%0 Journal Article %J Regional Environmental Change %D 2023 %T Beach erosion aggravates the drastic decline in marine turtle populations in French Guiana %A Chevallier, Damien %A Girondot, Marc %A Péron, Christina %A Martin, Jordan %A Bonola, Marc %A Chevalier, Johan %A de Thoisy, Benoît %A Kelle, Laurent %A Le Maho, Yvon %A Gardel, Antoine %A Anthony, Edward J. %B Regional Environmental Change %V 23 %8 Jan-09-2023 %G eng %U https://link.springer.com/10.1007/s10113-023-02105-3 %N 3 %! Reg Environ Change %R 10.1007/s10113-023-02105-3 %0 Journal Article %J arXiv %D 2023 %T A benchmark for computational analysis of animal behavior, using animal-borne tags %A Benjamin Hoffman %A Maddie Cusimano %A Vittorio Baglione %A Daniela Canestrari %A Chevallier, Damien %A Dominic L. DeSantis %A Lorène Jeantet %A Monique A. Ladds %A Takuya Maekawa %A Vicente Mata-Silva %A Víctor Moreno-González %A Eva Trapote %A Outi Vainio %A Antti Vehkaoja %A Ken Yoda %A Katherine Zacarian %A Ari Friedlaender %A Christian Rutz %K Accelerometers %K animal behavior %K Bio-loggers %K Clustering %K Machine Learning %K Time series %X Animal-borne sensors (‘bio-loggers’) 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. %B arXiv %8 05/2023 %G eng %0 Journal Article %J Journal of Crustacean Biology %D 2023 %T Benchmarking global biodiversity of decapod crustaceans (Crustacea: Decapoda) %A De Grave, Sammy %A Decock, Wim %A Dekeyzer, Stefanie %A Davie, Peter J F %A Fransen, Charles H J M %A Boyko, Christopher B %A Poore, Gary C B %A Macpherson, Enrique %A Ahyong, Shane T %A Crandall, Keith A %A de Mazancourt, Valentin %A Osawa, Masayuki %A Chan, Tin-Yam %A Ng, Peter K L %A Lemaitre, Rafael %A van der Meij, Sancia E T %A Santos, Sandro %B Journal of Crustacean Biology %V 43 %8 Aug-01-2023 %G eng %U https://academic.oup.com/jcb/article/doi/10.1093/jcbiol/ruad042/7234762 %N 3 %R 10.1093/jcbiol/ruad042 %0 Journal Article %J Aquatic Sciences %D 2023 %T Biogeographical snapshot of life-history traits of European silver eels: insights from otolith microchemistry %A Teichert, Nils %A Bourillon, Bastien %A Suzuki, Kyoko %A Acou, Anthony %A Alexandre Carpentier %A Kuroki, Mari %A Righton, David %A Thomas Trancart %A Virag, Laure-Sarah %A Walker, Alan %A Otake, Tsuguo %A Eric Feunteun %K Anguilla anguilla %K Biogeography %K Brackish habitat %K otolith %K phenotypic plasticity %K Sr:Ca ratio %X Life-history traits of eels display a high level of phenotypic plasticity in response to large-scale biogeographical drivers, as well as local conditions encountered during the continental phase. Here, we provided a biogeographical snapshot of the variability of life-history traits of eels (Anguilla anguilla), across a large proportion of their natural distribution range. Silver eels (n = 99) were collected across eleven European catchments to investigate how life-history traits vary along geographical and saline habitats, as it was inferred from the Sr:Ca ratio in otoliths. Among 13 life-history traits tested, 3 of them such as total length, body or liver weight were related to geographical coordinates. Overall, eels grow faster in southern Europe and migrate earlier suggesting that the silvering process is related to the local growth conditions more than fish age. The salinity profiles revealed by the otoliths’ Sr:Ca ratios indicate that eels with a brackish life-history generally grow faster, reach larger size-at-age, and have a better condition than eels living in freshwater. This observation associated with the lower abundance of the sanguivorous swimbladder nematode, Anguillicola crassus, confirms the importance of brackish areas for sustaining the eel production. A large proportion of the observed variation of life-history traits remained unexplained by the biogeographical trends and salinity condition, which suggests that other drivers act at the catchment scale.
%B Aquatic Sciences %V 85 %8 Jan-04-2023 %G eng %U https://link.springer.com/10.1007/s00027-023-00940-4 %N 2 %! Aquat Sci %R 10.1007/s00027-023-00940-4 %0 Journal Article %J Progress in Oceanography %D 2022 %T Bi-decadal changes in nutrient concentrations and ratios in marine coastal ecosystems: The case of the Arcachon bay, France %A Lheureux, A. %A David, V. %A Del Amo, Y. %A Soudant, D. %A Auby, I. %A Ganthy, F. %A Blanchet, H. %A Cordier, M-A. %A Costes, L. %A Ferreira, S. %A Mornet, L. %A Nowaczyk, A. %A Parra, M. %A D'Amico, F. %A Gouriou, L. %A Meteigner, C. %A Oger-Jeanneret, H. %A Rigouin, L. %A Rumebe, M. %A Tournaire, M-P. %A Trut, F. %A Trut, G. %A Savoye, N. %B Progress in Oceanography %V 201 %P 102740 %8 Jan-02-2022 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S0079661122000027 %! Progress in Oceanography %R 10.1016/j.pocean.2022.102740 %0 Journal Article %J ICES Journal of Marine Science %D 2022 %T Big data approaches to the spatial ecology and conservation of marine megafauna %A Grémillet, David %A Chevallier, Damien %A Guinet, Christophe %B ICES Journal of Marine Science %8 Jul-04-2022 %G eng %U https://academic.oup.com/icesjms/advance-article/doi/10.1093/icesjms/fsac059/6564869 %R 10.1093/icesjms/fsac059 %0 Journal Article %J PLoS ONE %D 2022 %T Biologging of emperor penguins – attachment techniques and associated deployment performance %A Houstin, Aymeric %A Zitterbart, Daniel %A Winterl, Alexander %A Richter, Sebastian %A Planas-Bielsa, Víctor %A Chevallier, Damien %A Ancel, André %A Fournier, Jérôme %A Fabry, Ben %A Le Bohec, Céline %B PLoS ONE %G eng %U https://hal.archives-ouvertes.fr/hal-03409952 %R 10.1101/2021.06.08.446548 %0 Journal Article %J Marine Ecology Progress Series %D 2021 %T Bi-decadal variability in physico-biogeochemical characteristics of temperate coastal ecosystems: from large-scale to local drivers %A Lheureux, Arnaud %A Savoye, Nicolas %A Del Amo, Yolanda %A Goberville, Eric %A Bozec, Yann %A Elsa Breton %A Conan, Pascal %A L’Helguen, Stéphane %A Mousseau, Laure %A Raimbault, Patrick %A Rimelin-Maury, Peggy %A Seuront, Laurent %A Vuillemin, Renaud %A Caparros, Jocelyne %A Cariou, Thierry %A Cordier, MA %A Corre, Anne-Marie %A Costes, Laurence %A Crispi, O. %A Muriel Crouvoisier %A de Latour, HdL %A Derriennic, Hervé %A Devesa, Jérémy %A Durozier, Maïa %A Ferreira, Sophie %A Garcia, Nicole %A Emilie Grossteffan %A Gueux, Aurore %A Lafont, M %A Lagadec, Véronique %A Lecuyer, Eric %A Leroux, Cédric %A Macé, Eric %A Maria, E %A Mornet, L %A Antoine Nowaczyk %A Parra, M %A Petit, Fabienne %A David, V %X Coastal marine ecosystems, which play a crucial role in the biogeochemical and ecological functioning of the earth system, are highly sensitive to the combined effects of climate and human activities. Because of their location, coastal ecosystems are directly influenced by human activities. Thus, it remains challenging to assess the spatial and temporal scales at which climate influences coastal ecosystems. Twelve sampling stations distributed in eight ecosystems of Western Europe were monitored during two decades for physico-biogeochemical parameters (temperature, salinity, concentrations of dissolved oxygen, nutrients and particulate material). The study encompasses a large diversity of temperate coastal ecosystems regarding geomorphology, trophic status, tidal regime, river influence, turbidity, and so on. Time-series analysis coupled with standardised 3-mode Principal Component Analyses, Partial Triadic Analyses and correlations were used to assess bi-decadal variability and ecosystems trajectories, and to detect the large-scale, regional and local drivers. Overall results highlight two abrupt changes in 2001 and 2005. The bi-decadal changes are related to changes in large-scale and regional climate; detected through proxies of temperature and atmospheric circulation, as well as through river discharge. Ecosystem trajectories usually move towards an increase in temperature, salinity and/or a decrease in chlorophyll-a, nutrients and particulate matter. However, the magnitude of change, the year-to-year variability and the sensitivity to the 2001 and 2005 changes vary among the ecosystems. This study highlights the need to perform long-term time series and combining data sets as well as multi-ecosystem and local studies to better understand long-term variability of coastal ecosystems and its associated drivers. %B Marine Ecology Progress Series %V 660 %P 19-35 %8 Feb-18-2021 %G eng %U https://doi.org/10.3354/meps13577 %! Mar. Ecol. Prog. Ser. %R 10.3354/meps13577 %0 Journal Article %J NeoBiota %D 2021 %T Biological invasions in France: Alarming costs and even more alarming knowledge gaps %A Renault, David %A Manfrini, Eléna %A Leroy, Boris %A Diagne, Christophe %A Ballesteros-Mejia, Liliana %A Angulo, Elena %A Courchamp, Franck %B NeoBiota %V 67 %P 191 - 224 %8 May-07-2023 %G eng %U https://neobiota.pensoft.net/article/59134/ %! NB %R 10.3897/neobiota.67.59134 %0 Journal Article %J Aquatic Botany %D 2021 %T Biosorption capacity of genus Dictyota facing organochlorine pesticide pollutions in coastal areas of the Lesser Antilles %A Contarini, Paul-Emile %A Charlotte R. Dromard %B Aquatic Botany %V 169 %P 103346 %8 Jan-02-2021 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S030437702030156X %! Aquatic Botany %R 10.1016/j.aquabot.2020.103346 %0 Journal Article %J Frontiers in Marine Science %D 2021 %T Born With Bristles: New Insights on the Kölliker's Organs of Octopus Skin %A Villanueva, Roger %A Coll-Lladó, Montserrat %A Laure Bonnaud-Ponticelli %A Carrasco, Sergio %A Escolar, Oscar %A Fernández-Álvarez, Fernando Á. %A Gleadall, Ian %A Nabhitabhata, Jaruwat %A Ortiz, Nicolás %A Rosas, Carlos %A Sánchez, Pilar %A Voight, Janet %A Swoger, Jim %B Frontiers in Marine Science %V 8 %G eng %U https://hal.archives-ouvertes.fr/hal-03326946 %R 10.3389/fmars.2021.645738 %0 Journal Article %J General and Comparative Endocrinology %D 2020 %T Basal teleosts provide new insights into the evolutionary history of teleost-duplicated aromatase %A Lin, Chien-Ju %A Maugars, Gersende %A Lafont, Anne-Gaelle %A Jeng, Shan-Ru %A Wu, Guan-Chung %A Sylvie Dufour %A Chang, Ching-Fong %B General and Comparative Endocrinology %V 291 %P 113395 %8 Jan-05-2020 %G eng %U https://linkinghub.elsevier.com/retrieve/pii/S0016648019303326 %! General and Comparative Endocrinology %R 10.1016/j.ygcen.2020.113395 %0 Journal Article %J Royal Society Open Science %D 2020 %T Behavioural inference from signal processing using animal-borne multi-sensor loggers: a novel solution to extend the knowledge of sea turtle ecology %A Jeantet, Lorène %A Planas-Bielsa, Víctor %A Benhamou, Simon %A Geiger, Sébastien %A Martin, Jordan %A Siegwalt, Flora %A Lelong, Pierre %A Gresser, Julie %A Etienne, Denis %A Hielard, Gaëlle %A Arqué, Alexandre %A Régis, Sidney %A Lecerf, Nicolas %A Frouin, Cédric %A Benhalilou, Abdelwahab %A Murgale, Céline %A Maillet, Thomas %A Andreani, Lucas %A Campistron, Guilhem %A Delvaux, Hélène %A Guyon, Christelle %A Richard, Sandrine %A Lefebvre, Fabien %A Aubert, Nathalie %A Habold, Caroline %A Le Maho, Yvon %A Chevallier, Damien %B Royal Society Open Science %V 7 %P 200139 %8 Jan-05-2020 %G eng %U https://royalsocietypublishing.org/doi/10.1098/rsos.200139 %N 5 %! R. Soc. open sci. %R 10.1098/rsos.200139 %0 Journal Article %J Collection Forum %D 2020 %T Benefits for the Management and Preservation of Fluid Collections Using QR Codes %A Pruvost, P. %B Collection Forum %V 34 %P 170 - 178 %8 Jan-01-2020 %G eng %U https://meridian.allenpress.com/collection-forum/article/34/1/170/476958/Benefits-for-the-Management-and-Preservation-of %N 1 %R 10.14351/0831-4985-34.1.170 %0 Journal Article %J Global Change Biology %D 2020 %T Benthic ecoregionalization based on echinoid fauna of the Southern Ocean supports current proposals of Antarctic Marine Protected Areas under IPCC scenarios of climate change %A Fabri-Ruiz, Salomé %A Danis, Bruno %A Navarro, Nicolas %A Koubbi, Philippe %A Laffont, Rémi %A Saucède, Thomas %B Global Change Biology %V 26 %P 2161 - 2180 %8 Jan-04-2020 %G eng %U https://onlinelibrary.wiley.com/toc/13652486/26/4 %N 4 %! Glob Change Biol %R 10.1111/gcb.v26.410.1111/gcb.14988 %0 Journal Article %J Evolutionary Applications %D 2020 %T 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 %A Delrieu‐Trottin, Erwan %A Durand, Jean‐Dominique %A Limmon, Gino %A Sukmono, Tedjo %A Kadarusman %A Sugeha, Hagi Yulia %A Chen, Wei‐Jen %A Busson, Frederic %A Borsa, Philippe %A Dahruddin, Hadi %A Sauri, Sopian %A Fitriana, Yuli %A Zein, Mochamad Syamsul Arifin %A Hocdé, Régis %A Pouyaud, Laurent %A Philippe Keith %A Wowor, Daisy %A Steinke, Dirk %A Hanner, Robert %A Hubert, Nicolas %K Coral Triangle %K Cryptic diversity %K DNA barcoding %K reference library %K taxonomic gap %X 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. %B Evolutionary Applications %8 Nov-02-2020 %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12926 %! Evol Appl %R 10.1111/eva.12926 %0 Journal Article %J Frontiers in Microbiology %D 2019 %T Bacterial–Fungal Interactions in the Kelp Endomicrobiota Drive Autoinducer-2 Quorum Sensing %A Tourneroche, Anne %A Lami, Raphaël %A Cédric Hubas %A Blanchet, Elodie %A Vallet, Marine %A Escoubeyrou, Karine %A Paris, Alain %A Prado, Soizic %X

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.

%B Frontiers in Microbiology %V 10 %P 1693 %G eng %U https://www.frontiersin.org/article/10.3389/fmicb.2019.01693 %R 10.3389/fmicb.2019.01693 %0 Journal Article %J Cybium %D 2019 %T Barbatula leoparda (Actinopterygii, Nemacheilidae), a new endemic species of stone loach of French Catalonia %A Gauliard, Camille %A Dettai, Agnès %A Persat, Henri %A Philippe Keith %A Denys, Gaël %K Barbatula leopard %K French Catalonia %K Freshwater %K Nemacheilidae %K New species %X

This study described a new stone loach species in France, Barbatula leoparda, which is endemic to French Catalonia (Têt and Tech river drainages). Seven specimens were compared to 49 specimens of B. barbatula (Linnaeus, 1758) and 71 specimens of B. quignardi (Băcescu-Meşter, 1967). This new species is characterized by the presence of blotches on the belly and the jugular area in individuals longer than 47 mm SL and by a greater interorbital distance (35.5 to 41.8% of the head length). We brought moreover the sequence of two mitochondrial markers (COI and 12S, respectively 652 and 950 bp) of the holotype, which are well distinct from all other species, for molecular identifications. This discovery is important for conservation.

%B Cybium %V 43 %P 169-177 %G eng %N 2 %0 Journal Article %J Journal of Coastal Research %D 2019 %T Beaches seasonal and paroxysmal morphosedimentary dynamics. results of 10 years Martinique coastal observation network. %A Franck Dolique %A Sedrati, M. %A Charpentier, J. %A Jeanson, Matthieu %A Cohen, O. %A Dupuy, L. %A Alami, S. %B Journal of Coastal Research %V SI 88 %P 172-184 %G eng %0 Journal Article %J Probiotics Antimicrob Proteins %D 2019 %T Behavior of Antimicrobial Peptide K4 in a Marine Environment. %A Houyvet, Baptiste %A Leduc, Alexandre %A Cornet, Valérie %A Pontin, Julien %A Bernay, Benoît %A Joël Henry %A Vetois, Emilie %A Céline Zatylny-Gaudin %X

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 μg 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

%B Probiotics Antimicrob Proteins %V 11 %P 676-686. %G eng %N 2 %R 10.1007/s12602-018-9454-3 %0 Journal Article %J Ecology of Freshwater Fish %D 2019 %T Behaviour of endangered European eels in proximity to a dam during downstream migration: Novel insights using high accuracy 3D acoustic telemetry %A Thomas Trancart %A Alexandre Carpentier %A Anthony Acou %A Danet, Valentin %A Elliott, Sophie %A Eric Feunteun %K 3D acoustic telemetry %K dam %K diadromous fish %K downstream migration %K European eel %X River infrastructures such as weirs, hydropower stations or water reservoirs represent obstructions to migration for diadromous fish. Knowledge of accurate behaviour of fish in front of such structures is required to protect migrants from hazardous areas, guide them towards safe passage or adapt structure to improve the escapement. We developed and made available a method to process acoustic telemetry data based on Time Difference Of Arrival analysis to accurately locate tagged fish. Improved accuracy allows the detection of escape routes and description of dam-crossing tactics. Sixteen tagged eels were tracked with high accuracy (1–2 m) and 1 location min−1 frequency during their exploration period on reaching the dam. Two migration routes (spillways and bottom compensation flow pipe) were used by 77% and 23% of eels respectively. Spillways were the preferred route, but a median of 16 days were required to pass the dam versus 1.1 days via the compensation pipe. A minimal water crest of 40 cm was required for passage via spillways. Eels passing through the compensation pipe were exclusively nocturnal and mainly explored the bottom of the dam. Eels passing through spillways explored the whole dam area by night and day, and were not attracted to the compensation pipe entrance. With global warming, more frequent drought periods are expected, potentially leading to decreased opportunities for eels to migrate across safer dams by spillways. To conserve this endangered species, dam management strategies that account for expected hydrologic conditions and distinct exploration behaviours are needed. %B Ecology of Freshwater Fish %V 29 %P 266-279 %G eng %U https://onlinelibrary.wiley.com/doi/abs/10.1111/eff.12512 %R 10.1111/eff.12512 %0 Journal Article %J Polar Biology %D 2019 %T Biochemical composition and energy content of size-fractionated zooplankton east of the Kerguelen Islands %A Harmelin-Vivien, Mireille %A Bӑnaru, Daniela %A Charlotte R. Dromard %A Ourgaud, Mélanie %A Carlotti, François %B Polar Biology %V 42 %P 603 - 617 %8 Jan-03-2019 %G eng %U http://link.springer.com/10.1007/s00300-019-02458-8 %N 3 %! Polar Biol %R 10.1007/s00300-019-02458-8 %0 Journal Article %J Ecological Indicators %D 2018 %T Benthic foraminifera to assess Ecological Quality Statuses in Italian transitional waters %A Vincent M.P. Bouchet %A Goberville, Eric %A Fabrizio Frontalini %K Diversity index %K Ecological quality status %K Italian transitional waters %K Living benthic foraminifera %K Marine strategy framework directive %K Water framework directive %X

Estuaries, lagoons and lakes, identified as transitional waters (TWs), are fragile ecotones at the interface between terrestrial and marine ecosystems. The assessment of their Ecological Quality status (EcoQ), required by marine legislations, is rather uncertain when based on traditional benthic macrofaunal indices. This study proposes to assess the EcoQ of marine waters using the diversity index Exp(H'bc) based on living benthic foraminifera. By testing this method on datasets from five Italian TWs, we showed that EcoQ's assessment based on foraminifera reflected changes in environmental conditions. Benthic foraminifera highlighted the degradation of most, if not all, study sites, ranking most of the TWs in “Moderate” to “Bad” EcoQs. Although the assessment of EcoQs estimated from diversity indices was similar when based on benthic foraminifera or macrofauna, discrepancies occurred if diversity index calculated on foraminifera and sensitivity-based indices applied on macrofauna were compared. Our results demonstrated that the Exp(H'bc) index based on living benthic foraminifera is a promising approach to assess EcoQs. Finally, we argue that benthic foraminifera, for their preservation potential as fossil within sediment, are a reliable option to define reference conditions and targets.

%B Ecological Indicators %V 84 %G eng %U https://www.sciencedirect.com/science/article/pii/S1470160X17304685 %R 10.1016/j.ecolind.2017.07.055 %0 Journal Article %J Ecology and Evolution %D 2018 %T Benthic species of the Kerguelen Plateau show contrasting distribution shifts in response to environmental changes %A Guillaumot, Charlène %A Fabri-Ruiz, Salomé %A Martin, Alexis %A Eleaume, Marc %A Danis, Bruno %A Feral, Jean-Pierre %A Saucède, Thomas %B Ecology and Evolution %V 8 %P 6210 - 6225 %8 Jan-06-2018 %G eng %U http://doi.wiley.com/10.1002/ece3.2018.8.issue-12 %N 12 %! Ecol Evol %R 10.1002/ece3.2018.8.issue-1210.1002/ece3.4091 %0 Journal Article %J Ecological Engineering %D 2018 %T Biofilm monitoring as a tool to assess the efficiency of artificial reefs as substrates: Toward 3D printed reefs %A Elisabeth Riera %A Lamy, Dominique %A Christophe Goulard %A Francour, P %A Cédric Hubas %K Artificial reef substrates %X

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’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.

%B Ecological Engineering %V 120 %P 230 - 237 %G eng %U https://www.sciencedirect.com/science/article/pii/S0925857418302167 %R https://doi.org/10.1016/j.ecoleng.2018.06.005 %0 Journal Article %J Connective Tissue Research %D 2018 %T Biomineralization in modern avian calcified eggshells: similarity versus diversity %A Dauphin, Y %A Luquet, G %A Perez-Huerta, A %A Salomé, M %X Avian eggshells are composed of several layers made of organic compounds and a mineral phase (calcite), and the general structure is basically the same in all species. A comparison of the structure, crystallography, and chemical composition shows that despite an overall similarity, each species has its own structure, crystallinity, and composition. Eggshells are a perfect example of the crystallographic versus biological concept of the formation and growth mechanisms of calcareous biominerals: the spherulitic-columnar structure is described as "a typical case of competitive crystal growth", but it is also said that the eggshell matrix components regulate eggshell mineralization. Electron back scattered diffraction (EBSD) analyses show that the crystallinity differs between different species. Nevertheless, the three layers are composed of rounded granules, and neither facets nor angles are visible. In-situ analyses show the heterogeneous distribution of chemical elements throughout the thickness of single eggshell. The presence of organic matrices other than the outer and inner membranes in eggshells is confirmed by thermograms and infrared spectrometry, and the differences in quality and quantity depend on the species. Thus, as in other biocrystals, crystal growth competition is not enough to explain these differences, and there is a strong biological control of the eggshell secretion. %B Connective Tissue Research %V 59 %P 67-73 %8 01/2018 %G eng %N Sup1 %9 Journal article %0 Journal Article %J Frontiers in Marine Science %D 2018 %T Blow Your Nose, Shrimp! Unexpectedly Dense Bacterial Communities Occur on the Antennae and Antennules of Hydrothermal Vent Shrimp %A Magali Zbinden %A Gallet, Alison %A Szafranski, Kamil M. %A Machon, Julia %A Juliette Ravaux %A Léger, Nelly %A Duperron, Sébastien %X In crustaceans, as in other animals, perception of environmental cues is of key importance for a wide range of interactions with the environment and congeners. Chemoreception involves mainly the antennae and antennules, which carry sensilla that detect water-borne chemicals. The functional importance of these as exchange surfaces in the shrimp’s sensory perception requires them to remain free of any microorganism and deposit that could impair the fixation of odorant molecules on sensory neurons. We report here the occurrence of an unexpected dense bacterial colonization on surface of the antennae and antennules of four hydrothermal vent shrimp species. Microscopic observation, qPCR and 16S rRNA barcoding reveal the abundance, diversity and taxonomic composition of these bacterial communities, that are compared with those found on a related coastal shrimp. Bacterial abundances vary among species. Bacteria are almost absent in coastal shrimp, meanwhile they fully cover the antennal flagella in some hydrothermal vent species. Epsilon- and Gammaproteobacteria dominate the hydrothermal shrimp-associated communities, whereas Alphaproteobacteria and Bacteroidetes are dominant in the coastal ones. Bacteria associated with vent shrimp species are most similar to known chemoautotrophic sulfur-oxidizers. Potential roles of these bacteria on the hydrothermal shrimp antennae and antennules and on sensory functions are discussed. %B Frontiers in Marine Science %V 5 %8 Aug-10-2018 %G eng %U https://www.frontiersin.org/article/10.3389/fmars.2018.00357/full %! Front. Mar. Sci. %R 10.3389/fmars.2018.00357 %0 Journal Article %J Fisheries Research %D 2017 %T A Bayesian two-stage biomass model for stock assessment of data-limited species: An application to cuttlefish (Sepia officinalis) in the English Channel %A Juliette Alemany %A Etienne Rivot %A Foucher, Eric %A Joël Vigneau %A Jean-Paul Robin %X Cuttlefish is a key commercial species in the English Channel fishery in terms of landings and value. Age-based assessment methods are limited by time-consuming age determination with statoliths and the lack of stock assessment models tailored to this data-limited species. A two-stage biomass model is developed in the Bayesian state-space modelling framework that allows inferences to be made on the stock biomass at the start, middle and end of each fishing seasons between 1992 and 2014, while accounting for both process and measurement errors and to assimilate various sources of information. A method that uses ancillary length-frequency data is developed to provide an informative prior distribution for the biomass growth rate parameter g (E = 0.89) and its annual variability (CV = 0.1). The new model is a substantial improvement on the existing stock assessment method used by the International Council for the Exploration of the Seas. Taking into consideration a time-varying g parameter provides a more ecologically meaningful model with regard to the sensitivity of the cuttlefish population dynamics to environmental fluctuations and improves model fit. The model also provides predictions of the unexploited biomass in winter, which is based on survey data, and helps manage the stock in the event of strong depletion. © 2017 Elsevier B.V. %B Fisheries Research %V 191 %P 131-143 %G eng %U http://www.sciencedirect.com/science/article/pii/S0165783617300772 %R 10.1016/j.fishres.2017.03.010 %0 Journal Article %J Marine Pollution Bulletin %D 2017 %T Before-After analysis of the trophic network of an experimental dumping site in the eastern part of the Bay of Seine (English Channel) %A Pezy, Jean-Philippe %A Raoux, Aurore %A Marmin, Stella %A Balay, Pierre %A Nathalie Niquil %A Jean-Claude Dauvin %X

An experimental study was conducted to assess the physical and biological impacts of muddy fine sand dredged material dumped on a medium sand site Machu offshore the Seine Estuary. Complementary trophic web modelling tools were applied to the Machu ecosystem to analyse the effects of dumping operations. Results show that, after the dumping operations, the biomass of fish increased while invertebrate biomass remained relatively stable through time. Nevertheless, the biomasses of benthic invertebrates, omnivores/scavengers and predators showed some increases, while non-selective deposit feeders and filter feeders decreased. At the ecosystem level, results show that the total ecosystem activity, the ascendency and the overall omnivorous character of the food-web structure increased after dumping operations, whereas recycling subsequently decreased. Finally, the fine and medium sand habitat offshore from the Seine estuary, which undergoes regular natural physical perturbations, shows a high resilience after a short dumping phase. (C) 2017 Elsevier Ltd. All rights reserved.

%B Marine Pollution Bulletin %V 118 %P 101-111 %8 05/2017 %G eng %R {10.1016/j.marpolbul.2017.02.042} %0 Journal Article %J Ecological indicators %D 2017 %T Benthic and fish aggregation inside an offshore wind farm: Which effects on the trophic web functioning? %A Raoux, Aurore %A Samuele Tecchio %A Pezy, Jean-Philippe %A Géraldine Lassalle %A Degraer, Steven %A Wilhelmsson, Dan %A Cachera, Marie %A Ernande, Bruno %A Le Guen, Camille %A Haraldsson, Matilda %A Karine Grangeré %A Le Loc'h, Francois %A Dauvin, Jean-Claude %A Nathalie Niquil %X

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 ``before{''} 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, ``before{''} and ``after{''}, 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.

%B Ecological indicators %V 72 %P 33-46 %8 01/2017 %G eng %R 10.1016/j.ecolind.2016.07.037 %0 Journal Article %J Chemosphere %D 2017 %T Bioaccumulation, distribution and elimination of chlordecone in the giant freshwater prawn Macrobrachium rosenbergii: Field and laboratory studies %A Anne Lafontaine %A Eric Gismondi %A Nathalie Dodet %A Célia Joaquim-Justo %A Céline Boulangé-Lecomte %A Fanny Caupos %A Lemoine, Soazig %A Laurent Lagadic %A Joëlle Forget-Leray %A Jean-Pierre Thomé %K Bioaccumulation factor %X

Abstract Chlordecone is a persistent organochlorine pesticide that has been widely used in Guadeloupe (French West Indies) to control the banana weevil Cosmopolites sordidus from 1972 to 1993. A few years after its introduction, widespread contamination of soils, rivers, wild animals and aquatic organisms was reported. Although high chlordecone concentrations have been reported in several crustacean species, its uptake, internal distribution, and elimination in aquatic species have never been described. This study aimed at investigating the accumulation and tissue distribution of chlordecone in the giant freshwater prawn Macrobrachium rosenbergii, using both laboratory (30 days exposure) and field (8 months exposure) approaches. In addition, depuration in chlordecone-free water was studied. Results showed that chlordecone bioconcentration in prawns was dose-dependent and time-dependent. Moreover, females appeared to be less contaminated than males after 5 and 7 months of exposure, probably due to successive spawning leading in the elimination of chlordecone through the eggs. Chlordecone distribution in tissues of exposed prawns showed that cephalothorax organs, mainly represented by the hepatopancreas, was the most contaminated. Results also showed that chlordecone was accumulated in cuticle, up to levels of 40% of the chlordecone body burden, which could be considered as a depuration mechanism since chlordecone is eliminated with the exuviae during successive moults. Finally, this study underlined the similarity of results obtained in laboratory and field approaches, which highlights their complementarities in the chlordecone behaviour understanding in M. rosenbergii.

%B Chemosphere %V 185 %P 888 - 898 %G eng %U http://www.sciencedirect.com/science/article/pii/S0045653517311529 %R https://doi.org/10.1016/j.chemosphere.2017.07.099 %0 Journal Article %J Deep Sea Research Part II: Topical Studies in Oceanography %D 2015 %T Behavioural study of two hydrothermal crustacean decapods: Mirocaris fortunata and Segonzacia mesatlantica, from the Lucky Strike vent field (Mid-Atlantic Ridge) %A Matabos Marjolaine %A Cuvelier Daphné %A Brouard Johan %A Bruce Shillito %A Juliette Ravaux %A Magali Zbinden %A Barthelemy Dominique %A Sarradin, Pierre-Marie %A Sarrazin, Jozee %K 32°16.3′W %K 37°17′N %K AbyssBox %K Biological interactions %K Deep-sea observatory %K Eiffel Tower edifice %K Experimental research %K Feeding behaviour %K Lucky Strike %K Mid-Atlantic Ridge %K Time series %K Video imagery %X Identifying the factors driving community dynamics in hydrothermal vent communities, and in particular biological interactions, is challenged by our ability to make direct observations and the difficulty to conduct experiments in those remote ecosystems. As a result, we have very limited knowledge on species׳ behaviour and interactions in these communities and how they in turn influence community dynamics. Interactions such as competition or predation significantly affect community structure in vent communities, and video time-series have successfully been used to gain insights in biological interactions and species behaviour, including responses to short-term changes in temperature or feeding strategies. In this study, we combined in situ and ex situ approaches to characterise the behaviour and interactions among two key species encountered along the Mid-Atlantic Ridge (MAR): the shrimp Mirocaris fortunata and the crab Segonzacia mesatlantica. In situ, species small-scale distribution, interactions and behaviour were studied using the TEMPO observatory module deployed on the seafloor at the base of the active Eiffel Tower edifice in the Lucky Strike vent field as part of the EMSO-Açores MoMAR observatory. TEMPO sampled 2min of video four times a day from July 2011 to April 2012. One week of observations per month was used for ‘long-term’ variations, and a full video data set was analysed for January 2012. In addition, observations of crab and shrimp individuals maintained for the first time under controlled conditions in atmospheric pressure (classic tank) and pressurised (AbyssBox) aquaria allowed better characterisation and description of the different types of behaviour and interactions observed in nature. While the identified in situ spatial distribution pattern was stable over the nine months, both species displayed a significant preference for mussel bed and anhydrite substrata, and preferentially occupied the area located directly in the fluid flow axis. The aggregation behaviour of M. fortunata resulted in the occurrence of numerous intraspecific interactions mainly involving the use of two pairs of sensory organs (antenna/antennule) and fleeing behaviours when in contact or close to individuals of S. mesatlantica. The higher level of passiveness observed in the ex situ artificial environment compared to the in situ environment was attributed to the lack of stimulation related to low densities of congeners and/or of sympatric species compared to the natural environment and the absence of continuous food supply, as both species displayed a significant higher level of activity during feeding time. This result emphasises the role of food supply as a driver of species distribution and behaviour. Direct in situ observations using cameras deployed on deep-sea observatories, combined with experimental set-up in pressurised aquaria, will help investigators understand the factors influencing community dynamics and species biology at vents as well as their underlying mechanisms. %B Deep Sea Research Part II: Topical Studies in Oceanography %V 121 %P 146 - 158 %G eng %U http://www.sciencedirect.com/science/article/pii/S0967064515001113 %R https://doi.org/10.1016/j.dsr2.2015.04.008 %0 Journal Article %J Estuarine, Coastal and Shelf Science %D 2015 %T Biogenic reefs affect multiple components of intertidal soft-bottom benthic assemblages: the Lanice conchilega case study %A De Smet, Bart %A D'Hondt, An Sophie %A Pieterjan, Verhelst %A Jérôme Fournier %A Laurent Godet %A Nicolas Desroy %A Rabaut, Marijn %A Magda, Vincx %A Jan, Vanaverbeke %K beaches %K benthos %K biogenic reefs %K community composition %K Lanice conchilega %K tidal flats %X

Biogenic reefs composed of the tube-building polychaete Lanice conchilega are important from a conservation point of view because they noticeably increase the biodiversity in otherwise species poor
environments. However, up to now, little or no attention has been paid to the intertidal epi- and hyperbenthic communities associated with the reefs. Therefore, this is the first study which focuses on
the effect of L. conchilega reefs on the entire bentho-pelagic community at two different locations. Environmental variables were measured and macro-, epi- and hyperbenthic communities were sampled
within a L. conchilega reef and a control area at two locations in France: the bay of the Mont Saint-Michel (BMSM) and Boulogne-sur-Mer (Boulogne). The effect of the reef presence on the benthic community
was studied with a 3-factor (Reef, Location and Period) Permanova. In addition, the relationship between the benthic community and the environmental variables was investigated using Distance-based linear
models (DistLM). Most collected organisms were sampled in the reef area (macrobenthos: 91%, epibenthos: 81% and hyperbenthos: 78.5%) indicating that, independent of the location, the L. conchilega
reefs positively affect all three associated benthic communities. However, the extent of the effect seems to be most pronounced for the macrobenthos and less distinct in case of the hyperbenthos. The macro-,
and epibenthos are mainly structured by biotic variables (L. conchilega density and macrobenthic food availability respectively), while the hyperbenthos is rather structured by environmental variables. In
general, L. conchilega reefs do not only affect abundances and diversity but they substantially steer the structure of the intertidal benthic sandy beach ecosystem.

%B Estuarine, Coastal and Shelf Science %V 152 %P 44-55 %8 01/2015 %G eng %R doi:10.1016/j.ecss.2014.11.002 %0 Journal Article %J FEMS Microbiol Ecol %D 2015 %T Biogeographical distribution of Rimicaris exoculata resident gut epibiont communities along the Mid-Atlantic Ridge hydrothermal vent sites. %A Durand, Lucile %A Roumagnac, Marie %A Cueff-Gauchard, Valérie %A Jan, Cyrielle %A Guri, Mathieu %A Tessier, Claire %A Haond, Marine %A Crassous, Philippe %A Magali Zbinden %A Arnaud-Haond, Sophie %A Cambon-Bonavita, Marie-Anne %X

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.

%B FEMS Microbiol Ecol %V 91 %8 2015 Oct %G eng %N 10 %R 10.1093/femsec/fiv101 %0 Journal Article %J Journal of Ornithology %D 2015 %T Bluethroats Luscinia svecica namnetum offset landscape constraints by expanding their home range %A Laurent Godet %A Matthieu Marquet %A Marie-Christine Eybert %A Elisa Grégoire %A Sarah Monnet %A Jérôme Fournier %X

The highly fragmented landscape structures of coastal salinas are known to result in decreased terrestrial bird abundance, species richness and diversity but to promote original assemblages dominated by specialist species, such as the Bluethroat Luscinia svecica namnetum. This species is mainly found at the core of these salinas, where the landscape characteristics are a priori the most hostile for terrestrial birds. The aim of this study was to test whether individuals of a specialized species like the Bluethroat may offset such landscape constraints by expanding their home ranges. We therefore radio-tracked 21 males in 2013 and 2014 in the salinas of the Marais du Mes (Parc Naturel Régional de Brière, Western France). The data of the 18 best-monitored males were used to carry out a hierarchical partitioning of variance to test the relative influence of landscape characteristics, individual characteristics and distance to other males on their home-range sizes. We found that landscape characteristics were the factors that best explained home range sizes. Home-range sizes were significantly smaller in diversified landscapes composed of tidal creeks and salt-marsh patches and tended to be larger in landscapes dominated by the aquatic matrix consisting of water ponds. The results of this study demonstrate that although a few bird species are able to
select a priori hostile landscapes, they can offset such constraints by expanding their home-range size.

%B Journal of Ornithology %V 156 %P 591-600 %8 06/2015 %G eng %0 Journal Article %J Mol Ecol Resour %D 2015 %T Bushmeat genetics: setting up a reference framework for the DNA typing of African forest bushmeat. %A Gaubert, Philippe %A Njiokou, Flobert %A Olayemi, Ayodeji %A Pagani, Paolo %A Dufour, Sylvain %A Danquah, Emmanuel %A Nutsuakor, Mac Elikem K %A Ngua, Gabriel %A Missoup, Alain-Didier %A Pablo Tedesco %A Dernat, Rémy %A Antunes, Agostinho %X

The bushmeat trade in tropical Africa represents illegal, unsustainable off-takes of millions of tons of wild game - mostly mammals - per year. We sequenced four mitochondrial gene fragments (cyt b, COI, 12S, 16S) in >300 bushmeat items representing nine mammalian orders and 59 morphological species from five western and central African countries (Guinea, Ghana, Nigeria, Cameroon and Equatorial Guinea). Our objectives were to assess the efficiency of cross-species PCR amplification and to evaluate the usefulness of our multilocus approach for reliable bushmeat species identification. We provide a straightforward amplification protocol using a single 'universal' primer pair per gene that generally yielded >90% PCR success rates across orders and was robust to different types of meat preprocessing and DNA extraction protocols. For taxonomic identification, we set up a decision pipeline combining similarity- and tree-based approaches with an assessment of taxonomic expertise and coverage of the GENBANK database. Our multilocus approach permitted us to: (i) adjust for existing taxonomic gaps in GENBANK databases, (ii) assign to the species level 67% of the morphological species hypotheses and (iii) successfully identify samples with uncertain taxonomic attribution (preprocessed carcasses and cryptic lineages). High levels of genetic polymorphism across genes and taxa, together with the excellent resolution observed among species-level clusters (neighbour-joining trees and Klee diagrams) advocate the usefulness of our markers for bushmeat DNA typing. We formalize our DNA typing decision pipeline through an expert-curated query database - DNAbushmeat - that shall permit the automated identification of African forest bushmeat items.

%B Mol Ecol Resour %V 15 %P 633-651 %8 2014 Sep 26 %G eng %R 10.1111/1755-0998.12334 %0 Journal Article %J Journal of Sea Research %D 2014 %T Bacterial dynamics in a microphytobenthic biofilm: A tidal mesocosm approach %A Hélène Agogué %A Clarisse Mallet %A Francis Orvain %A Margot de Crignis %A Françoise Mornet %A Christine Dupuy %B Journal of Sea Research %V 92 %P 144-157 %8 09/2014 %G eng %0 Book Section %B The Biogeographic Atlas of the Southern Ocean %D 2014 %T Biogeographic patterns of fish %A Percy-Alexander Hulley %A Causse, Romain %A Koubbi, Philippe %A Vacchi, Marino %B The Biogeographic Atlas of the Southern Ocean %G eng %0 Journal Article %J Geobiology %D 2014 %T Biomineralization of Schlumbergerella floresiana, a significant carbonate-producing benthic foraminifer. %A Sabbatini, A %A Bedouet, L %A Marie, A %A Bartolini, A %A Landemarre, L %A Weber, M X %A Gusti Ngurah Kade Mahardika, I %A Berland, Sophie %A Zito, F %A Vénec-Peyré, M-T %K Amino Acid Sequence %K Amino Acids %K Calcification, Physiologic %K Carbonates %K Electrophoresis, Polyacrylamide Gel %K Foraminifera %K Molecular Sequence Data %K Monosaccharides %X

Most foraminifera that produce a shell are efficient biomineralizers. We analyzed the calcitic shell of the large tropical benthic foraminifer Schlumbergerella floresiana. We found a suite of macromolecules containing many charged and polar amino acids and glycine that are also abundant in biomineralization proteins of other phyla. As neither genomic nor transcriptomic data are available for foraminiferal biomineralization yet, de novo-generated sequences, obtained from organic matrices submitted to ms blast database search, led to the characterization of 156 peptides. Very few homologous proteins were matched in the proteomic database, implying that the peptides are derived from unknown proteins present in the foraminiferal organic matrices. The amino acid distribution of these peptides was queried against the uniprot database and the mollusk uniprot database for comparison. The mollusks compose a well-studied phylum that yield a large variety of biomineralization proteins. These results showed that proteins extracted from S. floresiana shells contained sequences enriched with glycine, alanine, and proline, making a set of residues that provided a signature unique to foraminifera. Three of the de novo peptides exhibited sequence similarities to peptides found in proteins such as pre-collagen-P and a group of P-type ATPases including a calcium-transporting ATPase. Surprisingly, the peptide that was most similar to the collagen-like protein was a glycine-rich peptide reported from the test and spine proteome of sea urchin. The molecules, identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses, included acid-soluble N-glycoproteins with its sugar moieties represented by high-mannose-type glycans and carbohydrates. Describing the nature of the proteins, and associated molecules in the skeletal structure of living foraminifera, can elucidate the biomineralization mechanisms of these major carbonate producers in marine ecosystems. As fossil foraminifera provide important paleoenvironmental and paleoclimatic information, a better understanding of biomineralization in these organisms will have far-reaching impacts.

%B Geobiology %V 12 %P 289-307 %8 2014 Jul %G eng %N 4 %R 10.1111/gbi.12085 %0 Journal Article %J Journal of Coastal Research %D 2013 %T Beach morphological changes in response to marine turtles nesting: a preliminary study of Awala-Yalimapo beach, French Guiana (South America) %A Péron, Christina %A Chevallier, Damien %A Galpin, Martin %A Chatelet, Andy %A Anthony, Edward J. %A Le Maho, Yvon %A Gardel, Antoine %B Journal of Coastal Research %V 65 %P 99 - 104 %8 Feb-01-2013 %G eng %U http://www.bioone.org/doi/10.2112/SI65-018.1 %! Journal of Coastal Research %R 10.2112/SI65-018.1 %0 Conference Proceedings %B 6ème Conférence Internationale Cigogne noire %D 2012 %T The Black stork at the Nazinga ranch (Burkina Faso) %A Yameogo, Dieudonné %A Chevallier, Damien %A Brossault, Paul %B 6ème Conférence Internationale Cigogne noire %7 Ornithos %I Ornithos %C Châlons-en-Champagne, France %P 224 %8 2016 %G eng %6 1