pathways to the consumers. This seemed to increase the system{\textquoteright}s ability to return to a mix of trophic pathways, which theoretically increases the stability of the system.</p>
},
	doi = {10.1038/s41396-018-0045-9},
	url = {https://doi.org/10.1038/s41396-018-0045-9},
	author = {Haraldsson, Matilda and M{\'e}lanie Gerphagnon and Bazin, Pauline and Samuele Tecchio and T{\'e}l{\'e}sphore Sime-Ngando and Nathalie Niquil}
}
@article {6931,
	title = {Microhabitat characteristics of Stegastes planifrons and S. adustus territories},
	journal = {Environmental Biology of Fishes},
	volume = {101},
	year = {2018},
	month = {Jan-03-2018},
	pages = {441 - 448},
	issn = {0378-1909},
	doi = {10.1007/s10641-017-0709-8},
	url = {http://link.springer.com/10.1007/s10641-017-0709-8},
	author = {Charlotte R. Dromard and Bouchon-Navaro, Yolande and Cordonnier, S{\'e}bastien and Harmelin-Vivien, Mireille and Bouchon, Claude}
}
@inbook {5882,
	title = {Microphytobenthic Biofilms: Composition and Interactions},
	booktitle = {Mudflat Ecology},
	year = {2018},
	pages = {63{\textendash}90},
	publisher = {Springer International Publishing},
	organization = {Springer International Publishing},
	address = {Cham},
	abstract = {<p>Microphytobenthic biofilms in mudflats are characterised by a wide variety of microorganisms and the production of large quantities of extracellular polymeric substances (EPS). In this chapter, the diversity of microphytobenthos (MPB) is reviewed and the complex interactions that take place in mudflat biofilms between microalgae and bacteria are discussed. Microbial interaction in natural biofilms is an emerging field of study in mudflat ecosystems. Although emphasis is placed on EPS and EPS-mediated interactions, because they have received most of the research attention, more direct interactions such as communication and defence are also discussed. Most studies to date have dealt with monospecific or multispecific laboratory biofilms, and environmental studies are still very rare. The development of this field of study in mudflat ecosystems is clearly a major requirement in our understanding of the functioning of mudflat biofilms.</p>
},
	isbn = {978-3-319-99194-8},
	doi = {10.1007/978-3-319-99194-8_4},
	url = {https://doi.org/10.1007/978-3-319-99194-8_4},
	author = {C{\'e}dric Hubas and Passarelli, C and Paterson, David M},
	editor = {Beninger, Peter G.}
}
@article {5431,
	title = {Mission POLARIS : Invert{\'e}br{\'e}s antarctiques et r{\'e}chauffement global},
	volume = {278},
	year = {2018},
	month = {Juin},
	pages = {82-83},
	issn = {0990-0845},
	author = {St{\'e}phane Hourdez and J{\'e}r{\^o}me Fournier and Pierre Chevaldonn{\'e}}
}
@inbook {5883,
	title = {Mudflat Ecosystem Engineers and Services},
	booktitle = {Mudflat Ecology},
	year = {2018},
	pages = {243{\textendash}269},
	publisher = {Springer International Publishing},
	organization = {Springer International Publishing},
	address = {Cham},
	abstract = {<p>Ecosystem engineers play a fundamental role in the creation, maintenance and transformation of habitats in tidal flats. Highly diverse in terms of size, phylogeny, and effect on their environment, they can facilitate or hinder a number of organisms, but generally have a positive influence on both the abundance and the diversity of mudflat organisms. The magnitude of the engineering effect is, however, largely dependent on the biotic and abiotic environment of the engineer. In particular, stressful habitats such as mudflats host a large number of ecosystem engineers; understanding interactions between them, and how they vary with abiotic variables, is therefore of crucial importance, to evaluate how ecosystem engineers affect benthic communities and ecosystem functioning. Such understanding will also help human populations which benefit from mudflat organisms and/or functioning (i.e. which derive ecosystem services from them), to maintain and manage the sustainably of tidal flats, in a way which maintains human health and well-being.</p>
},
	isbn = {978-3-319-99194-8},
	doi = {10.1007/978-3-319-99194-8_10},
	url = {https://doi.org/10.1007/978-3-319-99194-8_10},
	author = {Passarelli, C and C{\'e}dric Hubas and Paterson, David M},
	editor = {Beninger, Peter G.}
}
@article {5924,
	title = {A new species of Schismatogobius (Teleostei: Gobiidae) from Halmahera (Indonesia)},
	journal = {Cybium},
	volume = {42},
	year = {2018},
	pages = {195-200},
	abstract = {<p>\&nbsp;</p>

<p>\&nbsp;Anew species of Schismatogobius, a freshwater goby, is described from Halmahera (Indonesia). It differs from other species belonging to the genus by a high percentage of genetic divergence in partial COIgene (652 bp) and by several characters, including the number of pectoral fin rays, the pattern of the ventral surface of the head, the pectoral fin colour pattern and the jaw length/head length ratio of male and female.</p>
},
	keywords = {Gobiidae, Halmahera, Indonesia, New species, Schismatogobius},
	author = {Philippe Keith and Darhuddin, H. and Limmon, G and Hubert, N}
}
@article {5864,
	title = {{OZCAR}: The French Network of Critical Zone Observatories},
	journal = {Vadose Zone Journal},
	volume = {17},
	year = {2018},
	doi = {10.2136/vzj2018.04.0067},
	url = {https://doi.org/10.2136/vzj2018.04.0067},
	author = {J. Gaillardet and I. Braud and F. Hankard and S. Anquetin and O. Bour and N. Dorfliger and J.R. de Dreuzy and S. Galle and C. Galy and S. Gogo and L. Gourcy and F. Habets and F. Laggoun and L. Longuevergne and T. Le Borgne and F. Naaim-Bouvet and G. Nord and V. Simonneaux and D. Six and T. Tallec and C. Valentin and Gwena{\"e}l Abril and P. Allemand and A. Ar{\`e}nes and B. Arfib and L. Arnaud and N. Arnaud and P. Arnaud and S. Audry and V. Bailly Comte and C. Batiot and A. Battais and H. Bellot and E. Bernard and C. Bertrand and H. Bessi{\`e}re and S. Binet and J. Bodin and X. Bodin and L. Boithias and J. Bouchez and B. Boudevillain and I. Bouzou Moussa and F. Branger and J. J. Braun and P. Brunet and B. Caceres and D. Calmels and B. Cappelaere and H. Celle-Jeanton and F. Chabaux and K. Chalikakis and C. Champollion and Y. Copard and C. Cotel and P. Davy and P. Deline and G. Delrieu and J. Demarty and C. Dessert and M. Dumont and C. Emblanch and J. Ezzahar and M. Est{\`e}ves and V. Favier and M. Faucheux and N. Filizola and P. Flammarion and P. Floury and O. Fovet and M. Fournier and A. J. Francez and L. Gandois and C. Gascuel and E. Gayer and C. Genthon and M. F. G{\'e}rard and D. Gilbert and I. Gouttevin and M. Grippa and G. Gruau and A. Jardani and L. Jeanneau and J. L. Join and H. Jourde and F. Karbou and D. Labat and Yvan Lagadeuc and E. Lajeunesse and R. Lastennet and W. Lavado and E. Lawin and T. Lebel and C. Le Bouteiller and C. Legout and Y. Lejeune and E. Le Meur and N. Le Moigne and J. Lions and A. Lucas and J. P. Malet and C. Marais-Sicre and J. C. Mar{\'e}chal and C. Marlin and P. Martin and J. Martins and J. M. Martinez and N. Massei and A. Mauclerc and N. Mazzilli and J. Mol{\'e}nat and P. Moreira-Turcq and E. Mougin and S. Morin and J. Ndam Ngoupayou and G. Panthou and C. Peugeot and G. Picard and M. C. Pierret and G. Porel and A. Probst and J. L. Probst and A. Rabatel and D. Raclot and L. Ravanel and F. Rejiba and P. Ren{\'e} and O. Ribolzi and J. Riotte and A. Rivi{\`e}re and H. Robain and L. Ruiz and J. M. Sanchez-Perez and W. Santini and S. Sauvage and P. Schoeneich and J. L. Seidel and M. Sekhar and O. Sengtaheuanghoung and N. Silvera and M. Steinmann and A. Soruco and G. Tallec and E. Thibert and D. Valdes Lao and C. Vincent and D. Viville and P. Wagnon and R. Zitouna}
}
@article {Meddeb201866,
	title = {Plankton food-web functioning in anthropogenically impacted coastal waters (SW Mediterranean Sea): An ecological network analysis},
	journal = {Progress in Oceanography},
	volume = {162},
	year = {2018},
	note = {cited By 4},
	pages = {66-82},
	publisher = {Elsevier Ltd},
	abstract = {The study is the first attempt to (i) model spring food webs in three SW Mediterranean ecosystems which are under different anthropogenic pressures and (ii) to project the consequence of this stress on their function. Linear inverse models were built using the Monte Carlo method coupled with Markov Chains to characterize the food-web status of the Lagoon, the Channel (inshore waters under high eutrophication and chemical contamination) and the Bay of Bizerte (offshore waters under less anthropogenic pressure). Ecological network analysis was used for the description of structural and functional properties of each food web and for inter-ecosystem comparisons. Our results showed that more carbon was produced by phytoplankton in the inshore waters (966{\textendash}1234 mg C m-2 d-1) compared to the Bay (727 mg C m-2 d-1). The total ecosystem carbon inputs into the three food webs was supported by high primary production, which was mainly due to \&gt;10 {\textmu}m algae. However, the three carbon pathways were characterized by low detritivory and a high herbivory which was mainly assigned to protozooplankton. This latter was efficient in channelling biogenic carbon. In the Lagoon and the Channel, foods webs acted almost as a multivorous structure with a tendency towards herbivorous one, whereas in the Bay the herbivorous pathway was more dominant. Ecological indices revealed that the Lagoon and the Channel food webs/systems had high total system throughput and thus were more active than the Bay. The Bay food web, which had a high relative ascendency value, was more organized and specialized. This inter{\textendash}ecosystem difference could be due to the varying levels of anthropogenic impact among sites. Indeed, the low value of Finn{\textquoteright}s cycling index indicated that the three systems are disturbed, but the Lagoon and the Channel, with low average path lengths, appeared to be more stressed, as both sites have undergone higher chemical pollution and nutrient loading. This study shows that ecosystem models combined with ecological indices provide a powerful approach to detect change in environmental status and anthropogenic impacts. {\textcopyright} 2018},
	keywords = {Algae, anthropogenic effect, Anthropogenic impacts, Anthropogenic pressures, Bizerte, Bizerte Bay, Chemical analysis, Chemical contamination, coastal water, community structure, Ecological network analysis, Ecology, ecosystem function, ecosystem modeling, Ecosystems, eutrophication, food web, Food webs, Functional properties, Inverse problems, Lakes, Linear inverse models, Markov processes, Mediterranean coastal waters, Mediterranean ecosystem, Mediterranean sea, Monte Carlo methods, network analysis, Phytoplankton, Plankton, primary production, Tunisia, Zooplankton},
	issn = {00796611},
	doi = {10.1016/j.pocean.2018.02.013},
	url = {https://www.sciencedirect.com/science/article/abs/pii/S0079661117300782},
	author = {Meddeb, M. and Grami, B. and Chaalali, A. and Haraldsson, M. and Nathalie Niquil and Pringault, O. and Sakka Hlaili, A.}
}
@article {6799,
	title = {Predicting krill swarm characteristics important for marine predators foraging off East Antarctica},
	journal = {Ecography},
	volume = {41},
	year = {2018},
	pages = {996 - 1012},
	issn = {0906-7590},
	url = {https://onlinelibrary.wiley.com/doi/full/10.1111/ecog.03080},
	author = {Bestley, Sophie and Raymond, Ben and Gales, NJ and Harcourt, RG and Hindell, Mark A and Jonsen, ID and Nicol, S and Clara P{\'e}ron and Sumner, MD and Weimerskirch, H. and Wotherspoon, S. and Cox, MJ}
}
@article {5515,
	title = {Strengths, weaknesses, and opportunities of French research in trophic ecology},
	journal = {Comptes Rendus Biologies},
	year = {2018},
	pages = {-},
	abstract = {<p class="rtejustify">The French National Institute of Ecology and Environment (INEE) aims at fostering pluridisciplinarity in Environmental Science and, for that purpose, funds ex muros research groups (GDR) on thematic topics. Trophic ecology has been identified as a scientific field in ecology that would greatly benefit from such networking activity, as being profoundly scattered. This has motivated the seeding of a GDR, entitled {\^a}GRET{\^a}. The contours of the GRET{\textquoteright}s action, and its ability to fill these gaps within trophic ecology at the French national scale, will depend on the causes of this relative scattering. This study relied on a nationally broadcasted poll aiming at characterizing the field of trophic ecology in France. Amongst all the unique individuals that fulfilled the poll, over 300 belonged at least partly to the field of trophic ecology. The sample included all French public research institutes and career stages. Three main disruptions within the community of scientist in trophic ecology were identified. The first highlighted the lack of interfaces between microbial and trophic ecology. The second evidenced that research questions were strongly linked to single study fields or ecosystem type. Last, research activities are still quite restricted to the ecosystem boundaries. All three rupture points limit the conceptual and applied progression in the field of trophic ecology. Here we show that most of the disruptions within French Trophic Ecology are culturally inherited, rather than motivated by scientific reasons or justified by socio-economic stakes. Comparison with the current literature confirms that these disruptions are not necessarily typical of the French research landscape, but instead echo the general weaknesses of the international research in ecology. Thereby, communication and networking actions within and toward the community of trophic ecologists, as planned within the GRET{\textquoteright}s objectives, should contribute to fill these gaps, by reintegrating microbes within trophic concepts and setting the seeds for trans- and meta-ecosystemic research opportunities. Once the community of trophic ecologists is aware of the scientific benefit in pushing its boundaries forwards, turning words and good intentions into concrete research projects will depend on the opportunities to obtain research funding.</p>
},
	keywords = {Community},
	issn = {1631-0691},
	doi = {https://doi.org/10.1016/j.crvi.2018.05.001},
	url = {https://www.sciencedirect.com/science/article/pii/S1631069118300830},
	author = {Marie-Elodie Perga and Michael Danger and Dubois, Stanislas and Cl{\'e}mentine Fritch and C{\'e}dric Gaucherel and C{\'e}dric Hubas and Franck Jabot and Lacroix, G{\'e}rard and S{\'e}bastien Lefebvre and P. Marmonier and Alexandre Bec}
}
@article {7180,
	title = {Subtidal Microphytobenthos: A Secret Garden Stimulated by the Engineer Species Crepidula fornicata},
	journal = {Frontiers in Marine Science},
	volume = {5},
	year = {2018},
	month = {Jun-12-2019},
	doi = {10.3389/fmars.2018.00475},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2018.00475/full},
	author = {Androuin, Thibault and Polerecky, Lubos and Decottignies, Priscilla and Dubois, Stanislas F. and Dupuy, Christine and C{\'e}dric Hubas and Jesus, Bruno and Le Gall, Erwan and Marzloff, Martin P. and Carlier, Antoine}
}
@article {6708,
	title = {Toxicological effects of CdSe nanocrystals on the marine diatom Phaeodactylum tricornutum: The first mass spectrometry-based proteomic approach},
	journal = {Ecotoxicology and Environmental Safety},
	volume = {152},
	year = {2018},
	month = {Jan-05-2018},
	pages = {78 - 90},
	issn = {01476513},
	doi = {10.1016/j.ecoenv.2018.01.043},
	url = {https://www.sciencedirect.com/science/article/abs/pii/S0147651318300514?via\%3Dihub},
	author = {Poirier, Isabelle and Pallud, Marie and Kuhn, Lauriane and Hammann, Philippe and Demorti{\`e}re, Arnaud and Jamali, Arash and Chicher, Johana and Christelle Caplat and Gallon, R{\'e}gis Kevin and Bertrand, Martine}
}
@article {5923,
	title = {The unique functioning of a pre-Columbian Amazonian floodplain fishery},
	journal = {Scientific Reports},
	volume = {8},
	year = {2018},
	doi = {10.1038/s41598-018-24454-4},
	url = {https://doi.org/10.1038/s41598-018-24454-4},
	author = {Rumsa{\"\i}s Blatrix and Bruno Roux and Philippe B{\'e}arez and Gabriela Prestes-Carneiro and Marcelo Amaya and Jose Luis Aramayo and Leonor Rodrigues and Umberto Lombardo and Jose Iriarte and Jonas Gregorio de Souza and Mark Robinson and Cyril Bernard and Marc Pouilly and M{\'e}lisse Dur{\'e}cu and Carl F. Huchzermeyer and Mashuta Kalebe and Alex Ovando and Doyle McKey}
}
@article {6686,
	title = {Without quality presence-absence data, discrimination metrics such as TSS can be misleading measures of model performance},
	journal = {Journal of Biogeography},
	volume = {45},
	year = {2018},
	month = {Jan-09-2018},
	pages = {1994 - 2002},
	doi = {10.1111/jbi.2018.45.issue-910.1111/jbi.13402},
	url = {http://doi.wiley.com/10.1111/jbi.2018.45.issue-9http://doi.wiley.com/10.1111/jbi.13402http://onlinelibrary.wiley.com/wol1/doi/10.1111/jbi.13402/fullpdfhttps://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111\%2Fjbi.13402},
	author = {Leroy, Boris and Delsol, Robin and Hugueny, Bernard and Meynard, Christine N. and Barhoumi, Ch{\'e}{\"\i}ma and Barbet-Massin, Morgane and Bellard, C{\'e}line}
}
@article {5037,
	title = {Benthic and fish aggregation inside an offshore wind farm: Which effects on the trophic web functioning?},
	journal = {Ecological indicators},
	volume = {72},
	year = {2017},
	month = {01/2017},
	pages = {33-46},
	abstract = {<p class="rtejustify">As part of the energy transition, the French government is planning the construction of three offshore wind farms in Normandy (Bay of Seine and eastern part of the English Channel, north-western France) in the next years. These offshore wind farms will be integrated into an ecosystem already facing multiple anthropogenic disturbances such as maritime transport, fisheries, oyster and mussel farming, and sediment dredging. Currently no integrated, ecosystem-based study on the effects of the construction and exploitation of offshore wind farms exists, where biological approaches generally focused on the conservation of some valuable species or groups of species. Complementary trophic web modelling tools were applied to the Bay of Seine ecosystem (to the 50 km(2) area covered by the wind farm) to analyse the potential impacts of benthos and fish aggregation caused by the introduction of additional hard substrates from the piles and the turbine scour protections. An Ecopath ecosystem model composed of 37 compartments, from phytoplankton to seabirds, was built to describe the situation {\textquoteleft}{\textquoteleft}before{{\textquoteright}{\textquoteright}} the construction of the wind farm. Then, an Ecosim projection over 30 years was performed after increasing the biomass of targeted benthic and fish compartments. Ecological Network Analysis (ENA) indices were calculated for the two periods, {\textquoteleft}{\textquoteleft}before{{\textquoteright}{\textquoteright}} and {\textquoteleft}{\textquoteleft}after{{\textquoteright}{\textquoteright}}, to compare network functioning and the overall structural properties of the food web. Our main results showed (1) that the total ecosystem activity, the overall system omnivory (proportion of generalist feeders), and the recycling increased after the construction of the wind farm; (2) that higher trophic levels such as piscivorous fish species, marine mammals, and seabirds responded positively to the aggregation of biomass on piles and turbine scour protections; and (3) a change in keystone groups after the construction towards more structuring and dominant compartments. Nonetheless, these changes could be considered as limited impacts of the wind farm installation on this coastal trophic web structure and functioning. (C) 2016 Elsevier Ltd. All rights reserved.</p>
},
	issn = {{1470-160X}},
	doi = {10.1016/j.ecolind.2016.07.037},
	author = {Raoux, Aurore and Samuele Tecchio and Pezy, Jean-Philippe and G{\'e}raldine Lassalle and Degraer, Steven and Wilhelmsson, Dan and Cachera, Marie and Ernande, Bruno and Le Guen, Camille and Haraldsson, Matilda and Karine Granger{\'e} and Le Loc{\textquoteright}h, Francois and Dauvin, Jean-Claude and Nathalie Niquil}
}
@article {5005,
	title = {Description of a new maternal larvophilic mouth-brooding cichlid species, Apistogramma megastoma sp. n. (Teleostei: Perciformes: Geophaginae), from Loreto, Peru},
	journal = {Vertebrate Zoology },
	volume = {67},
	year = {2017},
	author = {R{\"o}mer, CI and Estivals, G and Vela Diaz, A and Fabrice Duponchelle and Garcia Davila, C and Hahn, I and Renno, J-F},
	editor = {R{\"o}mer, U}
}
@article {5033,
	title = {Description of a new maternal larvophilic mouth-brooding cichlid species, Apistogramma megastoma sp. n. (Teleostei: Perciformes: Geophaginae), from Loreto, Peru},
	journal = {Vertebrate Zoology },
	volume = {67},
	year = {2017},
	author = {R{\"o}mer, Uwe and R{\"o}mer, CI and Estivals, G and Vela Diaz, A. and Fabrice Duponchelle and Garcia Davila, C and Hahn, I and Renno, Jean-Francois}
}
@article {5031,
	title = {Dynamics of DNA methylomes underlie oyster development},
	journal = {PLoS Genetics},
	volume = {13},
	year = {2017},
	month = {06/2017},
	pages = {e1006807},
	type = {Research Paper},
	url = {https:// doi.org/10.13 71/journal.p gen.1006807},
	author = {Guillaume Rivi{\`e}re and Yan He and Samuele Tecchio and Elizabeth Crowell and Micha{\"e}l Gras and Pascal Sourdaine and Guo, Ximing and Pascal Favrel}
}
@article {6667,
	title = {Dynamics of particulate organic matter composition in coastal systems: A spatio-temporal study at multi-systems scale},
	journal = {Progress in Oceanography},
	volume = {156},
	year = {2017},
	pages = {221-239},
	abstract = {In coastal systems, the multiplicity of sources fueling the pool of particulate organic matter (POM) leads to divergent estimations of POM composition. Eleven systems (two littoral systems, eight embayments and semi-enclosed systems and one estuary) distributed along the three maritime fa{\c c}ades of France were studied for two to eight years in order to quantify the relative contribution of organic matter sources to the surface-water POM pool in coastal systems. This study was based on carbon and nitrogen elemental and isotopic ratios, used for running mixing models. The POM of the estuary is dominated by terrestrial material (93\% on average), whereas the POM of the other systems is dominated by phytoplankton (84\% on average). Nevertheless, for the latter systems, the POM composition varies in space, with (1) systems where POM is highly composed of phytoplankton (>=93\%), (2) systems characterized by a non-negligible contribution of benthic (8{\textendash}19\%) and/or river (7{\textendash}19\%) POM sources, and (3) the Mediterranean systems characterized by the contribution of diazotroph organisms (ca. 14\%). A continent-to-ocean gradient of river and/or benthic POM contribution is observed. Finally, time series reveal (1) seasonal variations of POM composition, (2) differences in seasonality between systems, and (3) an inshore-offshore gradient of seasonality within each system that were sampled at several stations. Spatial and seasonal patterns of POM composition are mainly due to local to regional processes such as hydrodynamics and sedimentary hydrodynamic (e.g. resuspension processes, changes in river flows, wind patterns influencing along-shore currents) but also due to the geomorphology of the systems (depth of the water column, distance to the shore). Future studies investigating the link between these forcings and POM composition would help to better understand the dynamics of POM composition in coastal systems. {\textcopyright} 2017 Elsevier Ltd},
	keywords = {bacterium, benthos, biogeochemistry, Biological materials, C and n stable isotopes, C:N ratio, Carbon, carbon isotope, Coastal systems, coastal zone, Fluid dynamics, France, geomorphology, Hydrodynamics, Isotopes, isotopic ratio, Mediterranean sea, Meta analysis, meta-analysis, Mixing, Mixing models, nitrogen isotope, Organic compounds, particulate organic matter, Particulate organic matters, Phytoplankton, prokaryote, Rivers, seasonality, spatiotemporal analysis, stable isotope, Surface water, Surface waters, terrestrial deposit, Time series},
	issn = {00796611},
	doi = {10.1016/j.pocean.2017.03.001},
	url = {https://www.sciencedirect.com/science/article/abs/pii/S0079661116301914},
	author = {Li{\'e}nart, Camilla and Savoye, Nicolas and Bozec, Yann and Elsa Breton and Conan, Pascal and David, Val{\'e}rie and Eric Feunteun and Karine Granger{\'e} and Kerherv{\'e}, P. and Lebreton, B. and S{\'e}bastien Lefebvre and St{\'e}phane L{\textquoteright}Helguen and Mousseau, Laure and Raimbault, P and Richard, P. and Riera, P. and Sauriau, P.-G. and Gauthier Schaal and Aubert, F. and Aubin, S. and Bichon, S. and Boinet, C. and Bourasseau, L. and Br{\'e}ret, M. and Caparros, J. and Cariou, T. and Charlier, K. and Claquin, P. and Vincent Cornille and Corre, A.-M. and Costes, L. and Crispi, O. and Muriel Crouvoisier and Czamanski, M. and Del Amo, Y. and Derriennic, H. and Dindinaud, F. and Durozier, M. and Hanquiez, V. and Antoine Nowaczyk and Devesa, J. and Ferreira, S. and Fornier, M. and Garcia, F. and Garcia, N. and Geslin, S. and Emilie Grossteffan and Gueux, A. and Guillaudeau, J. and Guillou, G. and Joly, O. and Lachauss{\'e}e, N. and Lafont, M. and Lamoureux, J. and Lecuyer, E. and Lehodey, J.-P. and Lemeille, D. and Leroux, C. and Mac{\'e}, E. and Maria, E. and Pineau, P. and Petit, F. and Pujo-Pay, M. and Rimelin-Maury, P. and Sultan, E.}
}
@article {5908,
	title = {Geography and life history traits account for the accumulation of cryptic diversity among {Indo}-{West} {Pacific} coral reef fishes},
	journal = {Marine Ecology Progress Series},
	volume = {583},
	year = {2017},
	pages = {179{\textendash}193},
	author = {Hubert, Nicolas and Dettai, Agn{\`e}s and Patrice Pruvost and Cruaud, Corinne and Kulbicki, Michel and Myers, Robert F. and Borsa, Philippe}
}
@article {5969,
	title = {The homology and function of the lung plates in extant and fossil coelacanths},
	journal = {Scientific reports},
	volume = {7},
	year = {2017},
	pages = {9244},
	author = {Cupello, C and Meunier, Francois J. and Herbin, Marc and Janvier, Philippe and Cl{\'e}ment, Ga{\"e}l and Brito, Paulo M.}
}
@article {6820,
	title = {Identifying Toxic Impacts of Metals Potentially Released during Deep-Sea Mining{\textemdash}A Synthesis of the Challenges to Quantifying Risk},
	journal = {Frontiers in Marine Science},
	volume = {4},
	year = {2017},
	pages = {368},
	abstract = {In January 2017, the International Seabed Authority released a discussion paper on the development of Environmental Regulations for deep-sea mining (DSM) within the Area Beyond National Jurisdiction (the {\textquotedblleft}Area{\textquotedblright}). With the release of this paper, the prospect for commercial mining in the Area within the next decade has become very real. Moreover, within nations{\textquoteright} Exclusive Economic Zones, the exploitation of deep-sea mineral ore resources could take place on very much shorter time scales and, indeed, may have already started. However, potentially toxic metal mixtures may be released at sea during different stages of the mining process and in different physical phases (dissolved or particulate). As toxicants, metals can disrupt organism physiology and performance, and therefore may impact whole populations, leading to ecosystem scale effects. A challenge to the prediction of toxicity is that deep-sea ore deposits include complex mixtures of minerals, including potentially toxic metals such as copper, cadmium, zinc, and lead, as well as rare earth elements. Whereas the individual toxicity of some of these dissolved metals has been established in laboratory studies, the complex and variable mineral composition of seabed resources makes the a priori prediction of the toxic risk of DSM extremely challenging. Furthermore, although extensive data quantify the toxicity of metals in solution in shallow-water organisms, these may not be representative of the toxicity in deep-sea organisms, which may differ biochemically and physiologically and which will experience those toxicants under conditions of low temperature, high hydrostatic pressure, and potentially altered pH. In this synthesis, we present a summation of recent advances in our understanding of the potential toxic impacts of metal exposure to deep-sea meio- to megafauna at low temperature and high pressure, and consider the limitation of deriving lethal limits based on the paradigm of exposure to single metals in solution. We consider the potential for long-term and far-field impacts to key benthic invertebrates, including the very real prospect of sub-lethal impacts and behavioral perturbation of exposed species. In conclusion, we advocate the adoption of an existing practical framework for characterizing bulk resource toxicity in advance of exploitation.},
	issn = {2296-7745},
	doi = {10.3389/fmars.2017.00368},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2017.00368},
	author = {Hauton, Chris and Brown, Alastair and Thatje, Sven and Mestre, N{\'e}lia C. and Bebianno, Maria J. and Martins, In{\^e}s and Bettencourt, Raul and Canals, Miquel and Sanchez-Vidal, Anna and Bruce Shillito and Juliette Ravaux and Magali Zbinden and Duperron, S{\'e}bastien and Mevenkamp, Lisa and Vanreusel, Ann and Gambi, Cristina and Dell{\textquoteright}Anno, Antonio and Danovaro, Roberto and Gunn, Vikki and Weaver, Phil}
}
@article {5026,
	title = {The impact of suspended oyster farming on nitrogen cycling and nitrous oxide production in a sub-tropical Australian estuary},
	journal = {Estuarine, Coastal and Shelf Science},
	volume = {192},
	year = {2017},
	pages = {117 - 127},
	abstract = {<p>In this study we quantified nitrate (NO3-) reduction (denitrification, anammox and DNRA) and N2O production in sediments and epibiont communities associated with Sydney Rock Oyster (Saccostrea glomerata) farming. In sediments beneath an active suspended oyster farm, DNRA accounted for 98\% of NO3- reduction with rates of up to 169\&nbsp;{\textpm}\&nbsp;45\&nbsp;μmol\&nbsp;N m-2 h-1. Much of this DNRA was fuelled by NO3- derived from nitrification. Reference sediments had significantly lower DNRA rates of 83.8\&nbsp;{\textpm}\&nbsp;28.2\&nbsp;μmol\&nbsp;N m-2 h-1, however this constituted 96\% of the sites total NO3- reduction. Fatty acid analysis showed that sediment organic matter was more labile in the oyster impacted sediments, facilitating subtle shifts in sediment oxygen demand which increased the Fe2+ availability with respect to the reference sediments. The difference in DNRA rate between the sites was attributed to autotrophic oxidation of soluble Fe2+ in sediments underlying the oyster cultures. DNRA was absent in the oyster shell epibiont communities and rates of anammox and denitrification were lower than in the sediments. Production of NH4+ from the oysters and their associated epibionts was larger than DNRA and reached a rate of 206.2\&nbsp;μmol\&nbsp;N m-2 h-1. Nitrous oxide production rates were generally low compared to other aquaculture systems and the net flux of N2O for the combined oyster cultivation system (i.e. sediments plus epibionts) was negative, i.e. there was N2O consumption in the sediments beneath the oysters. Overall, subtropical suspended oyster farming systems favour inorganic N retention over N loss.</p>
},
	keywords = {Dissimilatory nitrate reduction to ammonium},
	issn = {0272-7714},
	doi = {http://dx.doi.org/10.1016/j.ecss.2017.05.007},
	url = {http://www.sciencedirect.com/science/article/pii/S0272771417301592},
	author = {Dirk V. Erler and David T. Welsh and William W. Bennet and Tarik Meziane and C{\'e}dric Hubas and Daniele Nizzoli and Angus J.P. Ferguson}
}
@article {8571,
	title = {Marine Mammals Exploring the Oceans Pole to Pole: A Review of the MEOP Consortium},
	journal = {Oceanography},
	volume = {30},
	year = {2017},
	month = {Jan-06-2017},
	pages = {132 - 138},
	issn = {10428275},
	doi = {10.5670/oceanog10.5670/oceanog.2017.234},
	url = {https://tos.org/oceanography/},
	author = {Treasure, Anne and Roquet, Fabien and Ansorge, Isabelle and Bester, Marth{\'a}n and Boehme, Lars and Bornemann, Horst and Charrassin, Jean-Beno{\^\i}t and Chevallier, Damien and Costa, Daniel and Fedak, Mike and Guinet, Christophe and Hammill, Mike and Harcourt, Robert and Hindell, Mark and Kovacs, Kit and Lea, Mary-Anne and Lovell, Phil and Lowther, Andrew and Lydersen, Christian and McIntyre, Trevor and McMahon, Clive and Muelbert, M{\^o}nica and Nicholls, Keith and Picard, Baptiste and Reverdin, Gilles and Trites, Andrew and Williams, Guy and de Bruyn, P.J. Nico}
}
@article {5231,
	title = {Mercury contamination level and speciation inventory in Lakes Titicaca and Uru-Uru (Bolivia): Current status and future trends},
	journal = {Environmental Pollution},
	volume = {231, Part 1},
	year = {2017},
	pages = {262 - 270},
	abstract = {<p>Aquatic ecosystems of the Bolivian Altiplano (\~{}3800 m a.s.l.) are characterized by extreme hydro-climatic constrains (e.g., high UV-radiations and low oxygen) and are under the pressure of increasing anthropogenic activities, unregulated mining, agricultural and urban development. We report here a complete inventory of mercury (Hg) levels and speciation in the water column, atmosphere, sediment and key sentinel organisms (i.e., plankton, fish and birds) of two endorheic Lakes of the same watershed differing with respect to their size, eutrophication and contamination levels. Total Hg (THg) and monomethylmercury (MMHg) concentrations in filtered water and sediment of Lake Titicaca are in the lowest range of reported levels in other large lakes worldwide. Downstream, Hg levels are 3-10 times higher in the shallow eutrophic Lake Uru-Uru than in Lake Titicaca due to high Hg inputs from the surrounding mining region. High percentages of MMHg were found in the filtered and unfiltered water rising up from \&lt;1 to \~{}50\% THg from the oligo/hetero-trophic Lake Titicaca to the eutrophic Lake Uru-Uru. Such high \%MMHg is explained by a high in situ MMHg production in relation to the sulfate rich substrate, the low oxygen levels of the water column, and the stabilization of MMHg due to abundant ligands present in these alkaline waters. Differences in MMHg concentrations in water and sediments compartments between Lake Titicaca and Uru-Uru were found to mirror the offset in MMHg levels that also exist in their respective food webs. This suggests that in situ MMHg baseline production is likely the main factor controlling MMHg levels in fish species consumed by the local population. Finally, the increase of anthropogenic pressure in Lake Titicaca may probably enhance eutrophication processes which favor MMHg production and thus accumulation in water and biota.</p>
},
	keywords = {Titicaca},
	issn = {0269-7491},
	doi = {https://doi.org/10.1016/j.envpol.2017.08.009},
	url = {https://www.sciencedirect.com/science/article/pii/S0269749117320572},
	author = {S. Gu{\'e}dron and D. Point and D. Acha and S. Bouchet and P.A. Baya and E. Tessier and M. Monperrus and C.I. Molina and A. Groleau and Laurent Chauvaud and J. Thebault and E. Amice and L. Alanoca and C. Duwig and G. Uzu and Lazzaro, Xavier and A. Bertrand and S. Bertrand and C. Barbraud and K. Delord and Gibon, Francois-Marie and C. Ibanez and M. Flores and P. Fernandez Saavedra and M.E. Ezpinoza and C. Heredia and F. Rocha and C. Zepita and D. Amouroux}
}
@article {G{\'e}rard20172211,
	title = {Metazoan parasite communities in Alosa alosa (Linnaeus, 1758) and Alosa fallax (Lac{\'e}p{\`e}de, 1803) (Clupeidae) from North-East Atlantic coastal waters and connected rivers},
	journal = {Parasitology Research},
	volume = {116},
	number = {8},
	year = {2017},
	note = {cited By 1},
	pages = {2211-2230},
	doi = {10.1007/s00436-017-5525-8},
	url = {https://link.springer.com/article/10.1007\%2Fs00436-017-5525-8},
	author = {G{\'e}rard, C. and Herv{\'e}, M. and Gay, M. and Bourgau, O. and Eric Feunteun and Anthony Acou and R{\'e}veillac, E.}
}
@article {4724,
	title = {Multi-approach analysis to assess diet of harbour porpoises Phocoena phocoena in the southern North Sea},
	journal = {Marine Ecology and Progress Series},
	volume = {563},
	year = {2017},
	month = {01/2017},
	pages = {249-259},
	abstract = {<p>Over the past decade, the distribution of harbour porpoises Phocoena phocoena has undergone a southward shift in the North Sea, which has led to an increase in the number of stranded porpoises in its southern part. Since the changes in distribution and relative abundance of porpoises may be linked to the changes in prey availability, the aim of the present work was to investigate whether any changes in the feeding habits of harbour porpoises along the North Sea occurred in the past decade. The diet of harbour porpoises stranded along the southern North Sea (northern France and Belgian coast) was assessed through 3 complementary methods: stomach content analysis, stable isotopes (carbon and nitrogen) analysis determined from muscle samples, and fatty acids analysis determined from blubber samples. Fatty acid patterns and stable isotope values from 52 porpoises were compared to 14 potential prey species collected from the southern North Sea. Our results showed that the diet of porpoises along the southern North Sea comprises fish species that are among the most abundant and widely distributed in the area, except for the sardine Sardina pilchardus that appeared to be a new potential prey. Moreover, our results suggested that the decline in sandeel (Ammodytidae) in the northern parts of the North Sea along with the re-invasion of the southern North Sea by sardine species might affect the distribution of harbour porpoises.</p>
},
	author = {Mahfouz, C and Tarik Meziane and Henry, F and Abi-Ghanem, C and Spitz, J and Jauniaux, T and Bouveroux, T and Khalef, G}
}
@article {5153,
	title = {{A nanoscale study of carbon and nitrogen fluxes in mats of purple sulfur bacteria: implications for carbon cycling at the surface of coastal sediments}},
	journal = {Frontiers in Microbiology},
	volume = {8},
	year = {2017},
	pages = {1995},
	abstract = {<p>Mass blooms of purple sulfur bacteria growing seasonally on green stranded macroalgae have a major impact on the microbial composition and functionality of intertidal mats. To explore the active anoxygenic phototrophic community in purple bacterial mats from the Roscoff Aber Bay (Brittany, France), we conducted a combined approach including molecular and high-resolution secondary ion mass spectrometry (NanoSIMS) analyses. To investigate the dynamics of carbon and nitrogen assimilation activities, NanoSIMS was coupled with a stable isotope probing (SIP) experiment and a compound specific isotope analysis (CSIA) of fatty acid methyl ester (FAME). Sediment samples were incubated with 13C- and/or 15N-labelled acetate, pyruvate, bicarbonate and ammonium. NanoSIMS analysis of 13C - and 15N -incubated samples showed elevated incorporations of 13C - and 15N in the light and of 13C -acetate in the dark into dense populations of spherical cells that unambiguously dominated the mats. These results confirmed CSIA data that ranked vaccenic acid, an unambiguous marker of purple sulfur bacteria, as the most strongly enriched in the light after 13C -acetate amendment and indicated that acetate uptake, the most active in the mat, was not light-dependent. Analysis of DNA- and cDNA-derived pufM gene sequences revealed that Thiohalocapsa-related clones dominated both libraries and were the most photosynthetically active members of the mat samples. This study provides novel insights into the contribution of purple sulfur bacteria to the carbon cycle during their seasonal developments at the sediment surface in the intertidal zone.</p>
},
	doi = {10.3389/fmicb.2017.01995},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2017.01995/abstract},
	author = {C{\'e}dric Hubas and Boeuf, Dominique and Bruno Jesus and Najet Thiney and Bozec, Yann and Christian Jeanthon}
}
@article {6928,
	title = {The nutritional quality of non-calcified macroalgae in Guadeloupe (Lesser Antilles) evaluated by their biochemical composition},
	journal = {Gulf and Caribbean Research},
	volume = {28},
	year = {2017},
	pages = {1-6},
	author = {Charlotte R. Dromard and Bouchon, Yolande and Harmelin-Vivien, Mireille and Bouchon, Claude}
}
@article {4341,
	title = {Physiological adjustments and transcriptome reprogramming are involved in the acclimation to salinity gradients in diatoms},
	journal = {Environmental Microbiology},
	volume = {19},
	year = {2017},
	month = {5},
	pages = {909-925},
	abstract = {<p>Salinity regimes in estuaries and coastal areas vary with river discharge patterns, seawater evaporation, the morphology of the coastal waterways, and the dynamics of marine water mixing. Therefore, microalgae have to respond to salinity variations at time scales ranging from daily to annual cycles. Microalgae may also have to adapt to physical alterations that induce the loss of connectivity between habitats and the enclosure of bodies of water. Here, we integrated physiological assays and measurements of morphological plasticity with a functional genomics approach to examine the regulatory changes that occur during the acclimation to salinity in the estuarine diatom Thalassiosira weissflogii. We found that cells exposed to different salinity regimes for a short or long period presented adjustments in their carbon fractions, silicon pools, pigment concentrations and/or photosynthetic parameters. Salinity-induced alterations in frustule symmetry were observed only in the long-term cultures. Whole transcriptome analyses revealed a down-regulation of nuclear and plastid encoded genes during the long-term response and identified only a few regulated genes that were in common between the short- and long-term responses. We propose that in diatoms, one strategy for acclimating to salinity gradients and maintaining optimal cellular fitness could be a reduction in the cost of transcription. This article is protected by copyright. All rights reserved.</p>
},
	issn = {1462-2920},
	doi = {10.1111/1462-2920.13398},
	url = {http://dx.doi.org/10.1111/1462-2920.13398},
	author = {Adrien Bussard and Corre, Erwan and C{\'e}dric Hubas and Duvernois-Berthet, Evelyne and Gildas Le Corguille and Jourdren, Laurent and Coulpier, Fanny and Pascal Claquin and Pascal Jean Lopez}
}
@article {5016,
	title = {Rapid de novo assembly of the European eel genome from nanopore sequencing reads},
	journal = {Scientific Reports},
	volume = {7},
	year = {2017},
	pages = {7213},
	author = {J. Jansen and M. Liem and S. Jong-Raadsen and Sylvie Dufour and Weltzien, Finn-Arne and W. Swinkels and A. Koelewijn and A. Palstra and B. Pelster and H. Spaink and G. van den Thillart and Dirks, Ron and Christiaan V Henkel}
}
@article {5366,
	title = {Regional and latitudinal patterns of soft-bottom macrobenthic invertebrates along French coasts: Results from the RESOMAR database},
	journal = {Journal of Sea Research},
	volume = {130},
	year = {2017},
	pages = {96 - 106},
	abstract = {<p>This study aims to describe the patterns of soft bottom macrozoobenthic richness along French coasts. It is based on a collaborative database developed by the {\textquotedblleft}R{\'e}seau des Stations et Observatoires Marins{\textquotedblright} (RESOMAR). We investigated patterns of species richness in sublittoral soft bottom habitats (EUNIS level 3) at two different spatial scales: 1) seaboards: English Channel, Bay of Biscay and Mediterranean Sea and 2) 0.5{\textdegree} latitudinal and longitudinal grid. Total observed richness, rarefaction curves and three incidence-based richness estimators (Chao2, ICE and Jacknife1) were used to compare soft bottom habitats species richness in each seaboard. Overall, the Mediterranean Sea has the highest richness and despite higher sampling effort, the English Channel hosts the lowest number of species. The distribution of species occurrence within and between seaboards was assessed for each major phylum using constrained rarefaction curves. The Mediterranean Sea hosts the highest number of exclusive species. In pairwise comparisons, it also shares a lower proportion of taxa with the Bay of Biscay (34.1\%) or the English Channel (27.6\%) than that shared between these two seaboards (49.7\%). Latitudinal species richness patterns along the Atlantic and English Channel coasts were investigated for each major phylum using partial LOESS regression controlling for sampling effort. This showed the existence of a bell-shaped latitudinal pattern, highlighting Brittany as a hotspot for macrobenthic richness at the confluence of two biogeographic provinces.</p>
},
	keywords = {France, Latitudinal pattern, Regional pattern, Soft-bottom, Species richness, Zoobenthos},
	issn = {1385-1101},
	doi = {https://doi.org/10.1016/j.seares.2017.03.011},
	url = {http://www.sciencedirect.com/science/article/pii/S1385110116302660},
	author = {R{\'e}gis K. Gallon and Nicolas Lavesque and Jacques Grall and C{\'e}line Labrune and Antoine Gr{\'e}mare and Guy Bachelet and Hugues Blanchet and Paulo Bonif{\'a}cio and Vincent M.P. Bouchet and Jean-Claude Dauvin and Nicolas Desroy and Franck Gentil and Laurent Guerin and C{\'e}line Houbin and J{\'e}r{\^o}me Jourde and Sandrine Laurand and Michel Le Duff and Vincent Le Garrec and Xavier de Montaudouin and Fr{\'e}d{\'e}ric Olivier and Francis Orvain and Pierre-Guy Sauriau and Eric Thi{\'e}baut and Olivier Gauthier}
}
@article {4780,
	title = {Resource use of three juvenile scarids (Cryptotomus roseus, Scarus iseri, Sparisoma radians) in Caribbean seagrass beds},
	journal = {Aquatic Botany},
	volume = {136},
	year = {2017},
	pages = {1-8},
	abstract = {<p>The bucktooth parrotfish\&nbsp;<em>Sparisoma radians</em>, the striped parrotfish\&nbsp;<em>Scarus iseri</em>\&nbsp;and the bluelip parrotfish\&nbsp;<em>Cryptotomus roseus</em>\&nbsp;are three herbivorous fishes commonly found at juvenile stages in Caribbean seagrass beds. While the diet of the three species as adults is relatively well known, few studies have been conducted on the feeding patterns of juveniles. In this study, the resource use of the juveniles of three scarid species were studied using two complementary methods: gut content and stable isotope analyses (13C:12C and\&nbsp;15N:14N ratios). Bayesian mixing model approaches were used to calculate the contribution of each food item to fish diets (SIAR, mixing models). The three parrotfish species appeared to rely essentially on the consumption of fleshy macrophytes.\&nbsp;<em>Cryptotomus roseus</em>\&nbsp;consumed more benthic invertebrates and presented a higher trophic level than the two other scarid species.\&nbsp;<em>Scarus iseri\&nbsp;</em>presented a higher assimilation of benthic biofilm, in accordance with the high percentage of sediment in its gut content, and\&nbsp;<em>Sparisoma radians</em>\&nbsp;assimilated more\&nbsp;<em>Thalassia testudinum</em>\&nbsp;leaves. This research highlighted a food resources partitioning among the juveniles of the three herbivorous fishes, probably to avoid inter-specific competitive interactions for the most palatable food at a critical stage of their life.</p>

<p><strong>Keywords:\&nbsp;</strong>Gut content analyses; Trophic niche; Stable isotopes analyses</p>
},
	doi = {DOI: 10.1016/j.aquabot.2016.08.003},
	author = {Charlotte R. Dromard and Vaslet, Amandine and Gautier, F and Yolande Bouchon-Navaro and Mireille Harmelin-Vivien and Claude Bouchon}
}
@article {8718,
	title = {Responses of primary cultured haemocytes derived from the marine gastropod Haliotis tuberculata to an industrial effluent exposure},
	journal = {Cytotechnology},
	volume = {69},
	year = {2017},
	month = {Jan-04-2017},
	pages = {191 - 200},
	issn = {0920-9069},
	doi = {10.1007/s10616-016-0050-7},
	url = {http://link.springer.com/10.1007/s10616-016-0050-7},
	author = {Ladhar-Chaabouni, Rim and Houel, Thomas and Serpentini, Antoine and Karray, Sahar and Lebel, Jean-Marc and Hamza-Chaffai, Amel}
}
@article {5024,
	title = {Schismatogobius (Gobiidae) from Indonesia, with description of four new species},
	journal = {Cybium},
	volume = {41},
	year = {2017},
	month = {06/2017},
	pages = {195-211},
	abstract = {<p class="rtejustify">The species of Schismatogobius from Indonesia are reviewed and compared to the known species described from the area. Eight species are recognized including four new species. These are described using genetic and morphomeristic approaches. The species differ by a high percentage of genetic divergence in partial COI gene (652 bp) and by several characters including the number of pectoral fin rays, the pattern of the ventral surface of the head in males and/or females, the pectoral fin colour pattern, the jaw length/head length ratio or the jaw length of male and/or female.</p>
},
	keywords = {Gobiidae, Indonesia, New species, Schismatogobius},
	author = {Philippe Keith and Clara Lord and Darhuddin, H. and Limmon, G and Sukmono, T and Hadiaty, Renny and Hubert, Nicolas}
}
@article {5000,
	title = {Seasonal and latitudinal variation in seagrass mechanical traits across Europe: The influence of local nutrient status and morphometric plasticity},
	journal = {Limnology and Oceanography},
	year = {2017},
	abstract = {<p>Seagrasses are marine flowering plants distributed worldwide. They are however threatened, mostly due to the increase of human activities. Seagrasses have the capacity to adapt their morphological, physiological, and mechanical traits to their local conditions. Mechanical traits have been identified as a good tool to investigate a plant-species capacity to withstand physical forces or disturbances but are still sparsely studied in seagrasses. With this study, we aimed to assess how the mechanical traits of a broadly spread seagrass species vary along a latitudinal gradient in relation to its morphometric plasticity and nutrient status. We found that seagrasses acclimate their mechanical traits in relation to their physiological or morphological traits, both over the growing season and across a latitudinal range: leaves were weaker and thinner in northern areas, particularly at the end of the growing season. Besides the influence of the latitudinal gradient, leaf mechanical strength and stiffness were both strongly affected by their morphometric plasticity. Moreover, we showed that leaves mechanical traits change depending on their nutrient status: leaves were stronger and stiffer in oligotrophic conditions as compared to more eutrophic conditions. Thus, our results imply that, under eutrophication, leaves become weaker and thus more vulnerable to physical forces. This vulnerability is higher in the north at the end of the growing season. The latter is consistent with the more ephemeral character of northern seagrass meadows, in contrast to the more evergreen southern meadows.</p>
},
	doi = {10.1002/lno.10611},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/lno.10611/full},
	author = {L.M. Soissons and M.M. van Katwijk and G. Peralta and F.G. Brun and P.G. Cardoso and T.F. Grilo and B. Ondiviela and M. Recio and M. Valle and J.M. Garmendia and F. Ganthy and I. Auby and L. Rigouin and Laurent Godet and J{\'e}r{\^o}me Fournier and Nicolas Desroy and L. Barill{\'e} and P. Kadel and R. Asmus and P.M.J. Herman and T.J. Bouma}
}
@article {4584,
	title = {Specific gravity and migratory patterns of amphidromous gobioid fish from Okinawa Island, Japan},
	journal = {Journal of Experimental Marine Biology and Ecology},
	volume = {486},
	year = {2017},
	pages = {160-169},
	abstract = {<p>Amphidromy is a diadromous life history pattern where fish spawn in freshwater, and their larvae drift downstream to the sea; the larvae develop in marine environments then migrate back in rivers to grow and reproduce. Two amphidromous types with different life history characteristics, such as egg and larval sizes, exist. To understand the ecology and early life history of amphidromous gobioid fish, six species from Okinawa Island were selected{\textemdash}two large egg-type species (Rhinogobius similis and Tridentiger kuroiwae) and four small egg-type species (Stiphodon percnopterygionus, Stenogobius sp., Sicyopterus lagocephalus, and Eleotris acanthopoma). The migratory pattern of four of these species was confirmed using otolith Sr:Ca and Ba:Ca ratios combined with water chemistry analysis. Although these species showed amphidromous migratory patterns, the timing of migration from estuarine to freshwater habitats was species-specific. The large egg-type, R. similis, showed three different migratory patterns: a long marine larval phase with a relatively fast migration from estuarine to freshwater habitats, a short marine larval phase with a relatively fast migration, and a gradual migration. Similar patterns of a long and fast migration or a gradual migration were seen in T. kuroiwae; however, the two small eggtype species, Sti. percnopterygionus and Stenogobius sp., showed rapid migration to freshwater after entering the river. To estimate larval ecology in the sea, ontogenetic changes in specific gravity (SG) were examined in all species. The SG was measured day and night for 1{\textendash}5 days until settlement in R. similis and T. kuroiwae, and until 10 days after hatching in the other species. The SG of all species ranged from 1.0138 to 1.0488, and varied among ontogenetic stages and between day and night and species. Larval SG was relatively similar between R. similis and T. kuroiwae, with low SG in the early stages and high SG after yolk absorption. During the late larval stages and until settlement, T. kuroiwae showed diel changes in SG, with higher SG during the day, whereas R. similis had a relatively constant pattern. The diel changes of T. kuroiwae larvae suggest different activity during the day and at night (e.g. diel vertical migration). In the four small egg-type species, SG was high at hatching and decreased thereafter, not showing large diel changes. The results suggest that sympatric amphidromous gobioid species have various early life histories that may be influenced by several larval traits, including SG.</p>
},
	keywords = {Buoyancy, diadromy, Early life history, Migratory history, otolith, Specific gravity},
	author = {Iida, Midori and Masashi Kondo and H{\'e}l{\`e}ne Tabouret and Maeda, Ken and P{\'e}cheyran, C and Atsushi Hagiwara and Philippe Keith and Katsunori Tachihara}
}
@article {4745,
	title = {Structural bias in aggregated species-level variables driven by repeated species co-occurrences: a pervasive problem in community and assemblage data},
	journal = {Journal of Biogeography},
	year = {2017},
	month = {02/2017},
	abstract = {Aim Species attributes are often used to explain diversity patterns across assemblages/communities. However, repeated species co-occurrences can generate spatial pattern and strong statistical relationships between aggregated attributes and richness in the absence of biological information. Our aim is to increase awareness of this problem. Location North America. Methods We generated empirical species richness patterns using two data structures: (1) birds gridded from range maps and (2) tree communities from the US Forest Service{\textquoteright}s Forest Inventory and Analysis. We analysed richness using linear regression, regression trees, generalized additive models, geographically weighted regression and simultaneous autoregression, with {\textquoteleft}random intrinsic variables{\textquoteright} as predictors generated by assigning random numbers to species and calculating averages in assemblages. We then generated simulations in which species with cohesive or patchy distributions are placed with respect to the North American temperature gradient with or without a broad-scale richness gradient. Random intrinsic variables are again used as predictors of richness. Finally, we analysed one simulated scenario with random intrinsic variables as both response and predictor variables. Results The models of bird and tree richness often explained moderate to large proportions of the variance. Regression trees, geographically weighted regression and simultaneous autoregression were very sensitive to the problem; generalized additive models were moderately affected, as was multiple regression to a lesser extent. In the virtual data, the variance explained increased with increasing species co-occurrences, but neither range cohesion, a richness gradient nor spatial autocorrelation in predictors had major impacts on the variance explained. The problem persisted when the response variable was also a random intrinsic variable. Main conclusions Repeated species co-occurrences can generate strong spurious relationships between richness and aggregated species attributes. It is important to realize that models utilizing assemblage variables aggregated from species-level values, as well as maps illustrating their spatial patterns, cannot be taken at face value.},
	keywords = {community structure, community weighted means, geographical ecology, intrinsic variables, spatial analysis, species co-occurrence, species composition, species richness gradients, trait analysis},
	issn = {1365-2699},
	doi = {10.1111/jbi.12953},
	url = {http://dx.doi.org/10.1111/jbi.12953},
	author = {Hawkins, Bradford A. and Leroy, Boris and Rodr{\'\i}guez, Miguel {\'A}. and Singer, Alexander and Vilela, Bruno and Villalobos, Fabricio and Wang, Xiangping and Zelen{\'y}, David}
}
@article {5046,
	title = {Towards ecosystem-based management: identifying operational food-web indicators for marine ecosystems},
	journal = {ICES Journal of Marine Science},
	year = {2017},
	pages = {fsw230},
	author = {Tam, Jamie C and Link, Jason S and Rossberg, Axel G. and Rogers, Stuart I and Levin, Philip S and Rochet, Marie-Jo{\"e}lle and Bundy, Alida and Belgrano, Andrea and Libralato, Simone and Maciej Tomasz Tomczak and van de Wolfshaar, K and Pranovi, F and Gorokhova, E and Large, S I and Nathalie Niquil and Greenstreet, SPR and Druon, JN and Lesutiene, J and Johansen, M and Preciado, I and Patr{\'\i}cio, Joana and Palialexis, A and Tett, P and Johansen, GO and Houle, J and Rindorf, A}
}
@article {Tam20172040,
	title = {Towards ecosystem-based management: Identifying operational food-web indicators for marine ecosystems},
	journal = {ICES Journal of Marine Science},
	volume = {74},
	number = {7},
	year = {2017},
	note = {cited By 25},
	pages = {2040-2052},
	publisher = {Oxford University Press},
	abstract = {Modern approaches to Ecosystem-Based Management and sustainable use of marine resources must account for the myriad of pressures (interspecies, human and environmental) affecting marine ecosystems. The network of feeding interactions between co-existing species and populations (food webs) are an important aspect of all marine ecosystems and biodiversity. Here we describe and discuss a process to evaluate the selection of operational food-web indicators for use in evaluating marine ecosystem status. This process brought together experts in food-web ecology, marine ecology, and resource management, to identify available indicators that can be used to inform marine management. Standard evaluation criteria (availability and quality of data, conceptual basis, communicability, relevancy to management) were implemented to identify practical food-web indicators ready for operational use and indicators that hold promise for future use in policy and management. The major attributes of the final suite of operational food-web indicators were structure and functioning. Indicators that represent resilience of the marine ecosystem were less developed. Over 60 potential food-web indicators were evaluated and the final selection of operational food-web indicators includes: the primary production required to sustain a fishery, the productivity of seabirds (or charismatic megafauna), zooplankton indicators, primary productivity, integrated trophic indicators, and the biomass of trophic guilds. More efforts should be made to develop thresholds-based reference points for achieving Good Environmental Status. There is also a need for international collaborations to develop indicators that will facilitate management in marine ecosystems used by multiple countries. {\textcopyright} 2017 International Council for the Exploration of the Sea. All rights reserved.},
	keywords = {Biomass, coexistence, ecosystem approach, ecosystem management, ecosystem resilience, environmental assessment, environmental indicator, food web, marine ecosystem, primary production, strategic approach, trophic status},
	issn = {10543139},
	doi = {10.1093/icesjms/fsw230},
	url = {https://academic.oup.com/icesjms/article-abstract/74/7/2040/2970046},
	author = {Tam, J.C. and Link, J.S. and Rossberg, A.G. and Rogers, S.I. and Levin, P.S. and Rochet, M.-J. and Bundy, A. and Belgrano, A. and Libralato, S. and Maciej Tomasz Tomczak and Van De Wolfshaar, K. and Pranovi, F. and Gorokhova, E. and Large, S.I. and Nathalie Niquil and Greenstreet, S.P.R. and Druon, J.-N. and Lesutiene, J. and Johansen, M. and Preciado, I. and Patricio, J. and Palialexis, A. and Tett, P. and Johansen, G.O. and Houle, J. and Rindorf, A.}
}
@article {4988,
	title = {Toxicity assessment of five emerging pollutants, alone and in binary or ternary mixtures, towards three aquatic organisms},
	journal = {Environmental Science and Pollution Research},
	year = {2017},
	abstract = {<p>Despite a growing scientific attention on ecological impact of emerging pollutants (EPs) such as pharmaceuticals, personal care products, and pesticides, knowledge gaps remain regarding mixture toxicity and effects on aquatic organisms. Several EPs were screened in seawater (Normandy, France), and the ecotoxicity of five compounds, chosen on their occurrence in ecosystems and use worldwide, was assessed and were the biocides methylparaben (MP) and triclosan (TCS), a pesticide degradation product (AMPA), and the pharmaceuticals venlafaxine (VEN) and carbamazepine (CBZ). The acute or sub-chronic toxicity, alone or in binary/ternary mixtures of three of them (CBZ, AMPA, and MP), was assessed on one marine and two freshwater organisms: Crassostrea gigas, Pseudokirchneriella subcapitata, and Daphnia magna. TCS and AMPA were, respectively, the most (EC50 \&lt; 1 mg L-1) and the least (EC50 \&gt; 50 mg L-1) toxic chemicals for the four endpoints (algal growth inhibition, daphnia immobilization, oyster embryotoxicity, and metamorphosis). The anxiolytic VEN (EC50 \&lt; 1 mg L-1) was particularly toxic to oyster larvae showing sensitivity difference between freshwater and marine organisms. If all the mixtures appeared to be in the same range of toxicity, the joint-toxic effects mainly led to synergistic or antagonistic interactions compared to single-compound toxicity. The data also highlighted species-dependent differing models of toxicity and underscored the need for an awareness of cocktail effects for better ecological risk assessment.</p>
},
	keywords = {Freshwater species, Marine bivalve, Mixture and single-compound toxicity, Personal care products, Pesticides, pharmaceuticals},
	doi = {DOI 10.1007/s11356-017-9306-9},
	author = {Di Poi, Carole and Katherine Costil and Bouchart, Valerie and Halm-Lemeille, Marie-Pierre}
}
@article {Houssard201749,
	title = {Trophic position increases with thermocline depth in yellowfin and bigeye tuna across the Western and Central Pacific Ocean},
	journal = {Progress in Oceanography},
	volume = {154},
	year = {2017},
	note = {cited By 12},
	pages = {49-63},
	doi = {10.1016/j.pocean.2017.04.008},
	url = {https://www.sciencedirect.com/science/article/pii/S007966111630177X},
	author = {Houssard, P. and Lorrain, A. and Tremblay-Boyer, L. and Allain, V. and Graham, B.S. and Menkes, C.E. and Pethybridge, H. and Couturier, L.I.E. and Point, D. and Leroy, Bruno and Receveur, A. and Hunt, B.P.V. and Vourey, E. and Bonnet, S. and Rodier, M. and Raimbault, P. and Eric Feunteun and Kuhnert, P.M. and Munaron, J.-M. and Lebreton, B. and Otake, T. and Letourneur, Y.}
}
@article {5044,
	title = {Uses of innovative modeling tools within the implementation of the marine strategy framework directive},
	journal = {Bridging the Gap Between Policy and Science in Assessing the Health Status of Marine Ecosystems},
	year = {2017},
	pages = {75},
	author = {Lynam, Christopher P. and Uusitalo, Laura and Patr{\'\i}cio, Joana and Piroddi, Chiara and Queir{\'o}s, Ana M and Teixeira, Heliana and Rossberg, Axel G. and Sagarminaga, Yolanda and Hyder, Kieran and Nathalie Niquil and M{\"o}llmann, C and Wilson, C and Chust, Guillem and Galpasoro, I and Forster, R and Verissimo, H and Tedesco, Letizia and Revilla, M and Neville, Suzanna}
}
@article {5045,
	title = {What Is Marine Biodiversity? Towards Common Concepts and Their Implications for Assessing Biodiversity Status. Front},
	journal = {Bridging the Gap Between Policy and Science in Assessing the Health Status of Marine Ecosystems},
	volume = {3},
	year = {2017},
	pages = {377},
	author = {Cochrane, SKJ and Andersen, JH and Berg, T and Hugues Blanchet and Borja, A and Carstensen, J and Elliott, M and Hummel, H and Nathalie Niquil and Renaud, PE}
}
@article {6707,
	title = {Ability of the marine bacterium Pseudomonas fluorescens BA3SM1 to counteract the toxicity of CdSe nanoparticles},
	journal = {Journal of Proteomics},
	volume = {148},
	year = {2016},
	month = {Jan-10-2016},
	pages = {213 - 227},
	issn = {18743919},
	doi = {10.1016/j.jprot.2016.07.021},
	url = {https://www.sciencedirect.com/science/article/pii/S187439191630330X?via\%3Dihub},
	author = {Poirier, Isabelle and Kuhn, Lauriane and Demorti{\`e}re, Arnaud and Mirvaux, Boris and Hammann, Philippe and Chicher, Johana and Christelle Caplat and Pallud, Marie and Bertrand, Martine}
}
@article {5814,
	title = {{Climate change and the ash dieback crisis}},
	journal = {Scientific Reports},
	volume = {6},
	year = {2016},
	abstract = {<p>{\textcopyright} The Author(s) 2016. Beyond the direct influence of climate change on species distribution and phenology, indirect effects may also arise from perturbations in species interactions. Infectious diseases are strong biotic forces that can precipitate population declines and lead to biodiversity loss. It has been shown in forest ecosystems worldwide that at least 10{\%} of trees are vulnerable to extinction and pathogens are increasingly implicated. In Europe, the emerging ash dieback disease caused by the fungus Hymenoscyphus fraxineus, commonly called Chalara fraxinea, is causing a severe mortality of common ash trees (Fraxinus excelsior); this is raising concerns for the persistence of this widespread tree, which is both a key component of forest ecosystems and economically important for timber production. Here, we show how the pathogen and climate change may interact to affect the future spatial distribution of the common ash. Using two presence-only models, seven General Circulation Models and four emission scenarios, we show that climate change, by affecting the host and the pathogen separately, may uncouple their spatial distribution to create a mismatch in species interaction and so a lowering of disease transmission. Consequently, as climate change expands the ranges of both species polewards it may alleviate the ash dieback crisis in southern and occidental regions at the same time.</p>
},
	issn = {20452322},
	doi = {10.1038/srep35303},
	author = {Goberville, Eric and Nina-Coralie Hautek{\`e}ete and Richard R Kirby and Yves Piquot and Christophe Luczak and Gr{\'e}gory Beaugrand}
}
@article {4265,
	title = {Coastal evolution and sedimentary mobility of Br{\o}gger Peninsula, northwest Spitsbergen},
	journal = {Polar Biology},
	year = {2016},
	month = {03/2016},
	pages = {1-10},
	abstract = {<p>Since the end of the Little Ice Age (LIA), Svalbard glaciers have undergone a net retreat in response to changing meteorological conditions. Located between 76{\textdegree}N and 80{\textdegree}N, western Spitsbergen has seen a climatic transition from a glacial to a paraglacial system. On the northern shore of the Br{\o}gger Peninsula (northwest Spitsbergen), the average temperature increased by 3\&nbsp;{\textdegree}C between 1965 and 2015, and cold-based valley glaciers have retreated more than 1\&nbsp;km from their LIA limits. This rapid deglaciation has exposed large areas of glacigenic sediments being easily reworked by runoff. This has led to the formation of extensive glacier-river delta systems and coastal progradation. Post-LIA coastal progradation and formation of new landforms in Kongsfjorden have been controlled predominantly by substantial availability of glacial sediment. A combination of aerial photographic and field data has been employed to estimate the post-LIA evolution of coastal sandur deltas and their submarine parts (named here {\textquotedblleft}prodeltas{\textquotedblright}). The data set reveals that delta shoreline advance could have reached around 5\&nbsp;m/year. between 1966 and 1990 for the most energetic delta of Austre Lovenbreen, and around 4\&nbsp;m/year between 2011 and 2014 for the most energetic delta of Midtre Lovenbreen. The prodeltas registered a net growth from 2009 to 2012: the biggest, located in the prolongation of deltas of Austre Lovenbreen, measured 1033\&nbsp;m in length in 2009 and 1180\&nbsp;m in length in 2012. This substantial amount of sediment supplied in the fjord has an impact on the fjord ecology, especially on the benthic ecosystem.</p>
},
	keywords = {High Arctic, Paraglacial, Sedimentary flux, Submarine and aerial coastal evolution, Svalbard},
	doi = {10.1007/s00300-016-1930-1},
	author = {Marine Bourriquen and Agn{\`e}s Baltzer and Denis Mercier and J{\'e}r{\^o}me Fournier and Laurent Perez and Sylvain Haquin and Eric Bernard and Maria Ansine Jensen}
}
@article {4530,
	title = {Differential protein expression during sperm maturation and capacitation in an hermaphroditic bivalve, Pecten maximus (Linnaeus, 1758)},
	journal = {Journal of Molluscan Studies},
	year = {2016},
	month = {09/2016},
	pages = {1-10},
	author = {Boonmee, A and Clothilde Heude-Berthelin and Kingtong, S and Pauletto, M and Bernay, B and Adeline, B and Suquet, M and Pascal Sourdaine and Kristell Kellner-Cousin}
}
@article {4413,
	title = {Effects of an environmentally relevant concentration of diuron on oyster genitors during gametogenesis: responses of early molecular and cellular markers and physiological impacts.},
	journal = {Environ Sci Pollut Res Int},
	volume = {23},
	year = {2016},
	month = {2016 Apr},
	pages = {8008-20},
	abstract = {<p>Genitors of the Pacific oyster Crassostrea gigas were submitted during gametogenesis to a short pulse exposure to the herbicide diuron at a realistic environmental concentration. Histological analysis showed no effect of diuron on gametogenesis course, sex ratio and reproductive effort. A non-significant increase in testosterone and progesterone levels was observed in genitors exposed to the herbicide. At cell level, diuron exposure was shown to modulate the phagocytic activity of circulating hemocytes. The results of a transcriptional analysis showed that diuron affected the expression of genes belonging to functions known to play a major role during oyster gametogenesis such as gene transcription regulation, DNA replication and repair, DNA methylation and cytokinesis. Taking into account the results we previously obtained on the same genitors, this study showed a negative effect of diuron on oyster reproduction by inducing both structural and functional modifications of the DNA.</p>
},
	issn = {1614-7499},
	doi = {10.1007/s11356-015-5969-2},
	author = {Akcha, F and Barranger, A and Bach{\`e}re, E and Clothilde Heude-Berthelin and Piquemal, D and Alonso, P and Sallan, R Rondon and Dimastrogiovanni, G and Porte, C and Menard, D and Szczybelski, A and Benabdelmouna, A and Auffret, M and Rouxel, J and Burgeot, T}
}
@article {4340,
	title = {The fate of C4 and C3 macrophyte carbon in central Amazon floodplain waters: Insights from a batch experiment},
	journal = {Limnologica - Ecology and Management of Inland Waters},
	volume = {59},
	year = {2016},
	pages = {90-98},
	abstract = {<p>The central Amazon floodplains are particularly productive ecosystems, where a large diversity of organic carbon sources are available for aquatic organisms. Despite the fact that C4 macrophytes generally produce larger biomasses than C3 macrophytes, food webs in the central Amazon floodplains appear dominantly based on a C3 carbon source.</p>

<p>In order to investigate the respective fate and degradation patterns of C4 and C3 aquatic plant-derived material in central Amazon floodplains, we developed a 23-days batch experiment. Fatty acid and carbon concentrations as well as stable isotope compositions were monitored over time in 60\&nbsp;L tanks. These tanks contained Amazon water, with different biomasses of C3 and C4 macrophyte, representative of in situ densities occurring in central Amazon floodplains.</p>

<p>In the C4Paspalum repens treatments, organic (POC, DOC) and inorganic carbon (DIC) got rapidly enriched in 13C, whereas in the C3Salvinia auriculata treatments, POC and DOC showed little change in concentration and isotopic composition, and DIC got depleted in 13C. The contribution of P. repens to POC and DOC was estimated to reach up to 94.2 and 70.7\%, respectively. In contrast, no differences were reported between the C3S. auriculata and control treatments, an observation attributed to the lower C3 biomass encountered in the field, to a slower degradation rate of C3 compared to C4 compounds, and to similar isotopic compositions for river POC and DOC, and C3 compounds.</p>

<p>The 13C enrichments of POC, DOC, and DIC from P. repens treatments were attributed to an enhanced bacterially-mediated hydrolysis and mineralization of C4 material. Evolutions of bacterial abundance and branched fatty acid concentrations confirmed the role of heterotrophic microbial communities in the high P. repens decomposition rate. Our experiment highlights the predominant role of C4 aquatic plants, as a large source of almost entirely biodegradable organic matter available for heterotrophic activity and CO2 outgassing to the atmosphere.</p>
},
	keywords = {Central amazon, Degradation, fatty acids, Floodplains, Macrophytes, Stables isotopes},
	doi = {doi:10.1016/j.limno.2016.03.008},
	author = {Jean-Michel Mortillaro and Passarelli, C and Gwena{\"e}l Abril and C{\'e}dric Hubas and Luis Felipe Artigas and Marc F Benedetti and Najet Thiney and Moreira-Turcq, P and P{\'e}rez, M A and Vidal, L and Tarik Meziane}
}
@article {4226,
	title = {Geographic variation in stable isotopic and fatty acid composition of anguilliform leptocephali and particulate organic matter in the South Pacific},
	journal = {Marine Ecology and Progress Series},
	volume = {544},
	year = {2016},
	pages = {225-241},
	abstract = {<p>The feeding ecology of leptocephali has remained poorly understood because they apparently feed on particulate organic matter (POM), which varies in composition, and it is unclear which components of the POM they assimilate. The δ13C and δ15N stable isotope (SI) and fatty acid (FA) compositions of 3 families of leptocephali and POM were compared in 3 latitudinal current zones of the western South Pacific. The δ15N signatures of leptocephali and POM overlapped, with both having their lowest values in the southern current zone. POM in general (across all zones) contained 38 FAs and was rich in saturated FAs (SFA) (16:0, 18:0, 14:0), while leptocephali contained 50 FAs, with high proportions of 16:0, and higher contributions of 22:6ω3, 20:5ω3, 18:1ω9, 16:1ω7 and other FAs than found in the POM. Serrivomeridae leptocephali in the north had higher δ15N signatures and were also distinguished from Nemichthyidae and Muraenidae larvae by their FA compositions (higher SFAs, lower 22:6ω3 and 20:5ω3). Although SI signatures of the Serrivomeridae larvae did not clearly vary with size, 16:0 and 18:0 FA proportions decreased with increasing larval size, and 22:6ω3 and 16:1ω7 increased in larger larvae. Correspondences between the latitudinal variations in nitrogen SI signatures and FA compositions of POM with those of leptocephali and the presence of FA markers of both autotrophic and heterotrophic organisms were consistent with leptocephali feeding on POM. POM can contain various materials from primary producers and heterotrophic microorganisms, but differences in the SI signatures and FA compositions in leptocephali remain to be explained through further research.</p>
},
	keywords = {Leptocephali {\textperiodcentered} Fatty acids {\textperiodcentered} Stable isotopes {\textperiodcentered} Biomarkers {\textperiodcentered} Trophic ecology {\textperiodcentered} Oceanic currents},
	isbn = {doi:10.3354/meps11575 },
	author = {Li{\'e}nart, Camilla and Eric Feunteun and Miller, M J and Aoyama, J and Jean-Michel Mortillaro and C{\'e}dric Hubas and Kuroki, M and Watanabe, S and Christine Dupuy and Alexandre Carpentier and Otake, T and Tsukamoto, K and Tarik Meziane}
}
@article {5813,
	title = {{Global impacts of the 1980s regime shift}},
	journal = {Global Change Biology},
	volume = {22},
	year = {2016},
	abstract = {<p>{\textcopyright} 2016 John Wiley {\&amp;} Sons Ltd. Despite evidence from a number of Earth systems that abrupt temporal changes known as regime shifts are important, their nature, scale and mechanisms remain poorly documented and understood. Applying principal component analysis, change-point analysis and a sequential t-test analysis of regime shifts to 72 time series, we confirm that the 1980s regime shift represented a major change in the Earth{\textquoteright}s biophysical systems from the upper atmosphere to the depths of the ocean and from the Arctic to the Antarctic, and occurred at slightly different times around the world. Using historical climate model simulations from the Coupled Model Intercomparison Project Phase 5 (CMIP5) and statistical modelling of historical temperatures, we then demonstrate that this event was triggered by rapid global warming from anthropogenic plus natural forcing, the latter associated with the recovery from the El Chich{\'o}n volcanic eruption. The shift in temperature that occurred at this time is hypothesized as the main forcing for a cascade of abrupt environmental changes. Within the context of the last century or more, the 1980s event was unique in terms of its global scope and scale; our observed consequences imply that if unavoidable natural events such as major volcanic eruptions interact with anthropogenic warming unforeseen multiplier effects may occur.</p>
},
	keywords = {Climate, Earth systems, Global change, Regime shift, Statistical analysis, Time series, Volcanic forcing},
	issn = {13652486},
	doi = {10.1111/gcb.13106},
	author = {Philip Chris Reid and Renata E. Hari and Gr{\'e}gory Beaugrand and David M. Livingstone and Christoph Marty and Dietmar Straile and Jonathan Barichivich and Goberville, Eric and Rita Adrian and Yasuyuki Aono and Ross Brown and James Foster and Pavel Groisman and Pierre H{\'e}laou{\"e}t and Huang-Hsiung Hsu and Richard R Kirby and Jeff Knight and Alexandra Kraberg and Jianping Li and Tzu-Ting Lo and Ranga B. Myneni and Ryan P. North and Alan J. Pounds and Tim Sparks and Ren{\'e} St{\"u}bi and Yongjun Tian and Karen H. Wiltshire and Dong Xiao and Zaichun Zhu}
}
@article {6814,
	title = {Ideas and perspectives: Southwestern tropical Atlantic coral growth response to atmospheric  circulation changes induced by ozone depletion in Antarctica},
	journal = {Biogeosciences},
	volume = {13},
	year = {2016},
	month = {Jan-01-2016},
	pages = {2379 - 2386},
	abstract = {Recent Southern Hemisphere (SH) atmospheric<br />
circulation, predominantly driven by stratospheric ozone de-<br />
pletion over Antarctica, has caused changes in climate across<br />
the extratropics. Here, we present evidence that the Brazilian<br />
coast (southwestern Atlantic) may have been impacted from<br />
both wind and sea-surface temperature changes derived from<br />
this process. Skeleton analysis of massive coral species liv-<br />
ing in shallow waters off Brazil are very sensitive to air{\textendash}sea<br />
interactions, and seem to record this impact. Growth rates<br />
of Brazilian corals show a trend reversal that fits the ozone<br />
depletion evolution, confirming that ozone impacts are far<br />
reaching and potentially affect coastal ecosystems in tropical<br />
environments},
	doi = {10.5194/bg-13-2379-2016},
	url = {http://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers16-05/010067169.pdf},
	author = {Evangelista, Heitor and Wainer, Ilana and Sifeddine, Abdelfettah and Corr{\`e}ge, Thierry and Cordeiro, Renato C. and Lamounier, Saulo and Godiva, Daniely and Shen, Chuan-Chou and Le Cornec, Florence and Turcq, Bruno and Claire E. Lazareth and Hu, Ching-Yi}
}
@article {8577,
	title = {The influence of oceanographic features on the foraging behavior of the olive ridley sea turtle Lepidochelys olivacea along the Guiana coast},
	journal = {Progress in Oceanography},
	volume = {142},
	year = {2016},
	month = {Jan-03-2016},
	pages = {58 - 71},
	issn = {00796611},
	doi = {10.1016/j.pocean.2016.01.006},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0079661115300094},
	author = {Chambault, Philippine and de Thoisy, Beno{\^\i}t and Heerah, Karine and Conchon, Anna and Barrioz, S{\'e}bastien and Dos Reis, Virginie and Berzins, Rachel and Kelle, Laurent and Picard, Baptiste and Roquet, Fabien and Le Maho, Yvon and Chevallier, Damien}
}
@article {4540,
	title = {International Perspectives on the Effects of Climate Change on Inland Fisheries},
	journal = {Fisheries},
	volume = {41},
	year = {2016},
	month = {07/2016},
	pages = {399-405},
	doi = {10.1080/03632415.2016.1182513},
	author = {I.J. Winfield and C. Baigun and P.A. Balykin and B. Becker and Y. Chen and A.F. Filipe and Y.V. Gerasimov and A.L. Godinho and R.M. Hugues and J.D. Koehn and D.N. Kutsyn and V. Mendoza-Portillo and Thierry Oberdorff and A.M. Orlov and A.P. Pedchenko and F. Pletterbauer and I.G. Prado and R. R{\"o}sch and S.J. Vatland}
}
@article {4396,
	title = {Meiofauna distribution in a mangrove forest exposed to shrimp farm effluents (New Caledonia)},
	journal = {Marine Environmental Research},
	volume = {119},
	year = {2016},
	pages = {100 - 113},
	abstract = {<p>Abstract Meiofauna abundance, biomass and individual size were studied in mangrove sediments subjected to shrimp farm effluents in New Caledonia. Two strategies were developed: i) meiofauna examination during the active (AP) and the non-active (NAP) periods of the farm in five mangrove stands characteristics of the mangrove zonation along this coastline, ii) meiofauna examination every two months during one year in the stand the closest to the pond (i.e. Avicennia marina). Thirteen taxonomic groups of meiofauna were identified, with nematodes and copepods being the most abundant ones. Meiofauna abundance and biomass increased from the land side to the sea side of the mangrove probably as a result of the increased length of tidal immersion. Abundance of total meiofauna was not significantly different before and after the rearing period. However, the effluent-receiving mangrove presented twice the meiofauna abundance and biomass than the control one. Among rare taxa, mites appeared extremely sensitive to this perturbation.</p>
},
	keywords = {New Caledonia},
	issn = {0141-1136},
	doi = {http://dx.doi.org/10.1016/j.marenvres.2016.05.028},
	url = {http://www.sciencedirect.com/science/article/pii/S0141113616300976},
	author = {L. Della Patrona and Cyril Marchand and C{\'e}dric Hubas and Nathalie Molnar and J. Deborde and Tarik Meziane}
}
@article {4594,
	title = {Morphological review of the freshwater fairy shrimp Dendrocephalus brasiliensis Pesta, 1921 (Anostraca: Thamnocephalidae)},
	journal = {Nauplius},
	volume = {24},
	year = {2016},
	month = {08/2016},
	pages = {1-10},
	abstract = {<p>Information concerning the morphology of Dendrocephalus brasiliensis Pesta, 1921 is currently fragmented. This study reviewed the morphological structures described previously and new features (e.g., antenna-like structures and gonopod). We review the distribution of this species and also expand the geographic distribution of D. brasiliensis in the state of Alagoas. The specimens were obtained from fish-breeding tanks in Porto Real do Col{\'e}gio, Alagoas, Brazil, in November 2012. Several morphological structures of D. brasiliensis are described in greater detail, including all branches and sub-branches from the frontal appendage and thoracopods from one population and compared to other species.</p>
},
	doi = {10.1590/2358-2936e2016008},
	author = {Samara de Paiva Barros-Alves and Douglas Fernandes Rodrigues Alves and Eduardo Ant{\^o}nio Bolla Jr and Nicolas Rabet and Gustavo Luis Hirose}
}
@article {8574,
	title = {Network Analysis Shows Asymmetrical Flows within a Bird Metapopulation},
	journal = {PLOS ONE},
	volume = {11},
	year = {2016},
	month = {Apr-11-2018},
	pages = {e0166701},
	doi = {10.1371/journal.pone.016670110.1371/journal.pone.0166701.g00110.1371/journal.pone.0166701.t00110.1371/journal.pone.0166701.t00210.1371/journal.pone.0166701.s001},
	url = {https://dx.plos.org/10.1371/journal.pone.0166701},
	author = {Rojas, Emilio R. and Sueur, C{\'e}dric and Henry, Pierre-Yves and Doligez, Blandine and Wey, G{\'e}rard and Dehorter, Olivier and Massemin, Sylvie and Chevallier, Damien and Clauss, Thierry and Dugu{\'e} Hubert and Merle, Christian},
	editor = {Margalida, Antoni}
}
@article {5438,
	title = {Neuropeptidome of the Cephalopod Sepia officinalis: Identification, Tissue Mapping, and Expression Pattern of Neuropeptides and Neurohormones during Egg Laying.},
	journal = {J Proteome Res. },
	volume = {15},
	year = {2016},
	pages = {48-67},
	author = {C{\'e}line Zatylny-Gaudin and Cornet, Val{\'e}rie and Leduc, Alexandre and Zanuttini, Bruno and Corre, Erwan and Corguill{\'e}, Gildas Le and Bernay, Beno{\^\i}t and Kraut, Alexandra and Cout{\'e}, Yohan and Jo{\"e}l Henry}
}
@article {7178,
	title = {Planktonic foraminiferal biogeography in the Indian sector of the Southern Ocean: Contribution from CPR data},
	journal = {Deep Sea Research Part I: Oceanographic Research Papers},
	volume = {110},
	year = {2016},
	month = {Jan-04-2016},
	pages = {75 - 89},
	issn = {09670637},
	doi = {10.1016/j.dsr.2015.12.014},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0967063716300280},
	author = {Meilland, Julie and Fabri-Ruiz, Salom{\'e} and Koubbi, Philippe and Monaco, Claire Lo and Cott{\'e}, C{\'e}dric and Hosie, Graham W. and Sanchez, Sophie and Howa, H{\'e}l{\`e}ne}
}
@article {4677,
	title = {Present-day African analogue of a pre-European Amazonian floodplain fishery shows convergence in cultural niche construction},
	journal = {Proceedings of the National Academy of Sciences},
	year = {2016},
	abstract = {<p>Erickson [Erickson CL (2000) Nature 408 (6809):190{\textendash}193] interpreted features in seasonal floodplains in Bolivia{\textquoteright}s Beni savannas as vestiges of pre-European earthen fish weirs, postulating that they supported a productive, sustainable fishery that warranted cooperation in the construction and maintenance of perennial structures. His inferences were bold, because no close ethnographic analogues were known. A similar present-day Zambian fishery, documented here, appears strikingly convergent. The Zambian fishery supports Erickson{\textquoteright}s key inferences about the pre-European fishery: It allows sustained high harvest levels; weir construction and operation require cooperation; and weirs are inherited across generations. However, our comparison suggests that the pre-European system may not have entailed intensive management, as Erickson postulated. The Zambian fishery{\textquoteright}s sustainability is based on exploiting an assemblage dominated by species with life histories combining high fecundity, multiple reproductive cycles, and seasonal use of floodplains. As water rises, adults migrate from permanent watercourses into floodplains, through gaps in weirs, to feed and spawn. Juveniles grow and then migrate back to dry-season refuges as water falls. At that moment fishermen set traps in the gaps, harvesting large numbers of fish, mostly juveniles. In nature, most juveniles die during the first dry season, so that their harvest just before migration has limited impact on future populations, facilitating sustainability and the adoption of a fishery based on inherited perennial structures. South American floodplain fishes with similar life histories were the likely targets of the pre-European fishery. Convergence in floodplain fish strategies in these two regions in turn drove convergence in cultural niche construction.</p>
},
	doi = {10.1073/pnas.1613169114},
	url = {http://www.pnas.org/content/early/2016/12/09/1613169114.abstract},
	author = {McKey, Doyle B. and Dur{\'e}cu, M{\'e}lisse and Marc Pouilly and Bearez, Philippe and Ovando, Alex and Kalebe, Mashuta and Carl F. Huchzermeyer}
}
@article {4365,
	title = {Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species.},
	journal = {Mol Ecol Resour},
	year = {2016},
	month = {2016 Mar 22},
	abstract = {<p>Among the 899 species of freshwater fishes reported from Sundaland biodiversity hotspot, nearly 50\% are endemics. The functional integrity of aquatic ecosystems is currently jeopardized by human activities and landscape conversion led to the decline of fish populations in several part of Sundaland, particularly in Java. The inventory of the Javanese ichthyofauna has been discontinuous and the taxonomic knowledge is scattered in the literature. The present study provides a DNA barcode reference library for the inland fishes of Java and Bali with the aim to streamline the inventory of fishes in this part of Sundaland. Owing to the lack of available checklist for estimating the taxonomic coverage of the present study, a checklist was compiled based on online catalogs. A total of 95 sites were visited and a library including 1,046 DNA barcodes for 159 species was assembled. Nearest neighbor distance was 28-fold higher than maximum intra-specific distance on average and a DNA barcoding gap was observed. The list of species with DNA barcodes displayed large discrepancies with the checklist compiled here as only 36\% (i.e. 77 species) and 60\% (i.e.24 species) of the known species were sampled in Java and Bali, respectively. This result was contrasted by a high number of new occurrences and the ceiling of the accumulation curves for both species and genera. These results highlight the poor taxonomic knowledge of this ichthyofauna and the apparent discrepancy between present and historical occurrence data is to be attributed to species extirpations, synonymy and misidentifications in previous studies. This article is protected by copyright. All rights reserved.</p>
},
	issn = {1755-0998},
	doi = {10.1111/1755-0998.12528},
	author = {Dahruddin, Hadi and Hutama, Aditya and Fr{\'e}d{\'e}ric Busson and Sauri, Sopian and Hanner, Robert and Philippe Keith and Hadiaty, Renny and Hubert, Nicolas}
}
@article {4280,
	title = {Trans-Amazonian natal homing in giant catfish},
	journal = {Journal of Applied Ecology},
	volume = {53},
	year = {2016},
	pages = {1511-1520},
	abstract = {<p>1.Knowledge of fish migration is a prerequisite to sustainable fisheries management and preservation, especially in large international river basins. In particular, understanding whether a migratory lifestyle is compulsory or facultative, and whether adults home to their natal geographic area is paramount to fully appraise disruptions of longitudinal connectivity resulting from damming.2.In the Amazon, the large migratory catfishes of the Brachyplatystoma genus are apex predators of considerable interest for fisheries. They are believed to use the entire length of the basin to perform their life cycle, with hypothesized homing behaviours. Here we tested these hypotheses, using the emblematic B. rousseauxii as a model species.3.We sampled adults close to major breeding areas in the Amazon basin (upper Madeira and upper Amazonas) and assessed their lifetime movements by measuring variations in 87Sr/86Sr along transverse sections of their otoliths (ear stones) using laser ablation multicollector mass spectrometry (LA-MC-ICPMS).4.We demonstrate that larvae migrate downstream from the Andean piedmont to the lower Amazon, where they grow over a protracted period before migrating upstream as adults. Contrary to prevailing inferences, not all fish spend their nursery stages in the Amazon estuary. By contrast, the passage in the lower or central Amazon seems an obligate part of the life cycle. We further evidence that most adults home to their natal geographic area within the Madeira sub-basin. Such long-distance natal homing is exceptional in purely freshwater fishes.5.Synthesis and applications. By using otolith microchemistry, we were able to demonstrate a seemingly compulsory basin-wide migratory life cycle of large Amazonian catfishes. This makes them the organisms performing the longest migrations (\&gt;8000 km) in fresh waters. This exceptional life history is already jeopardized by two dams recently built in the Madeira River, which block a major migration route and access to a substantial part of their spawning grounds. Major impacts can be anticipated from the current and forthcoming hydroelectric development in the Amazon basin, not only on the populations and fisheries of this apex predator, but also on Amazonian food webs through trophic cascades.This article is protected by copyright. All rights reserved.</p>
},
	keywords = {87Sr/86Sr ratios, Amazon, anthropogenic activities, Brachyplatystoma spp, freshwater fish, giant catfish, hydroelectric dams, Migration, otoliths},
	issn = {1365-2664},
	doi = {10.1111/1365-2664.12665},
	url = {http://dx.doi.org/10.1111/1365-2664.12665},
	author = {Fabrice Duponchelle and Marc Pouilly and Pecheyran, Christophe and Hauser, Marilia and Renno, Jean-Francois and Panfili, Jacques and Darnaude, Audrey M. and Garc{\'\i}a-Vasquez, Aurea and Carvajal-Vallejos, Fernando and Carmen Garc{\'\i}a-D{\'a}vila and Doria, Carolina and B{\'e}rail, Sylvain and Donard, Ariane and Sondag, Francis and Santos, Roberto V. and Jesus Nu{\~n}ez-Rodriguez and Point, David and Labonne, Maylis and Baras, Etienne}
}
@article {4448,
	title = {Unexpectedmovements of male Bluethroats Luscinia svecica namnetum during the breeding period},
	journal = {Alauda},
	volume = {84},
	year = {2016},
	pages = {195-202},
	abstract = {<p>During a radiotracking survey on 61 different males of Bluethroat Luscinia svecica namnetum from 2012 to 2015 in three different sites, we found that 8 males joined remote areas, at 300 to 900meters fromtheir regular territory and home range. Thesemovements occurred at dawn and dusk, but also at day. Such movements are not recorded in the literature and we propose four different hypotheses to explain them: the existence of {\textquotedblleft}hidden leks{\textquotedblright}, a male poly-territoriality, the look for food or for a shelter from predators.</p>
},
	author = {Cl{\'e}ment Harmange and Laurent Godet and Matthieu Marquet and Julie Dietrich and Sarah Monnet and Elisa Gr{\'e}goire and Marie-Christine Eybert and J{\'e}r{\^o}me Fournier}
}
@article {3747,
	title = {Acute combined pressure and temperature exposures on a shallow-water crustacean: novel insights into the stress response and high pressure neurological syndrome.},
	journal = {Comp Biochem Physiol A Mol Integr Physiol},
	volume = {181},
	year = {2015},
	month = {2015 Mar},
	pages = {9-17},
	abstract = {<p>Little is known about the ecological and physiological processes governing depth distribution limits in species. Temperature and hydrostatic pressure are considered to be two dominant factors. Research has shown that some marine ectotherms are shifting their bathymetric distributions in response to rapid anthropogenic ocean surface warming. Shallow-water species unable to undergo latitudinal range shifts may depend on bathymetric range shifts to seek refuge from warming surface waters. As a first step in constraining the molecular basis of pressure tolerance in shallow water crustaceans, we examined differential gene expression in response to acute pressure and temperature exposures in juveniles of the shallow-water shrimp Palaemonetes varians. Significant increases in the transcription of genes coding for an NMDA receptor-regulated protein, an ADP ribosylation factor, β-actin, two heat shock protein 70 kDa isoforms (HSP70), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were found in response to elevated pressure. NMDA receptors have been implicated in pathways of excitotoxic damage to neurons and the onset of high pressure neurological syndrome (HPNS) in mammals. These data indicate that the sub-lethal effects of acute barotrauma are associated with transcriptional disturbances within the nervous tissue of crustaceans, and cellular macromolecular damage. Such transcriptional changes lead to the onset of symptoms similar to that described as HPNS in mammals, and may act as a limit to shallow water organisms{\textquoteright} prolonged survival at depth.</p>
},
	issn = {1531-4332},
	doi = {10.1016/j.cbpa.2014.10.028},
	author = {Morris, J P and Thatje, S and Juliette Ravaux and Bruce Shillito and Fernando, D and Hauton, C}
}
@article {4235,
	title = {Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas.},
	journal = {BMC Genomics},
	volume = {16},
	year = {2015},
	month = {2015},
	pages = {808},
	abstract = {<p><strong>BACKGROUND: </strong>Originating from Northeast Asia, the Pacific oyster Crassostrea gigas has been introduced into a large number of countries for aquaculture purpose. Following introduction, the Pacific oyster has turned into an invasive species in an increasing number of coastal areas, notably recently in Northern Europe.</p>

<p><strong>METHODS: </strong>To explore potential adaptation of reproductive traits in populations with different histories, we set up a common garden experiment based on the comparison of progenies from two populations of Pacific oyster sampled in France and Denmark and their hybrids. Sex ratio, condition index and microarray gene expression in gonads, were analyzed in each progeny (n = 60).</p>

<p><strong>RESULTS: </strong>A female-biased sex-ratio and a higher condition index were observed in the Danish progeny, possibly reflecting an evolutionary reproductive strategy to increase the potential success of natural recruitment in recently settled population. Using multifarious statistical approaches and accounting for sex differences we identified several transcripts differentially expressed between the Danish and French progenies, for which additive genetic basis is suspected (showing intermediate expression levels in hybrids, and therefore additivity). Candidate transcripts included mRNA coding for sperm quality and insulin metabolism, known to be implicated in coordinated control and success of reproduction.</p>

<p><strong>CONCLUSIONS: </strong>Observed differences suggest that adaptation of invasive populations might have occurred during expansion acting on reproductive traits, and in particular on a female-biased sex-ratio, gamete quality and fertility.</p>
},
	issn = {1471-2164},
	doi = {10.1186/s12864-015-1972-8},
	author = {Sussarellu, Rossana and Huvet, Arnaud and Lap{\`e}gue, Sylvie and Virgile Quillien and Christophe Lelong and Cornette, Florence and Jensen, Lasse Fast and Bierne, Nicolas and Boudry, Pierre}
}
@article {4165,
	title = {Biogeographical distribution of Rimicaris exoculata resident gut epibiont communities along the Mid-Atlantic Ridge hydrothermal vent sites.},
	journal = {FEMS Microbiol Ecol},
	volume = {91},
	year = {2015},
	month = {2015 Oct},
	abstract = {<p>Rimicaris exoculata is a deep-sea hydrothermal vent shrimp whose enlarged gill chamber houses a complex trophic epibiotic community. Its gut harbours an autochthonous and distinct microbial community. This species dominates hydrothermal ecosystem megafauna along the Mid-Atlantic Ridge, regardless of contrasting geochemical conditions prevailing in them. Here, the resident gut epibiont community at four contrasted hydrothermal vent sites (Rainbow, TAG, Logatchev and Ashadze) was analysed and compiled with previous data to evaluate the possible influence of site location, using 16S rRNA surveys and microscopic observations (transmission electron microscopy, scanning electron microscopy and fluorescence in situ hybridization analyses). Filamentous epibionts inserted between the epithelial cell microvilli were observed on all examined samples. Results confirmed resident gut community affiliation to Deferribacteres, Mollicutes, Epsilonproteobacteria and to a lesser extent Gammaproteobacteria lineages. Still a single Deferribacteres phylotype was retrieved at all sites. Four Mollicutes-related operational taxonomic units were distinguished, one being only identified on Rainbow specimens. The topology of ribotype median-joining networks illustrated a community diversification possibly following demographic expansions, suggesting a more ancient evolutionary history and/or a larger effective population size at Rainbow. Finally, the gill chamber community distribution was also analysed through ribotype networks based on sequences from R. exoculata collected at the Rainbow, Snake Pit, TAG, Logatchev and Ashadze sites. Results allow the refining of hypotheses on the epibiont role and transmission pathways.</p>
},
	issn = {1574-6941},
	doi = {10.1093/femsec/fiv101},
	author = {Durand, Lucile and Roumagnac, Marie and Cueff-Gauchard, Val{\'e}rie and Jan, Cyrielle and Guri, Mathieu and Tessier, Claire and Haond, Marine and Crassous, Philippe and Magali Zbinden and Arnaud-Haond, Sophie and Cambon-Bonavita, Marie-Anne}
}
@article {6878,
	title = {Characterising multi-level effects of acute pressure exposure on a shallow-water invertebrate: insights into the kinetics and hierarchy of the stress response},
	journal = {Journal of Experimental Biology},
	volume = {218},
	year = {2015},
	month = {Jan-08-2015},
	pages = {2594 - 2602},
	issn = {0022-0949},
	doi = {10.1242/jeb.125914},
	url = {http://jeb.biologists.org/cgi/doi/10.1242/jeb.125914},
	author = {Morris, J. P. and Thatje, S. and Juliette Ravaux and Bruce Shillito and Hauton, C.}
}
@article {4358,
	title = {Comparative phylogeography of Javanese and Balinese freshwater fishes: DNA barcodes shed light on Quaternary range expansion dynamic in a biodiversity hotspot.},
	journal = {Genome},
	volume = {58},
	year = {2015},
	pages = {230},
	author = {Hutama, A. and Darhuddin, H. and Fr{\'e}d{\'e}ric Busson and Sauri, S and Hanner, R and Philippe Keith and Hadiaty, Renny and Hubert, N}
}
@article {3524,
	title = {Diversity of trophic niches among herbivorous fishes on a Caribbean reef (Guadeloupe, Lesser Antilles), evidenced by stable isotope and gut content analyses},
	journal = {Journal of Sea Reasearch},
	volume = {95},
	year = {2015},
	pages = {124-131},
	keywords = {Caribbean reefs, functional diversity, gut contents, herbivorous fishes, Stable isotopes, trophic niches},
	author = {Charlotte R. Dromard and Yolande Bouchon-Navaro and Mireille Harmelin-Vivien and Claude Bouchon}
}
@article {4102,
	title = {DNA Barcoding Indonesian freshwater fishes: challenges and prospects.},
	journal = {DNA barcode},
	volume = {3},
	year = {2015},
	pages = {144-169},
	keywords = {Checklist, DNA barcoding, Southeast Asia},
	author = {Hubert, Nicolas and Kadarusman and Wibowo, A and Fr{\'e}d{\'e}ric Busson and Caruso, D. and Sulandari, S. and Nafiqoh, N and R{\"u}ber, L and Pouyaud, L and Avarre, JC and Herder, F and Hanner, R and Philippe Keith and Hadiaty, Renny}
}
@article {4356,
	title = {DNA barcoding of Javanese and Balinese freshwater fishes: molecular insights into a poorly known ichthyofauna.},
	journal = {Genome},
	volume = {58},
	year = {2015},
	pages = {209},
	author = {Darhuddin, H. and Hutama, A. and Fr{\'e}d{\'e}ric Busson and Sauri, S and Philippe Keith and Hanner, R and Hadiaty, Renny and Hubert, Nicolas}
}
@article {3507,
	title = {Does a short-term exposure to cadmium chloride affects haemocyte parameters of the marine gastropod Haliotis tuberculata?},
	journal = {Environ Sci Pollut Res Int},
	year = {2015},
	month = {2014 Aug 19},
	abstract = {<p>In this study, a model based on primary cultured haemocytes from the gastropod mollusc Haliotis tuberculata was established to investigate the effects of cadmium chloride in vitro. Cells were exposed for 24\&nbsp;h to CdCl2 concentrations of 0, 1 and 100\&nbsp;μg\&nbsp;ml(-1). The effects of cadmium on haemocyte parameters were investigated using morphological, spectrophotometric and flow cytometry analysis. Results showed that cadmium has no significant effects on cell viability and phagocytotic activity under the tested conditions. However, haemocytes became more rounded after cadmium exposure, which could explain the significant decrease of cell area beginning at 1\&nbsp;μg\&nbsp;ml(-1) of CdCl2.</p>
},
	issn = {1614-7499},
	doi = {10.1007/s11356-014-3387-5},
	author = {Ladhar-Chaabouni, R and Machreki-Ajmi, Monia and Antoine Serpentini and Jean-Marc Lebel and Hamza-Chaffai, A}
}
@article {5237,
	title = {The endocrine-disrupting effect and other physiological responses of municipal effluent on the clam Ruditapes decussatus},
	journal = {Environ Sci Pollut Res Int. },
	volume = {22},
	year = {2015},
	pages = {19716-28},
	type = {research},
	author = {Mezghani-Chaari, Sawssan and Monia Machreki-Ajmi and Gauthier Tremolet and Kristell Kellner-Cousin and Alain Geffard and Christophe Minier and Hamza-Chaffai, Amel}
}
@article {4420,
	title = {The endocrine-disrupting effect and other physiological responses of municipal effluent on the clam Ruditapes decussatus.},
	journal = {Environ Sci Pollut Res Int},
	volume = {22},
	year = {2015},
	month = {2015 Dec},
	pages = {19716-28},
	abstract = {<p>In order to document the potential endocrine disrupting and toxic effect of the municipal wastewater effluents discharged into the Sfax coastal area (South of Tunisia), specimens of clam R. decussatus were collected from a reference site and were in vivo exposed to treated sewage effluent for 30 days. To this end, estrogenic and androgenic activities were measured in the gills to assess potential accumulation and regulation of active compounds. After effluent exposure androgenic activity in organic extracts increased up to fivefold compared to controls and remained elevated, while estrogenic activity was not significantly affected by exposure. As a consequence, remarkable disruptions in the gametogenesis activity, glycogen content, and Vitellogenin-like protein levels in male clams were observed. A parallel analysis of heavy metals in clam tissues was determined. A significant uptake of Ni, Zn, and Pb in soft tissues of exposed clams was observed. The significant increase of malondialdehyde (MDA) concentrations as a function of exposure time implies that clams have been exposed to an oxidative stress probably due to the presence of high metal concentrations in sewage effluent. Correlation analysis has revealed a statistically significant and positive relationship between MDA levels and metal concentrations in clams{\textquoteright} tissues. The acetylcholinesterase activity was not significantly affected by exposure. Altogether, these results showed that a short-term exposure to a mixture of chemical compounds released by the Sfax wastewater treatment plant induce adverse physiological and reproductive effects in R. decussatus. Further studies are underway in order to evaluate its long-term impacts on aquatic wildlife in the gulf of Gabes area.</p>
},
	issn = {1614-7499},
	doi = {10.1007/s11356-015-5199-7},
	author = {Mezghani-Chaari, Sawssan and Machreki-Ajmi, Monia and Tremolet, Gauthier and Kristell Kellner-Cousin and Geffard, Alain and Minier, Christophe and Hamza-Chaffai, Amel}
}
@article {4195,
	title = {Foraging habits of reef fishes associated with mangroves and seagrass beds in a Caribbean lagoon: a stable isotope approach.},
	journal = {Ciencias marinas},
	volume = {41},
	year = {2015},
	month = {2015},
	pages = {217-232},
	author = {Vaslet, Amandine and Yolande Bouchon-Navaro and Mireille Harmelin-Vivien and Lepoint, Gilles and Louis, Max and Claude Bouchon}
}
@article {4419,
	title = {GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas.},
	journal = {BMC Bioinformatics},
	volume = {16},
	year = {2015},
	month = {2015},
	pages = {401},
	abstract = {<p><strong>BACKGROUND: </strong>The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, which makes now C. gigas becoming a model organism among lophotrochozoans, the under-described sister clade of ecdysozoans within protostomes. These massive sequencing efforts offer the opportunity to assemble gene expression data and make such resource accessible and exploitable for the scientific community. Therefore, we undertook this assembly into an up-to-date publicly available transcriptome database: the GigaTON (Gigas TranscriptOme pipeliNe) database.</p>

<p><strong>DESCRIPTION: </strong>We assembled 2204 million sequences obtained from 114 publicly available RNA-seq libraries that were realized using all embryo-larval development stages, adult organs, different environmental stressors including heavy metals, temperature, salinity and exposure to air, which were mostly performed as part of the Crassostrea gigas genome project. This data was analyzed in silico and resulted into 56621 newly assembled contigs that were deposited into a publicly available database, the GigaTON database. This database also provides powerful and user-friendly request tools to browse and retrieve information about annotation, expression level, UTRs, splice and polymorphism, and gene ontology associated to all the contigs into each, and between all libraries.</p>

<p><strong>CONCLUSIONS: </strong>The GigaTON database provides a convenient, potent and versatile interface to browse, retrieve, confront and compare massive transcriptomic information in an extensive range of conditions, tissues and developmental stages in Crassostrea gigas. To our knowledge, the GigaTON database constitutes the most extensive transcriptomic database to date in marine invertebrates, thereby a new reference transcriptome in the oyster, a highly valuable resource to physiologists and evolutionary biologists.</p>
},
	keywords = {Animals, Base Sequence, Computational Biology, Crassostrea, Databases, Genetic, Gene Library, Gene Ontology, Genome, High-Throughput Nucleotide Sequencing, Molecular Sequence Data, Sequence Analysis, RNA, Software, Transcriptome},
	issn = {1471-2105},
	doi = {10.1186/s12859-015-0833-4},
	author = {Guillaume Rivi{\`e}re and Klopp, Christophe and Ibouniyamine, Nabihoudine and Huvet, Arnaud and Boudry, Pierre and Pascal Favrel}
}
@article {4553,
	title = {Global diversity patterns of freshwater fishes - potential victims of their own success},
	journal = {Diversity and Distributions},
	volume = {21},
	year = {2015},
	pages = {345{\textendash}356},
	issn = {1472-4642},
	doi = {10.1111/ddi.12271},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ddi.12271/abstract},
	author = {Pelayo-Villamil, Patricia and Guisande, Castor and Vari, Richard P. and Manjarrez-Hern{\~A}{\textexclamdown}ndez, Ana and Garcia-Rosello, Emilio and Gonzalez-Dacosta, Jacinto and Heine, Jurgen and Gonzalez Vilas, Luis and Patti, Bernardo and Quinci, Enza Maria and Jimenez, Luz Fernanda and Granado-Lorencio, Carlos and Pablo Tedesco and Lobo, Jorge M.}
}
@article {3864,
	title = {How Egg Case Proteins Can Protect Cuttlefish Offspring?},
	journal = {PLoS One},
	volume = {10},
	year = {2015},
	month = {2015},
	pages = {e0132836},
	abstract = {<p><em>Sepia officinalis</em> egg protection is ensured by a complex capsule produced by the female accessory genital glands and the ink bag. Our study is focused on the proteins constituting the main egg case. De novo transcriptomes from female genital glands provided essential databases for protein identification. A proteomic approach in SDS-PAGE coupled with MS unveiled a new egg case protein family: SepECPs, for <em>Sepia officinalis </em>Egg Case Proteins. N-glycosylation was demonstrated by PAS staining SDS-PAGE gels. These glycoproteins are mainly produced in the main nidamental glands. SepECPs share high sequence homology, especially in the signal peptide and the three cysteine-rich domains. SepECPs have a high number of cysteines, with conserved motifs involved in 3D-structure. SDS-PAGE showed that SepECPs could form dimers; this result was confirmed by TEM observations, which also revealed a protein network. This network is similar to the capsule network, and it associates these structural proteins with polysaccharides, melanin and bacteria to form a tight mesh. Its hardness and elasticity provide physical protection to the embryo. In addition, SepECPs also have bacteriostatic antimicrobial activity on GRAM- bacteria. By observing the SepECP / <em>Vibrio aestuarianus</em> complex in SEM, we demonstrated the ability of these proteins to agglomerate bacteria and thus inhibit their growth. These original proteins identified from the outer egg case ensure the survival of the species by providing physical and chemical protection to the embryos released in the environment without any maternal protection.</p>
},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0132836},
	author = {Cornet, Val{\'e}rie and Jo{\"e}l Henry and Goux, Didier and Duval, Emilie and Bernay, Beno{\^\i}t and Gildas Le Corguille and Corre, Erwan and C{\'e}line Zatylny-Gaudin}
}
@article {5043,
	title = {Hydrothermal Fe cycling and deep ocean organic carbon scavenging: Model-based evidence for significant POC supply to seafloor sediments},
	journal = {EARTH AND PLANETARY SCIENCE LETTERS},
	volume = {419},
	year = {2015},
	month = {JUN 1},
	pages = {143-153},
	abstract = {<p class="rtejustify">Submarine hydrothermal venting has recently been identified to have the potential to impact ocean biogeochemistry at the global scale. This is the case because processes active in hydrothermal plumes are so vigorous that the residence time of the ocean, with respect to cycling through hydrothermal plumes, is comparable to that of deep ocean mixing caused by thermohaline circulation. Recently, it has been argued that seafloor venting may provide a significant source of bio-essential Fe to the oceans as the result of a close coupling between Fe and organic carbon in hydrothermal plumes. But a complementary question remains to be addressed: does this same intimate Fe-C-org association in hydrothermal plumes cause any related impact to the global C cycle? To address this, SCOR-InterRidge Working Group 135 developed a modeling approach to synthesize site-specific field data from the East Pacific Rise 9 degrees 50{\textquoteright} N hydrothermal field, where the range of requisite data sets is most complete, and combine those inputs with global estimates for dissolved Fe inputs from venting to the oceans to establish a coherent model with which to investigate hydrothermal C-org cycling. The results place new constraints on submarine Fe vent fluxes worldwide, including an indication that the majority of Fe supplied to hydrothermal plumes should come from entrainment of diffuse flow. While this same entrainment is not predicted to enhance the supply of dissolved organic carbon to hydrothermal plumes by more than similar to 10\% over background values, what the model does indicate is that scavenging of carbon in association with Fe-rich hydrothermal plume particles should play a significant role in the delivery of particulate organic carbon to deep ocean sediments, worldwide. (C) 2015 Elsevier B.V. All rights reserved.</p>
},
	issn = {{0012-821X}},
	doi = {{10.1016/j.epsl.2015.03.012}},
	author = {German, C. R. and Legendre, L and Sander, S. G. and Nathalie Niquil and LutherIII, G. W. and Bharati, L. and Han, X. and Le Bris, Nadine}
}
@article {3779,
	title = {Immune and Stress Responses in Oysters with Insights on Adaptation.},
	journal = {Fish Shellfish Immunol},
	year = {2015},
	month = {2015 May 16},
	abstract = {<p>Oysters are representative bivalve molluscs that are widely distributed in world oceans. As successful colonizers of estuaries and intertidal zones, oysters are remarkably resilient against harsh environmental conditions including wide fluctuations in temperature and salinity as well as prolonged air exposure. Oysters have no adaptive immunity but can thrive in microbe-rich estuaries as filter-feeders. These unique adaptations make oysters interesting models to study the evolution of host-defense systems. Recent advances in genomic studies including sequencing of the oyster genome have provided insights into oyster{\textquoteright}s immune and stress responses underlying their amazing resilience. Studies show that the oyster genomes are highly polymorphic and complex, which may be key to their resilience. The oyster genome has a large gene repertoire that is enriched for immune and stress response genes. Thousands of genes are involved in oyster{\textquoteright}s immune and stress responses, through complex interactions, with many gene families expanded showing high sequence, structural and functional diversity. The high diversity of immune receptors and effectors may provide oysters with enhanced specificity in immune recognition and response to cope with diverse pathogens in the absence of adaptive immunity. Some members of expanded immune gene families have diverged to function at different temperatures and salinities or assumed new roles in abiotic stress response. Most canonical innate immunity pathways are conserved in oysters and supported by a large number of diverse and often novel genes. The great diversity in immune and stress response genes exhibited by expanded gene families as well as high sequence and structural polymorphisms may be central to oyster{\textquoteright}s adaptation to highly stressful and widely changing environments.</p>
},
	issn = {1095-9947},
	doi = {10.1016/j.fsi.2015.05.018},
	author = {Guo, Ximing and He, Yan and Zhang, Linlin and Christophe Lelong and Jouaux, Aude}
}
@article {4049,
	title = {Invertebrate assemblage responses and the dual roles of resistance and resilience to drying in intermittent rivers},
	journal = {Aquatic Sciences},
	year = {2015},
	abstract = {<p>ABSTRACT: Intermittent rivers are naturally dynamic ecosystems in which flow cessation and riverbed drying cause temporal fluctuations in aquatic biodiversity. We analysed datasets from intermittent rivers in different climate zones across the world to examine responses of aquatic macroinvertebrate assemblages to drying, in relation to both taxonomic composition and traits of resistance and resilience. First, we compared the differences in taxonomic richness and turnover and in trait diversity, richness and redundancy before and after intermittent sites dried with the differences in concurrently sampled perennial sites. We found such high levels of variation in the before-after differences at intermittent and perennial sites that we could not detect statistical differences between them. Second, we examined the effects of climate (arid, Mediterranean, temperate) and durations of dry and post-dry (flowing) periods on responses to drying at intermittent sites. Only climate had a detectable effect; the proportion of taxa at intermittent sites that persisted through drying-rewetting phases was greatest in arid-zone rivers. Regardless of climate, the invertebrates that persisted at intermittent sites were dominated by taxa resistant to drying. By contrast, taxa that persisted at perennial sites had fewer traits conferring resistance but more conferring resilience. The contributions of resistance and resilience combined with the presence of both intermittent and perennial reaches likely supports the long-term stability and persistence of communities in intermittent rivers, despite the inherently high variation in short-term responses to drying.</p>
},
	doi = {DOI:10.1007/s00027-015-0427-2 },
	author = {C. Leigh and N. Bonada and A.J. Boulton and B. Hugueny and S.T. Larned and R. Vander Vorste and T. Datry}
}
@article {3626,
	title = {Molecular characterization of peptide fractions of a Tilapia (Oreochromis niloticus) by-product hydrolysate and in vitro evaluation of antibacterial activity},
	journal = {Process Biochemistry},
	volume = {50},
	year = {2015},
	pages = {487-492},
	author = {Robert, Marie and C{\'e}line Zatylny-Gaudin and Fournier, Vincent and Corre, Erwan and Gildas Le Corguille and Bernay, Beno{\^\i}t and Jo{\"e}l Henry}
}
@article {4363,
	title = {A new species of Sicyopterus (Teleostei: Gobiidae) from Indonesia. },
	journal = {Cybium},
	volume = {39},
	year = {2015},
	pages = {243-248},
	author = {Philippe Keith and Clara Lord and Sauri, S and Fr{\'e}d{\'e}ric Busson and Hubert, Nicolas and Hadiaty, Renny}
}
@article {4360,
	title = {A new Stiphodon from Indonesia (Teleostei: Gobiidae)},
	journal = {Cybium},
	volume = {39},
	year = {2015},
	pages = {219-225},
	keywords = {Indonesia, New species, Stiphodon},
	author = {Philippe Keith and Clara Lord and Fr{\'e}d{\'e}ric Busson and Sauri, S and Hubert, Nicolas and Hadiaty, Renny}
}
@article {4103,
	title = {A new Stiphodon from Indonesia (Teleostei: Gobiidae)},
	journal = {Cybium},
	volume = {39.},
	year = {2015},
	pages = {219-225},
	keywords = {Freshwater, Gobiidae, Indonesia, New species, Stiphodon aureofuscus},
	author = {Philippe Keith and Fr{\'e}d{\'e}ric Busson and Sauri, S and Hubert, N and Hadiaty, Renny}
}
@article {4154,
	title = {The oldest notostracan (Upper Devonian Strud Locality, Belgium)},
	journal = {Palaeontology},
	volume = {58},
	year = {2015},
	month = {01/2015},
	pages = {497-509},
	author = {Linda Lagebro and Pierre Gueriau and Thomas Hegna and Nicolas Rabet and Aodh{\'a}n Butler and Graham Budd}
}
@article {4056,
	title = {Parental exposure to the herbicide diuron results in oxidative DNA damage to germinal cells of the Pacific oyster Crassostrea gigas.},
	journal = {Comp Biochem Physiol C Toxicol Pharmacol},
	year = {2015},
	month = {2015 Nov 21},
	abstract = {<p>Chemical pollution by pesticides has been identified as a possible contributing factor to the massive mortality outbreaks observed in Crassostrea gigas for several years. A previous study demonstrated the vertical transmission of DNA damage by subjecting oyster genitors to the herbicide diuron at environmental concentrations during gametogenesis. This trans-generational effect occurs through damage to genitor-exposed gametes, as measured by the comet-assay. The presence of DNA damage in gametes could be linked to the formation of DNA damage in other germ cells. In order to explore this question, the levels and cell distribution of the oxidized base lesion 8-oxodGuo were studied in the gonads of exposed genitors. High-performance liquid chromatography coupled with UV and electrochemical detection analysis showed an increase in 8-oxodGuo levels in both male and female gonads after exposure to diuron. Immunohistochemistry analysis showed the presence of 8-oxodGuo at all stages of male germ cells, from early to mature stages. Conversely, the oxidized base was only present in early germ cell stages in female gonads. These results indicate that male and female genitors underwent oxidative stress following exposure to diuron, resulting in DNA oxidation in both early germ cells and gametes, such as spermatozoa, which could explain the transmission of diuron-induced DNA damage to offspring. Furthermore, immunostaining of early germ cells seems indicates that damages caused by exposure to diuron on germ line not only affect the current sexual cycle but also could affect future gametogenesis.</p>
},
	issn = {1532-0456},
	doi = {10.1016/j.cbpc.2015.11.002},
	author = {Barranger, Audrey and Clothilde Heude-Berthelin and Rouxel, Julien and Adeline, B{\'e}atrice and Benabdelmouna, Abdellah and Burgeot, Thierry and Akcha, Farida}
}
@article {6880,
	title = {The potential for climate-driven bathymetric range shifts: sustained temperature and pressure exposures on a marine ectotherm, <i>Palaemonetes varians</i>},
	journal = {Royal Society Open Science},
	volume = {2},
	year = {2015},
	month = {Jan-11-2015},
	pages = {150472},
	issn = {2054-5703},
	doi = {10.1098/rsos.150472},
	url = {https://royalsocietypublishing.org/doi/10.1098/rsos.150472},
	author = {Morris, J. P. and Thatje, S. and Cottin, D. and Oliphant, A. and Brown, A. and Bruce Shillito and Juliette Ravaux and Hauton, C.}
}
@article {4400,
	title = {Re-description of Apistogramma payaminonis Kullander, 1986, with descriptions of two new cichlid species of the genus Apistogramma (Teleostei, Perciformes, Geophaginae) from northern Peru},
	journal = {Vertebrate Zoology},
	volume = {65},
	year = {2015},
	pages = {287-314},
	author = {R{\"o}mer, Uwe and Soares, D. P. and Garc{\'\i}a-D{\'a}vila, C. and Fabrice Duponchelle and Renno, Jean-Francois and Hanh, I.}
}
@article {3385,
	title = {Relationships between biodiversity and the stability of marine ecosystems: Comparisons at a European scale using meta-analysis},
	journal = {Journal of Sea Research},
	volume = {98},
	year = {2015},
	pages = {5-14},
	abstract = {<p>Abstract The relationship between biodiversity and stability of marine benthic assemblages was investigated through meta-analyses using existing data sets (n\&nbsp;=\&nbsp;28) covering various spatial (m{\textendash}km) and temporal (1973{\textendash}2006; ranging from 5 to \&gt;\&nbsp;250\&nbsp;months) scales in different benthic habitats (emergent rock, rock pools and sedimentary habitats) over different European marine systems (North Atlantic and western Mediterranean). Stability was measured by a lower variability in time, and variability was estimated as temporal variance of species richness, total abundance (density or \% cover) and community structure (using Bray{\textendash}Curtis dissimilarities on species composition and abundance). Stability generally decreased with species richness. Temporal variability in species richness increased with the number of species at both quadrat (\&lt;\&nbsp;1\&nbsp;m2) and site (\&nbsp;\&nbsp;100\&nbsp;m2) scales, while no relationship was observed by multivariate analyses. Positive relationships were also observed at the scale of site between temporal variability in species richness and variability in community structure with evenness estimates. This implies that the relationship between species richness or evenness and species richness variability is slightly positive and depends on the scale of observation. Thus, species richness does not stabilize temporal fluctuations in species number, rather species rich assemblages are those most likely to undergo the largest fluctuations in species numbers and abundance from time to time. Changes within community assemblages in terms of structure are, however, generally independent of biodiversity. Except for sedimentary and rock pool habitats, no relationship was observed between temporal variation of total abundances and diversity at either scale. Overall, our results emphasize that the relation between species richness and species-level measures of temporal variability depends on scale of measurements, type of habitats and the marine system (North Atlantic and Mediterranean) considered.</p>
},
	keywords = {Benthic Marine Coastal Habitats, Biodiversity Ecosystem Functioning, Community Variability, Diversity{\textendash}Stability Relationships, Temporal Variability},
	issn = {1385-1101},
	doi = {http://dx.doi.org/10.1016/j.seares.2014.08.004},
	url = {http://www.sciencedirect.com/science/article/pii/S1385110114001609},
	author = {Cusson, Mathieu and Tasman P. Crowe and Rita Ara{\'u}jo and Francisco Arenas and Rebbecca Aspden and Fabio Bulleri and Dominique Davoult and Kirstie Dyson and Simonetta Fraschetti and Kristjan Herk{\"u}l and C{\'e}dric Hubas and Stuart Jenkins and Jonne Kotta and Patrik Kraufvelin and Migne, A and Markus Molis and Olwyen Mulholland and Laure M.-L.J. No{\"e}l and Paterson, David M and James Saunders and Paul J. Somerfield and Isabel Sousa-Pinto and Nicolas Spilmont and Antonio Terlizzi and Lisandro Benedetti-Cecchi}
}
@article {4362,
	title = {Revision of vernacular names for the freshwater fish of French Guiana.},
	journal = {Cybium},
	volume = {39},
	year = {2015},
	pages = {279-300},
	author = {Grenand, Pierre and Chapuis, Jean and Cognat Andr{\'e} and Cristinoi Antonia and Davy Damien and Grenand Fran{\c c}oise and Michel J{\'e}gu and Philippe Keith and Martin, Emmanuel and Nemo Fran{\c c}ois and Pagezy H{\'e}l{\`e}ne and Le Bail, Pierre-Yves}
}
@article {3764,
	title = {The role of female cephalopod researchers: past and present},
	journal = {Journal of Natural History},
	volume = {49},
	year = {2015},
	pages = {1235{\textendash}1266},
	issn = {0022-2933},
	doi = {10.1080/00222933.2015.1037088},
	url = {http://dx.doi.org/10.1080/00222933.2015.1037088},
	author = {Allcock, A. Louise and von Boletzky, Sigurd and Laure Bonnaud-Ponticelli and Brunetti, Norma E. and Cazzaniga, N{\'e}stor J. and Hochberg, Eric and Ivanovic, Marcela and Lipinski, Marek and Marian, Jos{\'e} E. A. R. and Nigmatullin, Chingis and Nixon, Marion and Jean-Paul Robin and Rodhouse, Paul G. K. and Vidal, Erica A. G.}
}
@article {3383,
	title = {Seasonal variations of the composition of microbial biofilms in sandy tidal flats: Focus of fatty acids, pigments and exopolymers},
	journal = {Estuarine, Coastal and Shelf Science},
	volume = {153},
	year = {2015},
	pages = {29 - 37},
	abstract = {<p>Abstract Biofilms, or microbial mats, are common associations of microorganisms in tidal flats; they generally consist of a large diversity of organisms embedded in a matrix of Extracellular Polymeric Substances (EPS). These molecules are mainly composed of carbohydrates and proteins, but their detailed monomer compositions and seasonal variations are currently unknown. Yet this composition determines the numerous roles of biofilms in these systems. This study investigated the changes in composition of carbohydrates in intertidal microbial mats over a year to decipher seasonal variations in biofilms and in varying hydrodynamic conditions. This work also aimed to assess how these compositions are related to microbial assemblages. In this context, natural biofilms whose development was influenced or not by artificial structures mimicking polychaete tubes were sampled monthly for over a year in intertidal flats of the Chausey archipelago. Biofilms were compared through the analysis of their fatty acid and pigment contents, and the monosaccharide composition of their \{EPS\} carbohydrates. Carbohydrates from both colloidal and bound \{EPS\} contained mainly glucose and, to a lower extent, galactose and mannose but they showed significant differences in their detailed monosaccharide compositions. These two fractions displayed different seasonal evolution, even if glucose accumulated in both fractions in summer; bound \{EPS\} only were affected by artificial biogenic structures. Sediment composition in fatty acids and pigments showed that microbial communities were dominated by diatoms and heterotrophic bacteria. Their relative proportions, as well as those of other groups like cryptophytes, changed between times and treatments. The changes in \{EPS\} composition were not fully explained by modifications of microbial assemblages but also depended on the processes taking place in sediments and on environmental conditions. These variations of \{EPS\} compositions are likely to alter different ecosystem processes such as biostabilisation or pollutants trapping.</p>
},
	keywords = {biofilms, biogenic structures, EPS, fatty acids, monosaccharide composition, pigments},
	issn = {0272-7714},
	doi = {http://dx.doi.org/10.1016/j.ecss.2014.11.013},
	url = {http://www.sciencedirect.com/science/article/pii/S0272771414003412},
	author = {Passarelli, C and Tarik Meziane and Najet Thiney and Dominique Boeuf and B Jesus and Mickael Ruivo and Christian Jeanthon and C{\'e}dric Hubas}
}
@article {4554,
	title = {Shell growth, microstructure and composition over the development cycle of the European abalone Haliotis tuberculata},
	journal = {Marine Biology},
	volume = {162},
	year = {2015},
	pages = {687{\textendash}697},
	abstract = {<p>The shell of the European abalone Haliotis tuberculata is a model for studying mechanisms of mollusc shell formation, but the early steps of shell formation and calcification remain poorly documented. The microstructure and the mineralogical and geochemical composition of larval and juvenile shells were investigated by scanning electron microscopy, infrared spectroscopy and ion microprobe analyses (NanoSIMS). Analyses were performed on shells obtained from controlled fertilisations at the hatchery France-Haliotis (Plouguerneau, France) in July 2009 and 2010 using abalone from Roscoff. Shell cross sections revealed the microstructural arrangement of the developing shell, showing progressive biomineral organisation into two differentiated layers, i.e. the outer granular and the internal nacreous layer. Infrared analysis confirmed that the European abalone shell, at every stage of development, was mostly composed of CaCO3 in the form of aragonite. Variations in trace element composition, i.e. Sr/Ca, were measured in the different stages and correlated with micro-structural changes in the shells. Experimental manganese labelling of live abalones produced cathodoluminescence marks in the growing shell sections. The increase in shell thickness can be used to determine the growth rate of an early adult abalone shell.</p>
},
	issn = {1432-1793},
	doi = {10.1007/s00227-015-2615-y},
	url = {http://dx.doi.org/10.1007/s00227-015-2615-y},
	author = {St{\'e}phanie Auzoux-Bordenave and Brahmi, C. and Badou, Aicha and de Raf{\'e}lis, M. and Huchette, S.}
}
@article {3522,
	title = {Spatio-temporal variations in the composition of organic matter in surface sediments of a mangrove receiving shrimp farm effluents (New Caledonia)},
	journal = {Science of The Total Environment},
	volume = {512{\textendash}513},
	year = {2015},
	pages = {296 - 307},
	abstract = {<p>In order to investigate spatio-temporal variations in the composition and origin of the benthic organic matter (OM) at the sediment surface in mangrove receiving shrimp farm effluents, fatty acid (FA) biomarkers, natural stable isotopes (δ13C and δ15N), C:N ratios and chlorophyll-a (chl-a) concentrations were determined during the active and the non-active period of the farm. Fatty acid compositions in surface sediments within the mangrove forest indicated that organic matter inputs varied along the year as a result of farm activity. Effluents were the source of fresh particulate organic matter for the mangrove, as evidenced by the unsaturated fatty acid (UFA) distribution. The anthropogenic \{MUFA\} 18:1ω9 was not only accumulated at the sediment surface in some parts of the mangrove, but was also exported to the seafront. Direct release of bacteria and enhanced in situ production of fungi, as revealed by specific FAs, stimulated mangrove litter decomposition under effluent runoff condition. Also, microalgae released from ponds contributed to maintain high benthic chl-a concentrations in mangrove sediments in winter and to a shift in microphytobenthic community assemblage. Primary production was high whether the farm released effluent or not which questioned the temporary effect of shrimp farm effluent on benthic microalgae dynamic. This study outlined that mangrove benthic organic matter was qualitatively and quantitatively affected by shrimp farm effluent release and that responses to environmental condition changes likely depended on mangrove stand characteristics.</p>
},
	keywords = {Chlorophyll-a, fatty acids, Mangrove, Organic matter, Shrimp farming, Stable isotopes},
	issn = {0048-9697},
	doi = {http://dx.doi.org/10.1016/j.scitotenv.2014.12.082},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969714017938},
	author = {Ad{\'e}laide Aschenbroich and Cyril Marchand and Nathalie Molnar and Jonhatan Deborde and C{\'e}dric Hubas and Herv{\'e} Rybarczyk and Tarik Meziane}
}
@article {9379,
	title = {Spiralian Phylogeny Informs the Evolution of Microscopic Lineages},
	journal = {Current Biology},
	volume = {25},
	year = {2015},
	month = {Jan-08-2015},
	pages = {2000 - 2006},
	issn = {09609822},
	doi = {10.1016/j.cub.2015.06.068},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982215007952},
	author = {Laumer, Christopher~E. and Bekkouche, Nicolas and Kerbl, Alexandra and Goetz, Freya and Neves, Ricardo~C. and S{\o}rensen, Martin~V. and Kristensen, Reinhardt~M. and Hejnol, Andreas and Dunn, Casey~W. and Giribet, Gonzalo and Worsaae, Katrine}
}
@article {4052,
	title = {Stable isotopes reveal food web modifications along the upstream{\textendash} downstream gradient of a temperate stream},
	journal = {Aquatic Sciences},
	year = {2015},
	abstract = {<p>ABSTRACT: The upstream{\textendash}downstream gradient (UDG) is a key feature of streams. For instance food webs are assumed to change from upstream to downstream. We tested this hypothesis in a small European river catchment (937 km 2), and examined whether food web modifications are related to structural (i.e. food web composition) or functional changes (i.e. alteration of linkages within the web). We adopted a double approach at two levels of organisation (assemblage and species levels) using two isotopic metrics (isotopic space area and isotopic niche overlap), and proposed a new hypothesis-testing framework for exploring the dominant feeding strategy within a food web. We confirmed that the UDG influenced stream food webs, and found that food web modifications were related to both structural and functional changes. The structural change was mainly related to an increase in species richness, and induced functional modifications of the web (indirect effect). In addition, the UDG also modified the functional features of the web directly, without changing the web composition. The proposed framework allowed relating the direct effect of the UDG to a diet specialisation of the species, and the indirect effect via the structural changes to a generalist feeding strategy. The framework highlights the benefits of conducting the double approach, and provides a foundation for future studies investigating the dominant feeding strategy that underlies food web modifications.</p>
},
	doi = {DOI 10.1007/s00027-015-0421-8},
	author = {N. Hette and J{\'e}r{\^o}me Belliard and E. Tales and Thierry Oberdorff}
}
@article {3849,
	title = {Stiphodon annieae, a new species of freshwater goby from Indonesia (Teleostei: Gobiidae). },
	journal = {Cybium},
	volume = {38},
	year = {2015},
	pages = {267-272},
	keywords = {Freshwater, Halmahera, Indonesia, New species, Stiphodon annieae},
	author = {Philippe Keith and Hadiaty, Renny}
}
@article {3863,
	title = {The Toll/NF-κB pathway in cuttlefish symbiotic accessory nidamental gland.},
	journal = {Dev Comp Immunol},
	volume = {53},
	year = {2015},
	month = {2015 Jul 2},
	pages = {42-46},
	abstract = {<p>The female genital apparatus of decapod cephalopods contains a symbiotic accessory nidamental gland (ANG) that harbors bacterial symbionts. Although the ANG bacterial consortium is now well described, the impact of symbiosis on Sepia officinalis innate immunity pathways remains unknown. In silico analysis of the de novo transcriptome of ANG highlighted for the first time the existence of the NF-κB pathway in S. officinalis. Several signaling components were identified, i.e. five Toll-like receptors, eight signaling cascade features, and the immune response target gene iNOS, previously described as being involved in the initiation of bacterial symbiosis in a cephalopod gland. This work provides a first key for studying bacterial symbiosis and its impact on innate immunity in S. officinalis ANG.</p>
},
	issn = {1879-0089},
	doi = {10.1016/j.dci.2015.06.016},
	author = {Cornet, Val{\'e}rie and Jo{\"e}l Henry and Corre, Erwan and Gildas Le Corguille and C{\'e}line Zatylny-Gaudin}
}
@article {4048,
	title = {Towards understanding the organisation of metacommunities in  highly dynamic ecological systems },
	journal = {Oikos},
	year = {2015},
	abstract = {<p>ABSTRACT: Community ecology recognises today that local biological communities are not only affected by local biotic interactions and abiotic environmental conditions, but also by regional processes (e.g. dispersal). While much is known about how metacommunities are organised in space in terrestrial, marine and freshwater ecological systems, their temporal variations remain poorly studied. Here, we address the question of the dynamics of metacommunities in highly variable systems, using intermittent rivers (IRs), those rivers which temporarily stop flowing or dry up, as a model system. We first review how habitat heterogeneity in space and time influences metacommunity organisation. Second, we compare the metacommunities in IRs to those in perennial rivers (PRs) and develop the idea that IRs could undergo highly dynamic shifts due to the temporal variability in local and regional community processes. Third, we develop the idea that in IRs, metacommunities of the wet and dry phases of IRs are closely intertwined, thereby increasing even more their respective temporal dynamics. Last, we provide a roadmap to stimulate further conceptual and empirical developments of metacommunity research and identify possible applications for improving the management of IRs and other highly dynamic ecological systems.</p>
},
	doi = {doi: 10.1111/oik.02922},
	author = {T. Datry and N. Bonada and J. Heino}
}
@article {3828,
	title = {Transcriptome analysis reveals strong and complex antiviral response in a mollusc.},
	journal = {Fish Shellfish Immunol},
	year = {2015},
	month = {2015 May 22},
	abstract = {<p>Viruses are highly abundant in the oceans, and how filter-feeding molluscs without adaptive immunity defend themselves against viruses is not well understood. We studied the response of a mollusc Crassostrea gigas to Ostreid herpesvirus 1 {\textmu}Var (OsHV-1μVar) infections using transcriptome sequencing. OsHV-1μVar can replicate extremely rapidly after challenge of C.\&nbsp;gigas as evidenced by explosive viral transcription and DNA synthesis, which peaked at 24 and 48\&nbsp;h post-inoculation, respectively, accompanied by heavy oyster mortalities. At 120\&nbsp;h post-injection, however, viral gene transcription and DNA load, and oyster mortality, were greatly reduced indicating an end of active infections and effective control of viral replication in surviving oysters. Transcriptome analysis of the host revealed strong and complex responses involving the activation of all major innate immune pathways that are equipped with expanded and often novel receptors and adaptors. Novel Toll-like receptor (TLR) and MyD88-like genes lacking essential domains were highly up-regulated in the oyster, possibly interfering with TLR signal transduction. RIG-1/MDA5 receptors for viral RNA, interferon-regulatory factors, tissue necrosis factors and interleukin-17 were highly activated and likely central to the oyster{\textquoteright}s antiviral response. Genes related to anti-apoptosis, oxidation, RNA and protein destruction were also highly up-regulated, while genes related to anti-oxidation were down-regulated. The oxidative burst induced by the up-regulation of oxidases and severe down-regulation of anti-oxidant genes may be important for the destruction of viral components, but may also exacerbate oyster mortality. This study provides unprecedented insights into antiviral response in a mollusc. The mobilization and complex regulation of expanded innate immune-gene families highlights the oyster genome{\textquoteright}s adaptation to a virus-rich marine environment.</p>
},
	issn = {1095-9947},
	doi = {10.1016/j.fsi.2015.05.023},
	author = {He, Yan and Jouaux, Aude and Ford, Susan E and Christophe Lelong and Pascal Sourdaine and Mathieu, Michel and Guo, Ximing}
}
@article {5816,
	title = {{Uncertainties in the projection of species distributions related to general circulation models}},
	journal = {Ecology and Evolution},
	volume = {5},
	year = {2015},
	abstract = {<p>{\textcopyright} 2015 The Authors. Ecological Niche Models (ENMs) are increasingly used by ecologists to project species potential future distribution. However the application of such models may be challenging and some caveats have already been identified. While studies have generally shown that projections may be sensitive to the ENM applied or the emission scenario to name just a few the sensitivity of ENM-based scenarios to General Circulation Models (GCMs) has been often underappreciated. Here using a multi-GCM and multi-emission scenario approach we evaluated the variability in projected distributions under future climate conditions. We modeled the ecological realized niche (sensu Hutchinson) and predicted the baseline distribution of species with contrasting spatial patterns and representative of two major functional groups of European trees: the dwarf birch and the sweet chestnut. Their future distributions were then projected onto future climatic conditions derived from seven GCMs and four emissions scenarios using the new Representative Concentration Pathways (RCPs) developed for the Intergovernmental Panel on Climate Change (IPCC) AR5 report. Uncertainties arising from GCMs and those resulting from emissions scenarios were quantified and compared. Our study reveals that scenarios of future species distribution exhibit broad differences depending not only on emissions scenarios but also on GCMs. We found that the between-GCM variability was greater than the between-RCP variability for the next decades and both types of variability reached a similar level at the end of this century. Our result highlights that a combined multi-GCM and multi-RCP approach is needed to better consider potential trajectories and uncertainties in future species distributions. In all cases between-GCM variability increases with the level of warming and if nothing is done to alleviate global warming future species spatial distribution may become more and more difficult to anticipate. When future species spatial distributions are examined we propose to use a large number of GCMs and RCPs to better anticipate potential trajectories and quantify uncertainties.</p>
},
	keywords = {Biogeography, Climate Change, Ecological niche modeling, Global change models, Species distribution projections, Uncertainties},
	issn = {20457758},
	doi = {10.1002/ece3.1411},
	author = {Goberville, Eric and Gr{\'e}gory Beaugrand and Nina-Coralie Hautek{\`e}ete and Yves Piquot and Christophe Luczak}
}
@article {3510,
	title = {Acute toxicity of 8 antidepressants: what are their modes of action?},
	journal = {Chemosphere},
	volume = {108},
	year = {2014},
	month = {2014 Aug},
	pages = {314-9},
	abstract = {<p>Currently, the hazard posed by pharmaceutical residues is a major concern of ecotoxicology. Most of the antidepressants belong to a family named the Cationic Amphipathic Drugs known to have specific interactions with cell membranes. The present study assessed the impact of eight antidepressants belonging to selective serotonin reuptake inhibitors or serotonin norepinephrine reuptake inhibitors by the combination of multi-approaches (in vivo, in vitro, in silico) and gives some insights on the mode of action for these molecules. Antidepressants were from the most to the least toxic compound for Daphnia magna: Sertraline (EC50=1.15 mg L(-1))\&gt;Clomipramine (2.74 mg L(-1))\&gt;Amitriptyline (4.82 mg L(-1))\&gt;Fluoxetine (5.91 mg L(-1))\&gt;Paroxetine (6.24 mg L(-1))\&gt;Mianserine (7.81 mg L(-1))\&gt;Citalopram (30.14 mg L(-1)) and Venlafaxine (141.28 mg L(-1)). These acute toxicities were found correlated to Log Kow coefficients (R=0.93, p\&lt;0.001) and to cytotoxicity assessed on abalone hemocytes through the neutral red uptake assay (R=0.96, p\&lt;0.001). If narcosis as mode of action is typically expected during acute ecotoxicity bioassays, we showed by molecular modeling that particular interactions can exist between antidepressants and phosphatidylcholine, a major component of cell membranes, leading to a more specific mode of action corresponding to a potential acidic hydrolysis of ester functions.</p>
},
	keywords = {Animals, Antidepressive Agents, Cell Survival, Cells, Cultured, Daphnia, Environmental Pollutants, Gastropoda, Hemocytes, Lysosomes, Models, Molecular, Phosphatidylcholines, Serotonin Uptake Inhibitors},
	issn = {1879-1298},
	doi = {10.1016/j.chemosphere.2014.01.057},
	author = {Minguez, Laetitia and Farcy, E and Ballandonne, C{\'e}line and Lepailleur, Alban and Antoine Serpentini and Jean-Marc Lebel and Bureau, Ronan and Halm-Lemeille, Marie-Pierre}
}
@article {3512,
	title = {Assessment of cytotoxic and immunomodulatory properties of four antidepressants on primary cultures of abalone hemocytes (Haliotis tuberculata).},
	journal = {Aquat Toxicol},
	volume = {153},
	year = {2014},
	month = {2014 Aug},
	pages = {3-11},
	abstract = {<p>Pharmaceutical compounds like antidepressants found in surface waters raise concerns due to their potential toxicity on non-target aquatic organisms. This study aimed at investigating the in vitro cytotoxicity and immunomodulatory properties of four common antidepressants, namely Amitriptyline, Clomipramine, Citalopram and Paroxetine, on primary cultures of abalone hemocytes (Haliotis tuberculata), after 48 h-exposure. Effects on immunocompetence (phagocytosis, levels of reactive oxygen species, esterase activity and lysosomal membrane destabilization) were assessed. Results obtained by MTT assays revealed that acute toxicity is unlikely to occur in the environment since the LC50s of the four antidepressants are at the mg/L level. The different immunological endpoints displayed a biphasic response, with an increase at the lowest concentration (i.e. 1 μg/L) followed by a decrease at higher concentrations. Overall, Amitriptyline and Clomipramine, the two tricyclic antidepressants, had higher immunomodulatory capacities than the two selective serotonin reuptake inhibitors Citalopram and Paroxetine. Amitriptyline was the most potent and Citalopram the least potent drug in altering immune function in H. tuberculata.</p>
},
	keywords = {Animals, Antidepressive Agents, Cell Survival, Cells, Cultured, Enzyme Activation, Esterases, Gastropoda, Hemocytes, Immunity, Innate, Lethal Dose 50, Phagocytosis, Reactive Oxygen Species, Water Pollutants, Chemical},
	issn = {1879-1514},
	doi = {10.1016/j.aquatox.2013.10.020},
	author = {Minguez, Laetitia and Halm-Lemeille, Marie-Pierre and Katherine Costil and Bureau, Ronan and Jean-Marc Lebel and Antoine Serpentini}
}
@inbook {3857,
	title = { Biogeographic patterns of fish},
	booktitle = { The Biogeographic Atlas of the Southern Ocean  },
	year = {2014},
	author = {Percy-Alexander Hulley and Causse, Romain and Koubbi, Philippe and Vacchi, Marino}
}
@article {3374,
	title = {Cellular effects of bacterial N-3-Oxo-dodecanoyl-L-Homoserine lactone on the sponge Suberites domuncula (Olivi, 1792): insights into an intimate inter-kingdom dialogue.},
	journal = {PLoS One},
	volume = {9},
	year = {2014},
	month = {2014},
	pages = {e97662},
	abstract = {<p>Sponges and bacteria have lived together in complex consortia for 700 million years. As filter feeders, sponges prey on bacteria. Nevertheless, some bacteria are associated with sponges in symbiotic relationships. To enable this association, sponges and bacteria are likely to have developed molecular communication systems. These may include molecules such as N-acyl-L-homoserine lactones, produced by Gram-negative bacteria also within sponges. In this study, we examined the role of N-3-oxododecanoyl-L-homoserine lactone (3-oxo-C12-HSL) on the expression of immune and apoptotic genes of the host sponge Suberites domuncula. This molecule seemed to inhibit the sponge innate immune system through a decrease of the expression of genes coding for proteins sensing the bacterial membrane: a Toll-Like Receptor and a Toll-like Receptor Associated Factor 6 and for an anti-bacterial perforin-like molecule. The expression of the pro-apoptotic caspase-like 3/7 gene decreased as well, whereas the level of mRNA of anti-apoptotic genes Bcl-2 Homolog Proteins did not change. Then, we demonstrated the differential expression of proteins in presence of this 3-oxo-C12-HSL using 3D sponge cell cultures. Proteins involved in the first steps of the endocytosis process were highlighted using the 2D electrophoresis protein separation and the MALDI-TOF/TOF protein characterization: α and β subunits of the lysosomal ATPase, a cognin, cofilins-related proteins and cytoskeleton proteins actin, α tubulin and α actinin. The genetic expression of some of these proteins was subsequently followed. We propose that the 3-oxo-C12-HSL may participate in the tolerance of the sponge apoptotic and immune systems towards the presence of bacteria. Besides, the sponge may sense the 3-oxo-C12-HSL as a molecular evidence of the bacterial presence and/or density in order to regulate the populations of symbiotic bacteria in the sponge. This study is the first report of a bacterial secreted molecule acting on sponge cells and regulating the symbiotic relationship.</p>},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0097662},
	author = {Gard{\`e}res, Johan and Jo{\"e}l Henry and Bernay, Beno{\^\i}t and Ritter, Andr{\`e}s and C{\'e}line Zatylny-Gaudin and Wiens, Matthias and M{\"u}ller, Werner E G and Le Pennec, Ga{\"e}l}
}
@inbook {5148,
	title = {Chapter 7. Biogeographic patterns of fish},
	booktitle = {Biogeographic Atlas of the Southern Ocean},
	year = {2014},
	pages = {327{\textendash}362},
	edition = {In: De Broyer C., Koubbi P., Griffiths H.J., Raymond B., Udekem d{\textquoteright}Acoz C. d{\textquoteright}, et al. (eds.)},
	chapter = {7},
	isbn = {978-0-948277-28-3},
	author = {Guy Duhamel and Percy-Alexander Hulley and Causse, Romain and Koubbi, Philippe and Vacchi, Marino and Patrice Pruvost and Vigetta, Stephanie and Irisson, J.-O. and Mormede, Sophie and Belchier, Mark and others}
}
@article {3307,
	title = {Chapter Four : Transitions During Cephalopod Life History: The Role of Habitat, Environment, Functional Morphology and Behaviour},
	year = {2014},
	keywords = {Acquisition of behaviours, Adult, Cephalopod ontogeny, Cohort survival, Environmental variability, Habitat shifts, Juvenile, Life stages, Morphological changes, Paralarvae, Subadult},
	author = {Jean-Paul Robin and Roberts, Michael and Zeidberg, Lou and Bloor, Isobel and Rodriguez, Almendra and Brice{\~n}o, Felipe and Downey, Nicola and Mascar{\'o}, Maite and Guerra, Angel and Hofmeister, Jennifer and Barcellos, Diogo D. and Louren{\c c}o, Silvia A.P. and Roper, Clyde F.E. and Moltschaniwskyj, Natalie A. and Green, Corey P. and Mather, Jennifer}
}
@article {3490,
	title = {Characterisation and expression of the biomineralising gene Lustrin A during shell formation of the European abalone Haliotis tuberculata},
	journal = {Comparative Biochemistry and Physiology , Part B},
	volume = {169},
	year = {2014},
	month = {2014},
	pages = {1-8},
	type = {Research article},
	abstract = {<p>The molluscan shell is a remarkable product of a highly biomineralisation process, and is composed of calcium carbonate most commonly in the form of calcite or aragonite. The exceptional mechanical properties of this biomaterial are imparted by the embedded organic matrix which is secreted by the underlying mantle tissue. While many shell-matrix proteins have already been identified within adult molluscan shell, their presence and role in the early developmental stages of larval shell formation are not well understood. In the European abalone <em>Haliotis tuberculata</em>, the shell first forms in the early trochophore larva and develops into a mineralised protoconch in the veliger. Following metamorphosis, the juvenile shell rapidly changes as it becomes flattened and develops a more complex crystallographic profile including an external granular layer and an internal nacreous layer. Among the matrix proteins involved in abalone shell formation, Lustrin A is thought to participate in the formation of the nacreous layer. Here we have identified a partial cDNA coding for the <em>Lustrin A</em> gene in <em>H. tuberculata</em> and have analysed its spatial and temporal expression during abalone development. RT-PCR experiments indicate that <em>Lustrin A</em> is first expressed in juvenile (post-metamorphosis) stages, suggesting that Lustrin A is a component of the juvenile shell, but not of the larval shell. We also detected <em>Lustrin A</em> mRNAs in non-nacre forming cells at the distal-most edge of the juvenile mantle as well as in the nacre-forming region of the mantle. <em>Lustrin A</em> was also expressed in 7-day-old post-larvae, prior to the formation of nacre. These results suggest that Lustrin A plays multiple roles in the shell-forming process and further highlight the dynamic ontogenic nature of molluscan shell formation.</p>
},
	keywords = {biomineralisation, Haliotis tuberculata, larval development, Lustrin A, mollusc, organic matrix, shell},
	author = {Gaume, B{\'e}atrice and Denis, Fran{\c c}oise and Van Wormhoudt, Alain and Huchette, Sylvain and Jackson, Daniel and Avignon, Sol{\`e}ne and St{\'e}phanie Auzoux-Bordenave}
}
@article {3428,
	title = {Comparison of the sensitivity of seven marine and freshwater bioassays as regards antidepressant toxicity assessment.},
	journal = {Ecotoxicology},
	volume = {23},
	year = {2014},
	month = {2014 Nov},
	pages = {1744-54},
	abstract = {<p>The hazards linked to pharmaceutical residues like antidepressants are currently a major concern of ecotoxicology because they may have adverse effects on non-target aquatic organisms. Our study assesses the ecotoxicity of three antidepressants (fluoxetine, sertraline and clomipramine) using a battery of marine and freshwater species representing different trophic levels, and compares the bioassay sensitivity levels. We selected the following bioassays: the algal growth inhibition test (Skeletonema marinoi and Pseudokirchneriella subcapitata), the microcrustacean immobilization test (Artemia salina and Daphnia magna), development and adult survival tests on Hydra attenuata, embryotoxicity and metamorphosis tests on Crassostrea gigas, and in vitro assays on primary cultures of Haliotis tuberculata hemocytes. The results showed high inter-species variability in EC50-values ranging from 43 to 15,600\&nbsp;{\textmu}g/L for fluoxetine, from 67 to 4,400\&nbsp;{\textmu}g/L for sertraline, and from 4.70\&nbsp;{\textmu}g/L to more than 100,000\&nbsp;{\textmu}g/L for clomipramine. Algae (S. marinoi and P. subcapitata) and the embryo-larval stages of the oyster C. gigas were the most sensitive taxa. This raises an issue due to their ecological and/or economic importance. The marine crustacean A. salina was the least sensitive species. This difference in sensitivity between bioassays highlights the importance of using a test battery.</p>
},
	issn = {1573-3017},
	doi = {10.1007/s10646-014-1339-y},
	author = {Minguez, Laetitia and Di Poi, C and Farcy, E and Ballandonne, C{\'e}line and Benchouala, Amira and Bojic, Cl{\'e}ment and Cossu-Leguille, Carole and Katherine Costil and Antoine Serpentini and Jean-Marc Lebel and Halm-Lemeille, Marie-Pierre}
}
@article {9378,
	title = {Detailed reconstruction of the musculature in Limnognathia maerski (Micrognathozoa) and comparison with other Gnathifera},
	journal = {Frontiers in Zoology},
	volume = {11},
	year = {2014},
	month = {Jan-12-2014},
	doi = {10.1186/s12983-014-0071-z},
	url = {https://frontiersinzoology.biomedcentral.com/articles/10.1186/s12983-014-0071-z},
	author = {Bekkouche, Nicolas and Kristensen, Reinhardt M and Hejnol, Andreas and S{\o}rensen, Martin V and Worsaae, Katrine}
}
@article {4126,
	title = {Diversity of cultivable fungi associated with Antarctic marine sponges and screening for their antimicrobial, antitumoral and antioxidant potential.},
	journal = {World J Microbiol Biotechnol},
	volume = {30},
	year = {2014},
	month = {2014 Jan},
	pages = {65-76},
	abstract = {<p>The diversity of sponge-associated fungi has been poorly investigated in remote geographical areas like Antarctica. In this study, 101 phenotypically different fungal isolates were obtained from 11 sponge samples collected in King George Island, Antarctica. The analysis of ITS sequences revealed that they belong to the phylum Ascomycota. Sixty-five isolates belong to the genera Geomyces, Penicillium, Epicoccum, Pseudeurotium, Thelebolus, Cladosporium, Aspergillus, Aureobasidium, Phoma, and Trichocladium but 36 isolates could not be identified at genus level. In order to estimate the potential of these isolates as producers of interesting bioactivities, antimicrobial, antitumoral and antioxidant activities of fungal culture extracts were assayed. Around 51\% of the extracts, mainly from the genus Geomyces and non identified relatives, showed antimicrobial activity against some of the bacteria tested. On the other hand, around 42\% of the extracts showed potent antitumoral activity, Geomyces sp. having the best performance. Finally, the potential of the isolated fungi as producers of antioxidant activity seems to be moderate. Our results suggest that fungi associated with Antarctic sponges, particularly Geomyces, would be valuable sources of antimicrobial and antitumoral compounds. To our knowledge, this is the first report describing the biodiversity and the metabolic potential of fungi associated with Antarctic marine sponges.</p>
},
	keywords = {Animals, Antarctic Regions, Anti-Bacterial Agents, Antineoplastic Agents, Antioxidants, Ascomycota, DNA, Ribosomal Spacer, Porifera, Sequence Analysis, DNA},
	issn = {1573-0972},
	doi = {10.1007/s11274-013-1418-x},
	author = {Henr{\'\i}quez, Marlene and Vergara, Karen and Norambuena, Javiera and Beiza, Andrea and Maza, Felipe and Ubilla, Pamela and Araya, Ivanna and Ch{\'a}vez, Renato and San-Mart{\'\i}n, Aurelio and Darias, Jos{\'e} and Darias, Maria and Vaca, Inmaculada}
}
@article {3368,
	title = {Dual role of the cuttlefish salivary proteome in defense and predation.},
	journal = {J Proteomics},
	volume = {108},
	year = {2014},
	month = {2014 Aug 28},
	pages = {209-22},
	abstract = {<p><b>UNLABELLED: </b>We characterized the proteome of the posterior salivary glands of the cephalopod S. officinalis by combining de novo RNA sequencing and mass spectrometry. In silico analysis of the transcriptome revealed the occurrence of three main categories of proteins: enzymes, immune factors and toxins. Protein identification by SDS-PAGE and MALDI-TOF/TOF confirmed the occurrence of proteins essential to venom-like enzymes: peptidase S1 under four isoforms, phospholipase A2 and two toxins. The first toxin is a cystein rich secreted protein (CRISP), a common toxin found in all venomous animals. The second one is cephalotoxin, which is specific to decabrachia cephalopods. Secretions of the posterior salivary glands are transported to the cephalopodium; they are involved in prey catching but also in gamete storage, fertilization and egg-laying. The paralyzing activity and the antimicrobial effect of saliva suggest a dual role in predation and in immune defense in cuttlefish.</p><p><b>BIOLOGICAL SIGNIFICANCE: </b>The originality of this study lies in the use of a transcriptomic approach (de novo RNA sequencing) coupled to a proteomic approach to get an overview of posterior salivary glands in S. officinalis. In cephalopods, these glands are involved in predation, more precisely in paralyzing preys and digesting them. Our in silico analysis equally reveals a role in immune defense as observed in mammals{\textquoteright} saliva. Our study also shows the specificity of cuttlefish venom, with the identification of cephalotoxins, proteins that are not found in octopuses. Finally, we show that cuttlefish saliva is a complex mixture that has antibacterial and crippling properties, but no lethal effect.</p>},
	issn = {1876-7737},
	doi = {10.1016/j.jprot.2014.05.019},
	author = {Cornet, Val{\'e}rie and Jo{\"e}l Henry and Corre, Erwan and Gildas Le Corguille and Zanuttini, Bruno and C{\'e}line Zatylny-Gaudin}
}
@article {Personnic2014,
	title = {An ecosystem-based approach to assess the status of a mediterranean ecosystem, the Posidonia oceanica seagrass meadow},
	journal = {PLoS ONE},
	volume = {9},
	number = {6},
	year = {2014},
	note = {cited By 37},
	doi = {10.1371/journal.pone.0098994},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0098994},
	author = {Personnic, S. and Boudouresque, C.F. and Astruch, P. and Ballesteros, E. and Blouet, S. and Bellan-Santini, D. and Bonhomme, P. and Thibault-Botha, D. and Eric Feunteun and Mireille Harmelin-Vivien and Pergent, G. and Pergent-Martini, C. and Pastor, J. and Poggiale, J.-C. and Renaud, F. and Thibaut, T. and Ruitton, S.}
}
@article {3605,
	title = {The effect of cold stress on the proteome of the marine bacteriumPseudomonas fluorescens BA3SM1 and its ability to copewith metal excess},
	journal = {Aquatic Toxicology},
	volume = {157},
	year = {2014},
	month = {10/2014},
	pages = {120-133},
	abstract = {<p>This study examined the effect of cold stress on the proteome and metal tolerance of Pseudomonas fluo-rescens BA3SM1, a marine strain isolated from tidal flat sediments. When cold stress (+10{\textopenbullet}C for 36 h)was applied before moderate metal stress (0.4 mM Cd, 0.6 mM Cd, 1.5 mM Zn, and 1.5 mM Cu), growthdisturbances induced by metal, in comparison with respective controls, were reduced for Cd and Znwhile they were pronounced for Cu. This marine strain was able to respond to cold stress through a num-ber of changes in protein regulation. Analysis of the predicted differentially expressed protein functionsdemonstrated that some mechanisms developed under cold stress were similar to those developed inresponse to Cd, Zn, and Cu. Therefore, pre-cold stress could help this strain to better counteract toxicityof moderate concentrations of some metals. P. fluorescens BA3SM1 was able to remove up to 404.3 mgCd/g dry weight, 172.5 mg Zn/g dry weight, and 11.3 mg Cu/g dry weight and its metal biosorption abilityseemed to be related to the bacterial growth phase. Thus, P. fluorescens BA3SM1 appears as a promisingagent for bioremediation processes, even at low temperatures.</p>
},
	keywords = {Cold stress, Marine strain, Metal biosorptiona, Proteomics, Pseudomonas fluorescens},
	author = {Isabelle Poirier and Lauriane Kuhn and Christelle Caplat and Philippe Hammann and Martine Bertrand}
}
@article {3509,
	title = {The effect of different polychlorinated biphenyls on two aquatic models, the green alga Pseudokirchneriella subcapitata and the haemocytes from the European abalone Haliotis tuberculata.},
	journal = {Chemosphere},
	volume = {110},
	year = {2014},
	month = {2014 Sep},
	pages = {120-8},
	abstract = {<p>The present study was conducted to determine the toxicity of different polychlorinated biphenyls (PCBs) on the green algae, <em>Pseudokirchneriella subcapitata</em> and the haemocytes from the European abalone, <em>Haliotis tuberculata</em>. Using the algal growth inhibition test, the green algae median Effective Concentration (EC50) values ranged from 0.34μM for PCB28 to more than 100μM for PCBs 101 and 153. Considering the MTT viability test, the abalone EC50 values ranged from 1.67μM for PCB153 to 89μM for PCB28. Our results in contrast to previous observation in vertebrates did not show significant differences between the dioxin like- and non dioxin like-PCBs toxicities regardless of the model used. However, our results demonstrated that the toxicities of PCBs were species dependent. For example, PCB28 was the most toxic compound for P. subcapitata whereas PCBs 1, 180 and 153 were less toxic for that species. On the contrary, PCB153 was reported as the most toxic for H. tuberculata haemocytes and PCB28 the least toxic. To investigate the mode of action of these compounds, we used an in silico method. Our results suggested that PCBs have a non-specific mode of action (e.g., narcosis) on green algae, and another mode of action, probably more specific than narcosis, was reported for PCBs on the abalone haemocytes.</p>
},
	keywords = {Animals, Chlorophyta, Environmental Pollutants, Gastropoda, Hemocytes, Polychlorinated Biphenyls, Tetrachlorodibenzodioxin},
	issn = {1879-1298},
	doi = {10.1016/j.chemosphere.2014.02.023},
	author = {Halm-Lemeille, Marie-Pierre and Abbaszadeh Fard, Elham and Latire, T and Ferard, Jean-Fran{\c c}ois and Katherine Costil and Jean-Marc Lebel and Bureau, Ronan and Antoine Serpentini}
}
@article {3451,
	title = {Estimating how many undescribed species have gone extinct.},
	journal = {Conserv Biol},
	volume = {28},
	year = {2014},
	month = {2014 Oct},
	pages = {1360-70},
	abstract = {<p>Because both descriptions of species and modern human-driven extinctions started around the same time (i.e., eighteenth century), a logical expectation is that a large proportion of species may have gone extinct without ever having been recorded. Despite this evident and widely recognized assumption, the loss of undescribed species has never been estimated. We quantified this loss for several taxonomic groups and regions for which undescribed species extinctions are likely to have occurred. Across a wide range of taxonomic groups, we applied known extinction rates computed from recorded species losses to assumed exponential decay in the proportion of species remaining undiscovered. Because all previous modeling attempts to project total species richness implicitly assumed that undescribed species extinctions could be neglected, we also evaluated the effect of neglecting them. Finally, because we assumed constant description and extinction probabilities, we applied our model to simulated data that did not conform to this assumption. Actual species losses were severely underestimated by considering only known species extinctions. According to our estimates, the proportion of undiscovered extinct species over all extinctions ranged from 0.15 to 0.59, depending on the taxonomic group and the region considered. This means that recent extinctions may be up to twice as large as the number recorded. When species differed in their extinction or description probabilities, our model underestimated extinctions of undescribed species by up to 20\%.</p>
},
	issn = {1523-1739},
	doi = {10.1111/cobi.12285},
	author = {Pablo Tedesco and R{\'e}my Bigorne and Bogan, Arthur and Giam, Xingli and J{\'e}z{\'e}quel, C{\'e}line and Bernard Hugueny}
}
@article {3326,
	title = {Geographical origin of Amazonian freshwater fishes fingerprinted by $^{8}$$^{7}$Sr/$^{8}$$^{6}$Sr ratios on fish otoliths and scales.},
	journal = {Environ Sci Technol},
	volume = {48},
	year = {2014},
	month = {2014 Aug 19},
	pages = {8980-7},
	abstract = {<p>Calcified structures such as otoliths and scales grow continuously throughout the lifetime of fishes. The geochemical variations present in these biogenic structures are particularly relevant for studying fish migration and origin. In order to investigate the potential of the (87)Sr/(86)Sr ratio as a precise biogeochemical tag in Amazonian fishes, we compared this ratio between the water and fish otoliths and scales of two commercial fish species, Hoplias malabaricus and Schizodon fasciatus, from three major drainage basins of the Amazon: the Madeira, Solim{\~o}es, and Tapaj{\'o}s rivers, displaying contrasted (87)Sr/(86)Sr ratios. A comparison of the (87)Sr/(86)Sr ratios between the otoliths and scales of the same individuals revealed similar values and were very close to the Sr isotopic composition of the local river where they were captured. This indicates, first, the absence of Sr isotopic fractionation during biological uptake and incorporation into calcified structures and, second, that scales may represent an interesting nonlethal alternative for (87)Sr/(86)Sr ratio measurements in comparison to otoliths. Considering the wide range of (87)Sr/(86)Sr variations that exist across Amazonian rivers, we used variations of (87)Sr/(86)Sr to discriminate fish origin at the basin level, as well as at the sub-basin level between the river and savannah lakes of the Beni River (Madeira basin).</p>},
	issn = {1520-5851},
	doi = {10.1021/es500071w},
	author = {Marc Pouilly and Point, David and Sondag, Francis and Henry, Manuel and Santos, Roberto V}
}
@article {3252,
	title = {Global imprint of historical connectivity on freshwater fish biodiversity.},
	journal = {Ecol Lett},
	volume = {17},
	year = {2014},
	month = {2014 Sep},
	pages = {1130-40},
	abstract = {<p>The relative importance of contemporary and historical processes is central for understanding biodiversity patterns. While several studies show that past conditions can partly explain the current biodiversity patterns, the role of history remains elusive. We reconstructed palaeo-drainage basins under lower sea level conditions (Last Glacial Maximum) to test whether the historical connectivity between basins left an imprint on the global patterns of freshwater fish biodiversity. After controlling for contemporary and past environmental conditions, we found that palaeo-connected basins displayed greater species richness but lower levels of endemism and beta diversity than did palaeo-disconnected basins. Palaeo-connected basins exhibited shallower distance decay of compositional similarity, suggesting that palaeo-river connections favoured the exchange of fish species. Finally, we found that a longer period of palaeo-connection resulted in lower levels of beta diversity. These findings reveal the first unambiguous results of the role played by history in explaining the global contemporary patterns of biodiversity.</p>
},
	keywords = {Animals, Biodiversity, Environment, Fishes, Fresh Water, Models, Biological},
	issn = {1461-0248},
	doi = {10.1111/ele.12319},
	author = {Dias, Murilo S and Thierry Oberdorff and Bernard Hugueny and Leprieur, Fabien and J{\'e}z{\'e}quel, C{\'e}line and Cornu, Jean-Fran{\c c}ois and Brosse, S{\'e}bastien and Grenouillet, Gael and Pablo Tedesco}
}
@article {Saint-B{\'e}at2014144,
	title = {How does the resuspension of the biofilm alter the functioning of the benthos-pelagos coupled food web of a bare mudflat in Marennes-Ol{\'e}ron Bay (NE Atlantic)?},
	journal = {Journal of Sea Research},
	volume = {92},
	year = {2014},
	note = {cited By 17},
	pages = {144-157},
	doi = {10.1016/j.seares.2014.02.003},
	url = {https://www.sciencedirect.com/science/article/pii/S138511011400029X},
	author = {Saint-B{\'e}at, B. and Christine Dupuy and Agogu{\'e}, H. and Alexandre Carpentier and Chalumeau, J. and Como, S. and David, V. and De Crignis, M. and Duch{\^e}ne, J.-C. and Fontaine, C. and Eric Feunteun and Katell Guizien and Hartmann, H. and Lavaud, J. and S{\'e}bastien Lefebvre and Lefran{\c c}ois, C. and Mallet, C. and Montani{\'e}, H. and Mouget, J.-L. and Francis Orvain and Ory, P. and Pascal, P.-Y. and Radenac, G. and Richard, P. and V{\'e}zina, A.F. and Nathalie Niquil}
}
@article {4634,
	title = {In vitro effect of five pharmaceuticals on the viability of the European abalone hemocytes, Haliotis tuberculata},
	journal = {J xenobiotics},
	volume = {4},
	year = {2014},
	pages = {78-80},
	keywords = {cell viability, Haliotis tuberculata, hemocyte, in vitro, pharmaceuticals},
	doi = {10.4081/xeno.2014.4900},
	author = {Letullier, Amandine and Minguez, Laetitia and Katherine Costil and Halm-Lemeille, Marie-Pierre and Jean-Marc Lebel and Antoine Serpentini}
}
@article {3598,
	title = {Interacting Regional Scale Regime Shifts for Biodiversity and Ecosystem Services},
	journal = {BioScience},
	volume = {64},
	year = {2014},
	month = {08/2014},
	pages = {665-679},
	doi = {doi: 10.1093/biosci/biu093},
	author = {P. Leadley and V. Proen{\c c}a and Juan F. Fern{\'a}ndez-Manjarr{\'e}s and H.M. Pereira and R. Alkemade and R. Biggs and E. Bruley and W. Cheung and D. Cooper and J. Figueiredo and E. Gilman and S. Gu{\'e}nette and G. Hurtt and C. Mbow and Thierry Oberdorff and C. Revenga and J. Scharlemann and R. Scholes and M. Stafford-Smith and R. Sumaila and M. Walpole}
}
@article {3131,
	title = {Morphological and molecular evidence of three species of pikes <i>Esox</i> spp. (Actinopterygii, Esocidae) in France, including the description of a new species},
	journal = {Comptes Rendus Biologies},
	volume = {337},
	year = {2014},
	pages = {521-534},
	abstract = {<p>This integrative taxonomy study of French pikes compares morphological characters and molecular sequence data (mitochondrial COI and nuclear Plagl2 genes). In addition to the expected <em>E.\&nbsp;lucius</em>, DNA sequences and morphology both support a new species in France, <em>E.\&nbsp;aquitanicus</em> sp. nov. from the Charente to the Adour drainages. It is characterized by a color pattern of sides with narrow 1{\textendash}1.5-scale-wide oblique vertical bands, conferring it a marbled coat, a snout only 0.9 times larger than the postorbital length, an anal fin basis 1.1{\textendash}1.2 times larger than the caudal peduncle length, 101 to 121 lateral scales, 53 to 57 vertebrae, as well as 24 diagnostic sites in the COI gene and 3 in the Plagl2 gene. Partial COI sequences (131bp) from modern and historical specimens indicate also the presence of <em>E.\&nbsp;cisalpinus</em> and <em>E.\&nbsp;lucius</em> during the 19th century in Lake Geneva. Morphological and molecular data points to a possible hybridization between <em>E.\&nbsp;lucius</em> with both other local pike species, representing a risk for them. Their endangerment status should be evaluated rapidly in order to take conservation measures.</p>
},
	keywords = {Cytochrome c oxidase subunit 1, Esox aquitanicus, Esox cisalpinus, France, Integrative taxonomy, New species, Pleiomorphic adenoma gene-like 2},
	issn = {16310691},
	doi = {10.1016/j.crvi.2014.07.002},
	author = {Denys, Ga{\"e}l and Dettai, Agn{\`e}s and Persat, Henri and M{\'e}lyne Hautecoeur and Philippe Keith}
}
@article {4161,
	title = {A multilocus molecular phylogeny of combtooth blennies (Percomorpha: Blennioidei: Blenniidae): multiple invasions of intertidal habitats.},
	journal = {Mol Phylogenet Evol},
	volume = {70},
	year = {2014},
	month = {2014 Jan},
	pages = {47-56},
	abstract = {<p>The combtooth blennies (f. Blenniidae) is a diverse family of primarily marine fishes with approximately 387 species that inhabit subtidal, intertidal, supralittoral habitats in tropical and warm temperate regions throughout the world. The Blenniidae has typically been divided into six groups based on morphological characters: Blenniini, Nemophini, Omobranchini, Phenablenniini, Parablenniini, and Salariini. There is, however, considerable debate over the validity of these groups and their relationships. Since little is known about the relationships in this group, other aspects of their evolutionary history, such as habitat evolution and remain unexplored. Herein, we use Bayesian and maximum likelihood analyses of four nuclear loci (ENC1, myh6, ptr, and tbr1) from 102 species, representing 41 genera, to resolve the phylogeny of the Blenniidae, determine the validity of the previously recognized groupings, and explore the evolution of habitat association using ancestral state reconstruction. Bayesian and maximum likelihood analyses of the resulting 3100bp of DNA sequence produced nearly identical topologies, and identified many well-supported clades. Of these clades, Nemophini was the only traditionally recognized group strongly supported as monophyletic. This highly resolved and thoroughly sampled blenniid phylogeny provides strong evidence that the traditional rank-based classification does not adequately delimit monophyletic groups with the Blenniidae. This phylogeny redefines the taxonomy of the group and supports the use of 13 unranked clades for the classification of blenniids. Ancestral state reconstructions identified four independent invasions of intertidal habitats within the Blenniidae, and subsequent invasions into supralittoral and freshwater habitats from these groups. The independent invasions of intertidal habitats are likely to have played an important role in the evolutionary history of blennies.</p>
},
	keywords = {Animals, Bayes Theorem, Ecosystem, Likelihood Functions, Perciformes, Phylogeny, Sequence Analysis, DNA},
	issn = {1095-9513},
	doi = {10.1016/j.ympev.2013.09.001},
	author = {Hundt, Peter J and Samuel Iglesias and Hoey, Andrew S and Simons, Andrew M}
}
@article {3487,
	title = {Multiscale patterns in the diversity and organization of benthic intertidal fauna among French Atlantic estuaries},
	journal = {Journal of Sea Research},
	volume = {90},
	year = {2014},
	month = {07/2014},
	pages = {95 - 110},
	abstract = {<p>Based on a parallel sampling conducted during autumn 2008, a comparative study of the intertidal benthic macrofauna among 10 estuarine systems located along the Channel and Atlantic coasts of France was performed in order to assess the level of fauna similarity among these sites and to identify possible environmental factors involved in the observed pattern at both large (among sites) and smaller (benthic assemblages) scales. More precisely this study focused on unraveling the observed pattern of intertidal benthic fauna composition and diversity observed at among-site scale by exploring both biotic and abiotic factors acting at the among- and within-site scales. Results showed a limited level of similarity at the among-site level in terms of intertidal benthic fauna composition and diversity. The observed pattern did not fit with existing transitional water classification methods based on fish or benthic assemblages developed in the frame of the European Water Framework Directive (WFD). More particularly, the coastal plain estuaries displayed higher among-site similarity compared to ria systems. These coastal plain estuaries were characterized by higher influence of river discharge, lower communication with the ocean and high suspended particulate matter levels. On the other hand, the ria-type systems were more dissimilar and different from the coastal plain estuaries. The level of similarity among estuaries was mainly linked to the relative extent of the intertidal {\textquotedblleft}Scrobicularia plana{\textendash}Cerastoderma edule{\textquotedblright} and {\textquotedblleft}Tellina tenuis{\textquotedblright} or {\textquotedblleft}Venus{\textquotedblright} communities as a possible consequence of salinity regime, suspended matter concentrations and fine particles supply with consequences on the trophic functioning, structure and organization of benthic fauna. Despite biogeographical patterns, the results also suggest that, in the context of the WFD, these estuaries should only be compared on the basis of the most common intertidal habitat occurring throughout all estuarine systems and that the \{EUNIS\} biotope classification might be used for this purpose. In addition, an original inverse relation between γ-diversity and area was shown; however, its relevance might be questioned.</p>
},
	keywords = {Diversity, Estuaries, Macrozoobenthos, Structuring Factors, WFD},
	issn = {1385-1101},
	doi = {http://dx.doi.org/10.1016/j.seares.2014.02.014},
	url = {http://www.sciencedirect.com/science/article/pii/S1385110114000495},
	author = {Hugues Blanchet and Beno{\^\i}t Gouillieux and Sandrine Alizier and Jean-Michel Amouroux and Guy Bachelet and Anne-Laure Barill{\'e} and Jean-Claude Dauvin and Xavier de Montaudouin and Val{\'e}rie Derolez and Nicolas Desroy and Jacques Grall and Antoine Gr{\'e}mare and Pascal Hacquebart and J{\'e}r{\^o}me Jourde and C{\'e}line Labrune and Nicolas Lavesque and Antoine Meirland and Thiebaut Nebout and Fr{\'e}d{\'e}ric Olivier and Corine Pelaprat and Thierry Ruellet and Pierre-Guy Sauriau and S{\'e}bastien Thorin}
}
@article {3397,
	title = {Neuropeptides encoded by the genomes of the Akoya pearl oyster Pinctata fucata and Pacific oyster Crassostrea gigas: a bioinformatic and peptidomic survey.},
	journal = {BMC Genomics},
	volume = {15},
	year = {2014},
	month = {2014},
	pages = {840},
	abstract = {<p><strong>BACKGROUND: </strong>Oysters impart significant socio-ecological benefits from primary production of food supply, to estuarine ecosystems via reduction of water column nutrients, plankton and seston biomass. Little though is known at the molecular level of what genes are responsible for how oysters reproduce, filter nutrients, survive stressful physiological events and form reef communities. Neuropeptides represent a diverse class of chemical messengers, instrumental in orchestrating these complex physiological events in other species.</p>

<p><strong>RESULTS: </strong>By a combination of in silico data mining and peptide analysis of ganglia, 74 putative neuropeptide genes were identified from genome and transcriptome databases of the Akoya pearl oyster, Pinctata fucata and the Pacific oyster, Crassostrea gigas, encoding precursors for over 300 predicted bioactive peptide products, including three newly identified neuropeptide precursors PFGx8amide, RxIamide and Wx3Yamide. Our findings also include a gene for the gonadotropin-releasing hormone (GnRH) and two egg-laying hormones (ELH) which were identified from both oysters. Multiple sequence alignments and phylogenetic analysis supports similar global organization of these mature peptides. Computer-based peptide modeling of the molecular tertiary structures of ELH highlights the structural homologies within ELH family, which may facilitate ELH activity leading to the release of gametes.</p>

<p><strong>CONCLUSION: </strong>Our analysis demonstrates that oysters possess conserved molluscan neuropeptide domains and overall precursor organization whilst highlighting many previously unrecognized bivalve idiosyncrasies. This genomic analysis provides a solid foundation from which further studies aimed at the functional characterization of these molluscan neuropeptides can be conducted to further stimulate advances in understanding the ecology and cultivation of oysters.</p>
},
	issn = {1471-2164},
	doi = {10.1186/1471-2164-15-840},
	author = {Stewart, Michael J and Pascal Favrel and Rotgans, Bronwyn A and Wang, Tianfang and Zhao, Min and Sohail, Manzar and O{\textquoteright}Connor, Wayne A and Elizur, Abigail and Jo{\"e}l Henry and Cummins, Scott F}
}
@article {3724,
	title = {A new species of Sicyopus (Gobioidei) from Java and Bali},
	journal = {Cybium},
	volume = {38},
	year = {2014},
	pages = {173-178},
	abstract = {<p>Sicyopus rubicundus n. sp., a sicydiine goby, is described from specimens collected in streams of\&nbsp;Java and Bali (Indonesia). It differs from other species of this amphidromous genus by a combination of characters\&nbsp;including a first dorsal fin with five spines in both sexes, a second dorsal fin with one spine and nine segmented\&nbsp;rays, an anal fin with one spine and nine segmented rays, and a distinctive body colour in male.</p>
},
	keywords = {Freshwater, Gobiidae, Indonesia, New species, Sicyopus rubicundus},
	author = {Philippe Keith and Hadiaty, Renny and Fr{\'e}d{\'e}ric Busson and Hubert, Nicolas}
}
@article {Passarelli2013,
	title = {{Organisms as cooperative ecosystem engineers in intertidal flats}},
	journal = {Journal of Sea Research},
	volume = {92},
	year = {2014},
	month = {09/2014},
	pages = {92-101},
	abstract = {<p>The importance of facilitative interactions and organismal ecosystem engineering for establishing the structure of communities is increasingly being recognised for many different ecosystems. For example, soft-bottom tidal flats host a wide range of ecosystem engineers, probably because the harsh physico-chemical environmental conditions render these species of particular importance for community structure and function. These environments are therefore interesting when focusing on how ecosystem engineers interact and the consequences of these interactions on community dynamics. In this review, we initially detail the influence on benthic systems of two kinds of ecosystem engineers that are particularly common in tidal flats. Firstly, we examine species providing biogenic structures, which are often the only source of habitat complexity in these environments. Secondly, we focus on species whose activities alter sediment stability, which is a crucial feature structuring the dynamics of communities in tidal flats. The impacts of these engineers on both environment and communities were assessed but in addition the interaction between ecosystem engineers was examined. Habitat cascades occur when one engineer favours the development of another, which in turn creates or modifies and improves habitat for other species. Non-hierarchical interactions have often been shown to display non-additive effects, so that the effects of the association cannot be predicted from the effects of individual organisms. Here we propose the term of {\textquotedblleft}cooperative ecosystem engineering{\textquotedblright} when two species interact in a way which enhances habitat suitability as a result of a combined engineering effect. Finally, we conclude by describing the potential threats for ecosystem engineers in intertidal areas, potential effects on their interactions and their influence on communities and ecosystem function.</p>
},
	keywords = {Biogenic Structure, Cooperative Ecosystem Engineers, Habitat Cascade, Sediment stability, tidal flats},
	doi = {10.1016/j.seares.2013.07.010},
	author = {Passarelli, C and Fr{\'e}d{\'e}ric Olivier and Paterson, D M and Tarik Meziane and C{\'e}dric Hubas}
}
@article {3370,
	title = {Protecting honey bees: identification of a new varroacide by in silico, in vitro, and in vivo studies.},
	journal = {Parasitol Res},
	volume = {113},
	year = {2014},
	month = {2014 Dec},
	pages = {4601-10},
	abstract = {<p>Varroa destructor is the main concern related to the gradual decline of honeybees. Nowadays, among the various acaricides used in the control of V. destructor, most presents increasing resistance. An interesting alternative could be the identification of existent molecules as new acaricides with no effect on honeybee health. We have previously constructed the first 3D model of AChE for honeybee. By analyzing data concerning amino acid mutations implicated in the resistance associated to pesticides, it appears that pirimicarb should be a good candidate for varroacide. To check this hypothesis, we characterized the AChE gene of V. destructor. In the same way, we proposed a 3D model for the AChE of V. destructor. Starting from the definition of these two 3D models of AChE in honeybee and varroa, a comparison between the gorges of the active site highlighted some major differences and particularly different shapes. Following this result, docking studies have shown that pirimicarb adopts two distinct positions with the strongest intermolecular interactions with VdAChE. This result was confirmed with in vitro and in vivo data for which a clear inhibition of VdAChE by pirimicarb at 10 μM (contrary to HbAChE) and a 100\% mortality of varroa (dose corresponding to the LD50 (contact) for honeybee divided by a factor 100) were observed. These results demonstrate that primicarb could be a new varroacide candidate and reinforce the high relationships between in silico, in vitro, and in vivo data for the design of new selective pesticides.</p>},
	issn = {1432-1955},
	doi = {10.1007/s00436-014-4150-z},
	author = {Dulin, Fabienne and C{\'e}line Zatylny-Gaudin and Ballandonne, C{\'e}line and Guillet, Bertrand and Bonafos, Romain and Bureau, Ronan and Halm, Marie Pierre}
}
@article {3309,
	title = {Seasonal variation of marine snow-associated and ambient water prokaryotic communities in the northern Adriatic Sea},
	journal = {Aquatic Microbial Ecology},
	volume = {73},
	year = {2014},
	month = {11/2014},
	pages = {211-224},
	author = {Vojvoda, Jana and Lamy, Dominique and Sintes, Eva and Garcia, Juan AL and Turk, Valentina and Gerhard J Herndl}
}
@article {3430,
	title = {The skeleton of the staghorn coral Acropora millepora: molecular and structural characterization.},
	journal = {PLoS One},
	volume = {9},
	year = {2014},
	month = {2014},
	pages = {e97454},
	abstract = {<p>The scleractinian coral Acropora millepora is one of the most studied species from the Great Barrier Reef. This species has been used to understand evolutionary, immune and developmental processes in cnidarians. It has also been subject of several ecological studies in order to elucidate reef responses to environmental changes such as temperature rise and ocean acidification (OA). In these contexts, several nucleic acid resources were made available. When combined to a recent proteomic analysis of the coral skeletal organic matrix (SOM), they enabled the identification of several skeletal matrix proteins, making A. millepora into an emerging model for biomineralization studies. Here we describe the skeletal microstructure of A. millepora skeleton, together with a functional and biochemical characterization of its occluded SOM that focuses on the protein and saccharidic moieties. The skeletal matrix proteins show a large range of isoelectric points, compositional patterns and signatures. Besides secreted proteins, there are a significant number of proteins with membrane attachment sites such as transmembrane domains and GPI anchors as well as proteins with integrin binding sites. These features show that the skeletal proteins must have strong adhesion properties in order to function in the calcifying space. Moreover this data suggest a molecular connection between the calcifying epithelium and the skeletal tissue during biocalcification. In terms of sugar moieties, the enrichment of the SOM in arabinose is striking, and the monosaccharide composition exhibits the same signature as that of mucus of acroporid corals. Finally, we observe that the interaction of the acetic acid soluble SOM on the morphology of in vitro grown CaCO3 crystals is very pronounced when compared with the calcifying matrices of some mollusks. In light of these results, we wish to commend Acropora millepora as a model for biocalcification studies in scleractinians, from molecular and structural viewpoints.</p>
},
	keywords = {Acetic Acid, Amination, Animals, Anthozoa, Bone and Bones, Calcium Carbonate, Crystallization, Gels, Monosaccharides, Proteins, Solubility, Spectroscopy, Fourier Transform Infrared, Spectrum Analysis, Raman},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0097454},
	author = {Ramos-Silva, Paula and Kaandorp, Jaap and Herbst, Fr{\'e}d{\'e}ric and Plasseraud, Laurent and Alcaraz, G and Stern, Christine and Corneillat, Marion and Guichard, N and Durlet, Christophe and Gilles Luquet and Marin, F}
}
@article {3723,
	title = {Three new species of Lentipes (Teleostei: Gobiidae) from Indonesia. },
	journal = {Cybium},
	volume = {38},
	year = {2014},
	pages = {133-146},
	abstract = {<p>Three new species of Lentipes (L. argenteus, L. ikeae and L. mekonggaensis), freshwater gobies, are<br />
described from streams of Sumatra, Java, Bali and Sulawesi (Indonesia). They differ from other species of the<br />
genus by a combination of characters including an urogenital papilla lacking lateral lobes and retractable into a<br />
sheath-like groove, the number of pectoral fin rays, the number of scales, tricuspid teeth in the upper jaw, and a<br />
specific body colour in males.</p>
},
	keywords = {Bali, Freshwater, Gobiidae, Java, Lentipes, New species, Sulawesi, Sumatra},
	author = {Philippe Keith and Hadiaty, Renny and Hubert, Nicolas and Fr{\'e}d{\'e}ric Busson and Clara Lord}
}
@article {3371,
	title = {Transcriptomic and peptidomic analysis of protein hydrolysates from the white shrimp (L. vannamei).},
	journal = {J Biotechnol},
	volume = {186},
	year = {2014},
	month = {2014 Sep 30},
	pages = {30-7},
	abstract = {<p>An RNAseq approach associated to mass spectrometry was conducted to assess the composition, molecular mass distribution and primary sequence of hydrolytic peptides issued from hydrolysates of white shrimp (Litopenaeus vannamei) by-products. High performance size exclusion chromatography (HPSEC) analyses indicated that 69.2\% of the 214-nm-absorbing components had apparent molecular masses below 1000 Da, and 88.3\% below 2000 Da. OFFGEL-nLC-MALDI-TOF/TOF and nLC-ESI-MS/MS analyses led to the identification of 808 peptides based on the NCBI EST databank (161,397 entries) completed by the new L. vannamei databank (58,508 entries) that we created from the RNAs of tissues used for hydrolysate production. Whereas most of hydrolytic peptides have a MW below 2000 Da, preliminary investigations of antimicrobial properties revealed three antibacterial fractions that demonstrate functional activities. The abundance of small peptides as well as the biological activities detected could imply very interesting applications for shrimp hydrolysate in the field of aquaculture feeding.</p>},
	issn = {1873-4863},
	doi = {10.1016/j.jbiotec.2014.06.020},
	author = {Robert, Marie and C{\'e}line Zatylny-Gaudin and Fournier, Vincent and Corre, Erwan and Gildas Le Corguille and Bernay, Beno{\^\i}t and Jo{\"e}l Henry}
}
@article {7331,
	title = {Highly Dynamic Cellular-Level Response of Symbiotic Coral to a Sudden Increase in Environmental NitrogenABSTRACT},
	journal = {mBio},
	volume = {4},
	year = {2013},
	month = {Jan-07-2013},
	doi = {10.1128/mBio.00052-13},
	url = {https://mbio.asm.org/content/4/3/e00052-13},
	author = {Kopp, C. and Pernice, M. and Domart-Coulon, I. and Djediat, C. and Spangenberg, J. E. and Alexander, D. T. L. and Hignette, M. and Tarik Meziane and Meibom, A.},
	editor = {Orphan, Victoria and McFall-Ngai, Margaret J.}
}
@article {7341,
	title = {Responses of juvenile sea bass, Dicentrarchus labrax, exposed to acute concentrations of crude oil, as assessed by molecular and physiological biomarkers},
	journal = {Chemosphere},
	volume = {87},
	year = {2012},
	month = {Jan-05-2012},
	pages = {692 - 702},
	issn = {00456535},
	doi = {10.1016/j.chemosphere.2011.12.059},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0045653511014287},
	author = {Kerambrun, E. and Le Floch, S. and Sanchez, W. and Thomas Guyon, H. and Tarik Meziane and Henry, F. and Amara, R.}
}
@article {7351,
	title = {Surface adhesion of microphytobenthic biofilms is enhanced under Hediste diversicolor (O.F. M{\"u}ller) trophic pressure},
	journal = {Journal of Experimental Marine Biology and Ecology},
	volume = {438},
	year = {2012},
	month = {Jan-12-2012},
	pages = {52 - 60},
	issn = {00220981},
	doi = {10.1016/j.jembe.2012.10.005},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022098112003577},
	author = {Passarelli, Claire and C{\'e}dric Hubas and Nicolas Segui, Audrey and Grange, Julie and Tarik Meziane}
}
@article {8588,
	title = {Testing a Global Positioning System on free-ranging badgers Meles meles},
	journal = {Mammal Notes},
	year = {2012},
	month = {2012},
	pages = {1-5},
	type = {Short note},
	url = {https://www.mammal.org.uk/wp-content/uploads/2016/04/Note-5-Brendel-MN-2012-1.pdf},
	author = {Brendel, Carole and Helder, R{\'e}mi and Chevallier, Damien and Zaytoon, Janan and Georges, Jean-Yves and Handrich, Yves}
}
@article {8592,
	title = {Influence of weather conditions on the flight of migrating black storks},
	journal = {Proceedings of the Royal Society B: Biological Sciences},
	volume = {277},
	year = {2010},
	month = {Oct-09-2011},
	pages = {2755 - 2764},
	issn = {0962-8452},
	doi = {10.1098/rspb.2010.0422},
	url = {https://royalsocietypublishing.org/doi/10.1098/rspb.2010.0422},
	author = {Chevallier, D. and Handrich, Y. and Georges, J.-Y. and Baillon, F. and Brossault, P. and Aurouet, A. and Le Maho, Y. and Massemin, S.}
}
@article {7325,
	title = {Growth and condition indices in juvenile sole Solea solea measured to assess the quality of essential fish habitat},
	journal = {Marine Ecology Progress Series},
	volume = {351},
	year = {2007},
	month = {Jun-12-2007},
	pages = {201 - 208},
	issn = {0171-8630},
	doi = {10.3354/meps07154},
	url = {http://www.int-res.com/abstracts/meps/v351/p201-208/},
	author = {Amara, R and Tarik Meziane and Gilliers, C and Hermel, G and Laffargue, P}
}
@article {7328,
	title = {Fatty acids as trophic tracers in an experimental estuarine food chain: Tracer transfer},
	journal = {Journal of Experimental Marine Biology and Ecology},
	volume = {336},
	year = {2006},
	month = {Jan-08-2006},
	pages = {42 - 53},
	issn = {00220981},
	doi = {10.1016/j.jembe.2006.04.004},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022098106002012},
	author = {Hall, David and Lee, S.Y. and Tarik Meziane}
}
@article {9185,
	title = {DNA barcoding of two amphidromous goby post-larvae (penja) morphotypes from Mandar River, West Sulawesi, Indonesia.},
	volume = {45},
	year = {201},
	month = {08/2021},
	pages = {243-249},
	author = {Nurjirana and Philippe Keith and Burhanuddin, A I and Afrisal, Muhammad and Haris, A}
}
