@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\ microphytobenthos\ (MPB), a\ microbial community\ of primary producers, play a key role in\ coastal ecosystem\ 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\ energy dissipation\ 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\ min to a light gradient of photosynthetically active radiation (PAR) from 50 to 1000\ μmol photons m-2\ 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\ acclimation\ of migrational MPB biofilms. Since alka(e)nes are produced from FAs\ 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 {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\ 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 {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 {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 {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 {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 {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 {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 {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 {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\ 13C and\ 15N in the albumen gland and gonadal follicles of the sea slug\ 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\ E. timida\ 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 {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\ 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\ C. fornicata\ 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\ C. fornicata\ 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\ C. fornicata\ 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.
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 {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{\textendash}2.s{\textendash}1 and high light, HL at 800 μmol.photons.m{\textendash}2.s{\textendash}1) 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{\textendash}2.s{\textendash}1 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 {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\ 13C and\ 15N assimilation over a 12-h incubation period of\ Elysia viridis\ 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\ 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\ 13C- and\ 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\ 13C-labeled long-chain FA, absent from\ E. viridis\ 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 {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,\ Paradendryphiella salina, a fungal endophyte was isolated from\ Saccharina latissima\ (L.) and\ Laminaria digitata\ (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\ P. salina\ 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 {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 {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 {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 {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} } @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 = {

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.

}, 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 {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 = {

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.

}, 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 = {

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.

}, 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 {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 = {

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\ 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.

}, 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.} } @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 = {

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.

}, 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.} } @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 = {

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.

}, 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 {5515, title = {Strengths, weaknesses, and opportunities of French research in trophic ecology}, journal = {Comptes Rendus Biologies}, year = {2018}, pages = {-}, abstract = {

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}€œGRET{\^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.

}, 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 {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 = {

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\ {\textpm}\ 45\ μmol\ 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\ {\textpm}\ 28.2\ μmol\ 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\ μmol\ 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.

}, 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 {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 = {

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.

}, 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 {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 = {

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.

}, 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 {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 = {

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.

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\ 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.

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.

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.

}, 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 = {

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.

}, 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 {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 = {

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.

}, 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 {3984, title = {Environmental microbiology as a mosaic of explored ecosystems and issues}, journal = {Environmental Science and Pollution Research}, volume = {22}, year = {2015}, pages = {13577-13598}, keywords = {Critical zone, Environmental microbiology, Microbial ecology, Microbial ecosystems}, issn = {0944-1344}, doi = {10.1007/s11356-015-5164-5}, url = {http://dx.doi.org/10.1007/s11356-015-5164-5}, author = {Faure, Denis and Bonin, Patricia and Duran, Robert and The EC2CO consortium} } @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 = {

Abstract The relationship between biodiversity and stability of marine benthic assemblages was investigated through meta-analyses using existing data sets (n\ =\ 28) covering various spatial (m{\textendash}km) and temporal (1973{\textendash}2006; ranging from 5 to \>\ 250\ 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 (\<\ 1\ m2) and site (\ \ 100\ 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.

}, 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 {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 = {

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.

}, 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 {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 = {

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.

}, 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 {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 = {

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.

}, 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 {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} }