Author: "Cédric Hubas" - Searchworks@Jio Institute Digital Library Search Results

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1. Establishing complexity targets to enhance artificial reef designs

Author: Elisabeth Riera, Benjamin Mauroy, Patrice Francour, and Cédric Hubas
Subjects: Artificial reef, Habitat complexity, 3-Dimensional computer-aided design model, Medicine, Science
Abstract: Abstract Artificial reefs (AR), which are integral tools for fish management, ecological reconciliation and restoration efforts, require non-polluting materials and intricate designs that mimic natural habitats. Despite their three-dimensional complexity, current designs nowadays rely on empirical methods that lack standardised pre-immersion assessment. To improve ecosystem integration, we propose to evaluate 3-dimensional Computer-aided Design (3D CAD) models using a method inspired by functional ecology principles. Based on existing metrics, we assess geometric (C-convexity, P-packing, D-fractal dimension) and informational complexity (R-specific richness, H- diversity, J-evenness). Applying these metrics to different reefs constructed for habitat protection, biomass production and bio-mimicry purposes, we identify potential complexity target points (CTPs). This method provides a framework for improving the effectiveness of artificial reef design by allowing for the adjustment of structural properties. These CTPs represent the first step in enhancing AR designs. We can refine them by evaluating complexity metrics derived from 3D reconstructions of natural habitats to advance bio-mimicry efforts. In situ, post-immersion studies can help make the CTPs more specific for certain species of interest by exploring complexity-diversity or complexity-species distribution relationships at the artificial reef scale.
Published: 2024
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2. Novel α-Hydroxy γ-Butenolides of Kelp Endophytes Disrupt Bacterial Cell-to-Cell Signaling

Author: Marine Vallet, Yee-Meng Chong, Anne Tourneroche, Grégory Genta-Jouve, Cédric Hubas, Raphael Lami, Claire M. M. Gachon, Tatyana Klochkova, Kok-Gan Chan, and Soizic Prado
Subjects: fungal endophytes, marine macrophytes, endomicrobiota, Paradendryphiella salina, α-hydroxy γ-butenolide, quorum sensing, Science, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract: A wide range of microbial symbionts such as bacteria and fungi colonize the tissues of macrophytes. The chemical interactions between these endophytes remain underexplored. The obligate marine fungus Paradendryphiella salina was isolated from several healthy brown macrophyte species. Novel α-hydroxy γ-butenolides produced by P. salina were purified and characterized by nuclear magnetic resonance (NMR). These compounds interfere with the bacterial quorum sensing system as shown in bioassays with pathogenic bacterial model Pseudomonas aeruginosa. Ultra-performance liquid chromatography–high-resolution mass spectrometry (UHPLC-HRMS)-based comparative metabolomics revealed the presence of the main α-hydroxy γ-butenolides among all the P. salina strains isolated from different hosts as well as a high metabolic variability related to the alga-host species. Collectively, these findings highlight the key role of microbial chemical signaling that may occur within the algal holobiont.
Published: 2020
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3. Effect of Light Intensity and Light Quality on Diatom Behavioral and Physiological Photoprotection

Author: Antoine Prins, Paul Deleris, Cédric Hubas, and Bruno Jesus
Subjects: diatoms, fluorescence, PAM, migration, photoprotection, Science, General. Including nature conservation, geographical distribution, QH1-199.5
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–2.s–1 and high light, HL at 800 μmol.photons.m–2.s–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–2.s–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.
Published: 2020
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4. An Untargeted Metabolomic Approach for Microphytobenthic Biofilms in Intertidal Mudflats

Author: Julie Gaubert-Boussarie, Soizic Prado, and Cédric Hubas
Subjects: microphytobenthos, biofilms, mudflats, metabolomics, diatoms, Science, General. Including nature conservation, geographical distribution, QH1-199.5
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.
Published: 2020
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5. Bacterial–Fungal Interactions in the Kelp Endomicrobiota Drive Autoinducer-2 Quorum Sensing

Author: Anne Tourneroche, Raphaël Lami, Cédric Hubas, Elodie Blanchet, Marine Vallet, Karine Escoubeyrou, Alain Paris, and Soizic Prado
Subjects: quorum sensing (QS), AI-2, bacterial–fungal interaction, kelp microbiota, algal holobiont, Microbiology, QR1-502
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.
Published: 2019
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6. Laminariales Host Does Impact Lipid Temperature Trajectories of the Fungal Endophyte Paradendryphiella salina (Sutherland.)

Author: Marine Vallet, Tarik Meziane, Najet Thiney, Soizic Prado, and Cédric Hubas
Subjects: fatty acids, fungal endophytes, laminariales, Paradendryphiella salina, Biology (General), QH301-705.5
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.
Published: 2020
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7. Subtidal Microphytobenthos: A Secret Garden Stimulated by the Engineer Species Crepidula fornicata

Author: Thibault Androuin, Lubos Polerecky, Priscilla Decottignies, Stanislas F. Dubois, Christine Dupuy, Cédric Hubas, Bruno Jesus, Erwan Le Gall, Martin P. Marzloff, and Antoine Carlier
Subjects: Crepidula fornicata, engineer species, subtidal microphytobenthos, fertilization, hyperspectral imaging, Science, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract: The slipper limpet Crepidula fornicata is an emblematic invasive species along the northeast Atlantic coast. This gregarious gastropod lives in stacks of several individuals and forms extended beds in shallow subtidal areas. The effects of this engineer species on the colonized habitat can be physical (e.g., presence of hard-shell substrates with uneven topography) or biological (e.g., nutrient enrichment by direct excretion or via biodeposition). We hypothesized that through biological activity, nutrient fluxes at the sediment-water interface are enhanced, leading to stimulated primary productivity by microphytobenthos (MPB) associated with Crepidula beds. To test this fertilization hypothesis, we conducted a 10-day mesocosm experiment using C. fornicata (live and dead) placed on top of sieved and homogenized sediment collected in situ. We used hyperspectral imaging to non-invasively map the development of MPB biomass, and to assess the potential influence of C. fornicata and its spatial extent. Our results showed that live C. fornicata significantly promote MPB growth through both physical and biological effects, with the biological effect dominating over the pure physical one. The highest stimulation was observed on the shells, suggesting that dissolved metabolic products excreted by C. fornicata were likely the main factor stimulating MPB growth in our short-term experiment. Our findings provide first direct evidence that stimulation of MPB growth by the biological activity of larger benthic epifauna occurs not only in intertidal but also in shallow subtidal habitats. More research is needed to assess the contribution of this fertilization effect to the trophic functioning of subtidal benthic systems.
Published: 2018
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8. A Nanoscale Study of Carbon and Nitrogen Fluxes in Mats of Purple Sulfur Bacteria: Implications for Carbon Cycling at the Surface of Coastal Sediments

Author: Cédric Hubas, Dominique Boeuf, Bruno Jesus, Najet Thiney, Yann Bozec, and Christian Jeanthon
Subjects: microbial mats, Chromatiaceae, Thiohalocapsa, stable isotope probing (SIP), NanoSIMS, compound specific isotope analysis (CSIA), Microbiology, QR1-502
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-labeled 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.
Published: 2017
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9. Proliferation of purple sulphur bacteria at the sediment surface affects intertidal mat diversity and functionality.

Author: Cédric Hubas, Bruno Jesus, Mickael Ruivo, Tarik Meziane, Najet Thiney, Dominique Davoult, Nicolas Spilmont, David M Paterson, and Christian Jeanthon
Subjects: Medicine, Science
Abstract: There is a relative absence of studies dealing with mats of purple sulphur bacteria in the intertidal zone. These bacteria display an array of metabolic pathways that allow them to disperse and develop under a wide variety of conditions, making these mats important in terms of ecosystem processes and functions. Mass blooms of purple sulphur bacteria develop during summer on sediments in the intertidal zone especially on macroalgal deposits. The microbial composition of different types of mats differentially affected by the development of purple sulphur bacteria was examined, at low tide, using a set of biochemical markers (fatty acids, pigments) and composition was assessed against their influence on ecosystem functions (sediment cohesiveness, CO2 fixation). We demonstrated that proliferation of purple sulphur bacteria has a major impact on intertidal mats diversity and functions. Indeed, assemblages dominated by purple sulphur bacteria (Chromatiaceae) were efficient exopolymer producers and their biostabilisation potential was significant. In addition, the massive growth of purple sulphur bacteria resulted in a net CO2 degassing whereas diatom dominated biofilms represented a net CO2 sink.
Published: 2013
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10. Trophic structure and mercury biomagnification in tropical fish assemblages, Iténez River, Bolivia.

Author: Marc Pouilly, Danny Rejas, Tamara Pérez, Jean-Louis Duprey, Carlos I Molina, Cédric Hubas, and Jean-Remy D Guimarães
Subjects: Medicine, Science
Abstract: We examined mercury concentrations in three fish assemblages to estimate biomagnification rates in the Iténez main river, affected by anthropogenic activities, and two unperturbed rivers from the Iténez basin, Bolivian Amazon. Rivers presented low to moderate water mercury concentrations (from 1.25 ng L(-1) to 2.96 ng L(-1)) and natural differences in terms of sediment load. Mercury biomagnification rates were confronted to trophic structure depicted by carbon and nitrogen stable isotopes composition (δ(15)N; δ(13)C) of primary trophic sources, invertebrates and fishes. Results showed a slight fish contamination in the Iténez River compared to the unperturbed rivers, with higher mercury concentrations in piscivore species (0.15 µg g(-1) vs. 0.11 µg g(-1) in the unperturbed rivers) and a higher biomagnification rate. Trophic structure analysis showed that the higher biomagnification rate in the Iténez River could not be attributed to a longer food chain. Nevertheless, it revealed for the Iténez River a higher contribution of periphyton to the diet of the primary consumers fish species; and more negative δ(13)C values for primary trophic sources, invertebrates and fishes that could indicate a higher contribution of methanotrophic bacteria. These two factors may enhance methylation and methyl mercury transfer in the food web and thus, alternatively or complementarily to the impact of the anthropogenic activities, may explain mercury differences observed in fishes from the Iténez River in comparison to the two other rivers.
Published: 2013
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11. Impairment of the bacterial biofilm stability by triclosan.

Author: Helen V Lubarsky, Sabine U Gerbersdorf, Cédric Hubas, Sebastian Behrens, Francesco Ricciardi, and David M Paterson
Subjects: Medicine, Science
Abstract: The accumulation of the widely-used antibacterial and antifungal compound triclosan (TCS) in freshwaters raises concerns about the impact of this harmful chemical on the biofilms that are the dominant life style of microorganisms in aquatic systems. However, investigations to-date rarely go beyond effects at the cellular, physiological or morphological level. The present paper focuses on bacterial biofilms addressing the possible chemical impairment of their functionality, while also examining their substratum stabilization potential as one example of an important ecosystem service. The development of a bacterial assemblage of natural composition--isolated from sediments of the Eden Estuary (Scotland, UK)--on non-cohesive glass beads (
Published: 2012
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12. The stabilisation potential of individual and mixed assemblages of natural bacteria and microalgae.

Author: Helen V Lubarsky, Cédric Hubas, Melanie Chocholek, Fredrik Larson, Werner Manz, David M Paterson, and Sabine U Gerbersdorf
Subjects: Medicine, Science
Abstract: It is recognized that microorganisms inhabiting natural sediments significantly mediate the erosive response of the bed ("ecosystem engineers") through the secretion of naturally adhesive organic material (EPS: extracellular polymeric substances). However, little is known about the individual engineering capability of the main biofilm components (heterotrophic bacteria and autotrophic microalgae) in terms of their individual contribution to the EPS pool and their relative functional contribution to substratum stabilisation. This paper investigates the engineering effects on a non-cohesive test bed as the surface was colonised by natural benthic assemblages (prokaryotic, eukaryotic and mixed cultures) of bacteria and microalgae. MagPI (Magnetic Particle Induction) and CSM (Cohesive Strength Meter) respectively determined the adhesive capacity and the cohesive strength of the culture surface. Stabilisation was significantly higher for the bacterial assemblages (up to a factor of 2) than for axenic microalgal assemblages. The EPS concentration and the EPS composition (carbohydrates and proteins) were both important in determining stabilisation. The peak of engineering effect was significantly greater in the mixed assemblage as compared to the bacterial (x 1.2) and axenic diatom (x 1.7) cultures. The possibility of synergistic effects between the bacterial and algal cultures in terms of stability was examined and rejected although the concentration of EPS did show a synergistic elevation in mixed culture. The rapid development and overall stabilisation potential of the various assemblages was impressive (x 7.5 and ×9.5, for MagPI and CSM, respectively, as compared to controls). We confirmed the important role of heterotrophic bacteria in "biostabilisation" and highlighted the interactions between autotrophic and heterotrophic biofilm consortia. This information contributes to the conceptual understanding of the microbial sediment engineering that represents an important ecosystem function and service in aquatic habitats.
Published: 2010
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13. Analyse par imagerie hyperspectrale sous-marine : Révéler la variabilité de l'efficacité des récifs artificiels

Author: Elisabeth RIERA, Cédric Hubas, Mischa Ungerman, Guy Rigot, Alexis Pey, Patrice Francour, Francesca Rossi, Ecology and Conservation Science for Sustainable Seas (ECOSEAS), Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Muséum national d'Histoire naturelle (MNHN), Auteur indépendant, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Stazione Zoologica Anton Dohrn (SZN), and Institut de l'Océan, Sorbonne Université
Subjects: [SDE]Environmental Sciences, Imagerie Hyperspectrale sous marine, Récifs artificiels
Abstract: Poster illustrant l'usage de l'imagerie hyperspectral sous marine pour évaluerl'efficacité des récifs artificiels à imiter le signal photosynthétique des assemblages des habitats naturels adjacents. Etude de cas effectué en Principauté de Monaco en 2020.
Published: 2023
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14. Sex-specific seasonal variations in the fatty acid and carotenoid composition of sea cucumber gonads and implications for aquaculture

Author: Frank David, Gwen Herault, Nadia Ameziane, Tarik Meziane, Aïcha Badou, and Cédric Hubas
Subjects: Ecology, Aquatic Science, Ecology, Evolution, Behavior and Systematics
Published: 2023
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15. Meiofauna and Biofilms—The Slimy Universe

Author: Nabil Majdi, Cédric Hubas, Tom Moens, and Daniela Zeppilli
Published: 2023
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16. Identification of microbial exopolymer producers in sandy and muddy intertidal sediments by compound-specific isotope analysis

Author: Cédric Hubas, Julie Gaubert-Boussarie, An-Sofie D’Hondt, Bruno Jesus, Dominique Lamy, Vona Meleder, Antoine Prins, Philippe Rosa, Willem Stock, and Koen Sabbe
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 production and degradation are supported by very different communities in muddy and sandy sediments and that EPS sources are more diverse in the sand. In mud, bound EPS are mainly derived from diatoms, while colloidal EPS are the result of degradation of bound exopolymers by certain specialised bacteria. In sand, bound EPS are rather of bacterial or cyanobacterial origin and diatoms contribute mainly to colloidal EPS. These differences are thought to be related to differences in the functioning of the epipelic and epipsammic communities and in particular to the use of EPS either for motility or for cell attachment purposes.
Published: 2022
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17. Upstream/downstream food quality differences in a Caribbean Island River

Author: Etienne Bezault, Alexandre Bec, Lou Frotté, Cédric Hubas, Sébastien Cordonnier, Fanny Perrière, Dominique Monti, Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Université des Antilles (Pôle Guadeloupe), Université des Antilles (UA), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Muséum national d'Histoire naturelle (MNHN), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: 0106 biological sciences, Limiting factor, Aquatic Science, 01 natural sciences, 03 medical and health sciences, Organic matter, Ecosystem, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, health care economics and organizations, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Upstream (petroleum industry), chemistry.chemical_classification, 0303 health sciences, Fish migration, Caribbean island, Ecology, 010604 marine biology & hydrobiology, Shrimp, chemistry, 13. Climate action, Environmental science, lipids (amino acids, peptides, and proteins), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Food quality
Abstract: International audience; Caribbean rivers are inhabited by native macrofauna with a diadromous life cycle. The factors influencing the upstream migration of diadromous species are not well understood. Suggested primary factors include species density, habitat suitability and food availability. We hypothesized that food quality could be a key parameter in the upstream migration of macrocrustaceans. We sampled the main shrimp species and their potential food sources along an altitudinal gradient in the Grand Carbet River of Guadeloupe. Lipid analyses of the different food items reveal that biofilm and drifting organic matter are main sources of eicosapentaenoic acid (EPA). Biofilm is richer in EPA upstream, while drifting material is richer in EPA downstream. These opposed altitudinal gradients are reflected in shrimp lipids depending on whether they feed on biofilm or drifting organic matter. In addition, low EPA levels in shrimp suggest that dietary EPA could be a limiting factor in this system and that this differential altitudinal distribution of EPA could influence shrimp settlement.
Published: 2021
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18. The metabolites of light: untargeted metabolomic approaches bring new clues to understand light-driven adaptation of intertidal mudflat biofilm

Author: Cédric Hubas and Caroline Doose
Abstract: The microphytobenthos (MPB) is a microbial community of primary producers playing a key role in coastal ecosystem functioning. The intertidal mudflats are subject to challenging variations of irradiance, forcing the micro-organisms to develop photoprotective mechanisms. 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 a lot of 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 exposures. On the one hand, the production of FAs from bacterial origin corresponding to good photosynthesis state of MPB under low light (LL) and medium light (ML). On the other hand, alka(e)nes and a fatty alcohol were produced under light-induced stress triggered by high light (HL). The physiological and ecological roles of these compounds are poorly described in literature. This study showed that they seem to play important unexplored roles in light-induced stress adaptation 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 adaptation to light.
Published: 2022
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19. Functional kleptoplasts intermediate incorporation of carbon and nitrogen in cells of the Sacoglossa sea slug Elysia viridis

Author: Cédric Hubas, Michael Kühl, Stéphane Escrig, Sónia Cruz, Sofie L. Jakobsen, Bruno Jesus, Najet Thiney, Anders Meibom, Paulo Cartaxana, Ricardo Calado, Charlotte LeKieffre, Centre for Environmental and Marine Studies [Aveiro] (CESAM), Universidade de Aveiro, Laboratoire de Planétologie et Géodynamique - Angers (LPG-ANGERS), Laboratoire de Planétologie et Géodynamique [UMR 6112] (LPG), Université d'Angers (UA)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Angers (UA)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), University of Copenhagen = Københavns Universitet (KU), Ecole Polytechnique Fédérale de Lausanne (EPFL), Mer, molécules et santé EA 2160 (MMS), Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN), FEDER, through COMPETE2020 - Programa Operacional Competitividade e InternacionalizacAo (POCI), Programa Operacional Regional (POR) de Lisboa national funds (OE), through FCT/MCTES PTDC/BIA-ANM/4622/2014POCI-01-0145-FEDER-016754CESAM through national funds (OE) via FCT/MCTES UIDB/50017/2020+UIDP/50017/2020Sapere-Aude advanced grant from the Independent Research Fund Denmark DFF-8021-00308BFCT/MCTES through Programa Investigador IF/00899/2014Portuguese Foundation for Science and TechnologyEuropean Commission, Muséum national d'Histoire naturelle (MNHN), University of Copenhagen = Københavns Universitet (UCPH), Institut Des Substances et Organismes de la Mer - UR 2160 (ISOMER), Nantes Université - UFR des Sciences Pharmaceutiques et Biologiques (Nantes Univ - UFR Pharmacie), Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, and Nantes Université (Nantes Univ)
Subjects: 0106 biological sciences, 0301 basic medicine, CODIUM-FRAGILE, Physiology, lcsh:Medicine, 01 natural sciences, CHLOROPLASTS, lcsh:Science, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Multidisciplinary, Ecology, opisthobranchia, [SDV.BA]Life Sciences [q-bio]/Animal biology, Fatty Acids, ASSOCIATION, Chloroplast, Biochemistry, chloroplasts, FATTY-ACIDS, Kleptoplasty, Elysia viridis, Nitrogen, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, METABOLISM, Biology, Photosynthesis, 010603 evolutionary biology, GASTROPODA, Article, 03 medical and health sciences, Animals, codium-fragile, [CHIM]Chemical Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, BIOSYNTHESIS, OPISTHOBRANCHIA, photosynthesis, Sacoglossa, PHOTOSYNTHESIS, lcsh:R, association, ORGANELLES, Assimilation (biology), Marine invertebrates, fatty-acids, biology.organism_classification, Carbon, Sea slug, 030104 developmental biology, organelles, gastropoda, lcsh:Q, biosynthesis, Plant sciences, Zoology, metabolism
Abstract: Some sacoglossan sea slugs incorporate intracellular functional algal chloroplasts, a process termed kleptoplasty. “Stolen” 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.
Published: 2020
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20. Mangrove microbiota along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America): Drivers and potential bioindicators

Author: Guillaume Dirberg, Tony Robinet, Lars-Eric Heimbürger-Boavida, Ronan Jézéquel, Amonda El Houssainy, Maud Fiard, Romain Walcker, Cécile Militon, Cédric Hubas, Léa Sylvi, Isabelle Bihannic, Franck Gilbert, Philippe Cuny, Emma Michaud, Dominique Lamy, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Centre de documentation de recherche et d'expérimentations sur les pollutions accidentelles des eaux (Cedre), Cedre, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Aix-Marseille Université - AMU (FRANCE), Centre de Documentation, de Recherche et d'Expérimentations sur les pollutions accidentelles des eaux - CEDRE (FRANCE), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut Français de Recherche pour l'Exploitation de la MER - IFREMER (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement - INRAE (FRANCE), Institut de Recherche pour le Développement - IRD (FRANCE), Université Paris 1 Panthéon-Sorbonne (FRANCE), Sorbonne Université (FRANCE), Université de Bretagne Occidentale - UBO (FRANCE), Université Paris Est Créteil Val de Marne - UPEC (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Université de Caen Basse-Normandie (FRANCE), Museum National d'Histoire Naturelle - MNHN (FRANCE), Université de Toulon - UTLN (FRANCE), Université des Antilles et de la Guyane (FRANCE), Université de Paris - U-Paris (FRANCE), Institut d'Ecologie et des Sciences de l'Environnement de Paris - IEES (Paris, France), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Muséum national d'Histoire naturelle (MNHN), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP)
Subjects: Geologic Sediments, Environmental Engineering, [SDE.MCG]Environmental Sciences/Global Changes, Biodiversité et Ecologie, 03 medical and health sciences, Dieldrin, chemistry.chemical_compound, Estuarine mangrove sediments, PAHs contamination, Humans, Environmental Chemistry, Organic matter, 14. Life underwater, Waste Management and Disposal, 030304 developmental biology, chemistry.chemical_classification, Ecologie, Environnement, 0303 health sciences, geography, geography.geographical_feature_category, Environmental Biomarkers, biology, Planctomycetes, 030306 microbiology, Ecology, Anthropogenic Effects, Microbiota, Organochlorine contaminants, Estuary, 15. Life on land, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, Pollution, 6. Clean water, French Guiana, chemistry, 13. Climate action, Wetlands, Low organic matter enrichment, Desulfobacteraceae, Environmental science, Proteobacteria, Mangrove, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Estuaries, Bioindicator, Acidobacteria
Abstract: International audience; The microbial communities inhabiting the Atlantic-East Pacific (AEP) mangroves have been poorly studied, and mostly comprise chronically polluted mangroves. In this study, we characterized changes in the structure and diversity of microbial communities of mangroves along the urban-to-rural gradient of the Cayenne estuary (French Guiana, South America) that experience low human impact. The microbial communities were assigned into 50 phyla. Proteobacteria, Chloroflexi, Acidobacteria, Bacteroidetes, and Planctomycetes were the most abundant taxa. The environmental determinants found to significantly correlated to the microbial communities at these mangroves were granulometry, dieldrin concentration, pH, and total carbon (TC) content. Furthermore, a precise analysis of the sediment highlights the existence of three types of anthropogenic pressure among the stations: (i) organic matter (OM) enrichment due to the proximity to the city and its wastewater treatment plant, (ii) dieldrin contamination, and (iii) naphthalene contamination. These forms of weak anthropogenic pressure seemed to impact the bacterial population size and microbial assemblages. A decrease in Bathyarchaeota, “Candidatus Nitrosopumilus”, and Nitrospira genera was observed in mangroves subjected to OM enrichment. Mangroves polluted with organic contaminants were enriched in Desulfobacteraceae, Desulfarculaceae, and Acanthopleuribacteraceae (with dieldrin or polychlorobiphenyl contamination), and Chitinophagaceae and Geobacteraceae (with naphthalene contamination). These findings provide insights into the main environmental factors shaping microbial communities of mangroves in the AEP that experience low human impact and allow for the identification of several potential microbial bioindicators of weak anthropogenic pressure.
Published: 2022
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21. Climate change influences chlorophylls and bacteriochlorophylls metabolism in hypersaline microbial mat

Author: M.A. Perdrau, Cédric Hubas, C. Mazière, M. Bodo, Christine Dupuy, Robert Duran, Cristiana Cravo-Laureau, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: 0106 biological sciences, Chlorophyll, Chlorophyll a, Environmental Engineering, Climate Change, [SDE.MCG]Environmental Sciences/Global Changes, Chlorosome, 01 natural sciences, Hypersaline microbial mats, 03 medical and health sciences, chemistry.chemical_compound, Phototrophic communities, Environmental Chemistry, Humans, Seawater, Microbial mat, Waste Management and Disposal, Bacteriochlorophylls, 030304 developmental biology, 0303 health sciences, Phototroph, Chlorophyll derivatives, 010604 marine biology & hydrobiology, Chlorophyll A, Ocean acidification, Hydrogen-Ion Concentration, Pollution, Anoxygenic photosynthesis, Mesocosms, chemistry, 13. Climate action, Environmental chemistry, [SDE]Environmental Sciences, Bacteriochlorophyll, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; This study aimed to determine the effect of the climatic change on the phototrophic communities of hypersaline microbial mats. Ocean acidification and warming were simulated alone and together on microbial mats placed into mesocosms. As expected, the temperature in the warming treatments increased by 4 °C from the initial temperature. Surprisingly, no significance difference was observed between the water pH of the different treatments despite of a decrease of 0.4 unit pH in the water reserves of acidification treatments. The salinity increased on the warming treatments and the dissolved oxygen concentration increased and was higher on the acidification treatments. A total of 37 pigments were identified belonging to chlorophylls, carotenes and xanthophylls families. The higher abundance of unknown chlorophyll molecules called chlorophyll derivatives was observed in the acidification alone treatment with a decrease in chlorophyll a abundance. This change in pigmentary composition was accompanied by a higher production of bound extracellular carbohydrates but didn't affect the photosynthetic efficiency of the microbial mats. A careful analysis of the absorption properties of these molecules indicated that these chlorophyll derivatives were likely bacteriochlorophyll c contained in the chlorosomes of green anoxygenic phototroph bacteria. Two hypotheses can be drawn from these results: 1/ the phototrophic communities of the microbial mats were modified under acidification treatment leading to a higher relative abundance of green anoxygenic bacteria, or 2/ the highest availability of CO2 in the environment has led to a shift in the metabolism of green anoxygenic bacteria being more competitive than other phototrophs.
Published: 2022
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22. The response of microphytobenthos to physical disturbance, herbicide, and titanium dioxide nanoparticle exposure

Author: James E.V. Rimmer, Cédric Hubas, Adam J. Wyness, Bruno Jesus, Morgan Hartley, Andrew J. Blight, Antoine Prins, David M. Paterson, European Commission, John Templeton Foundation, NERC, University of St Andrews. School of Biology, University of St Andrews. Sediment Ecology Research Group, University of St Andrews. Scottish Oceans Institute, University of St Andrews. Coastal Resources Management Group, University of St Andrews. Marine Alliance for Science & Technology Scotland, University of St Andrews. St Andrews Sustainability Institute, University of Saint Andrews, Scottish Oceans Institute [University of St Andrews] (SOI), School of Biology [University of St Andrews], University of St Andrews [Scotland]-University of St Andrews [Scotland], Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Muséum national d'Histoire naturelle (MNHN), Scottish Association for Marine Science (SAMS), Nantes Université (Nantes Univ), Institut Des Substances et Organismes de la Mer - UR 2160 (ISOMER), Nantes Université - UFR des Sciences Pharmaceutiques et Biologiques (Nantes Univ - UFR Pharmacie), Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, and European Project: 227799,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2008-1,ASSEMBLE(2009)
Subjects: Diatoms, MCC, Glyphosate, Herbicides, [SDE.MCG]Environmental Sciences/Global Changes, QH301 Biology, Microphytobenthos, NDAS, Aquatic Science, Oceanography, Pollution, QH301, Stressor, Biofilms, Titanium dioxide, Nanoparticles, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Funding: The research leading to these results received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 730984, ASSEMBLE Plus project. AJW was funded by the John Templeton Grant 60501, “Putting the Extended Evolutionary Synthesis to the Test”. DMP and AJB were supported by the NERC Blue-coast award (NE/N016009/1). 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 – such as duration and exposure sequence – 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. Publisher PDF
Published: 2022
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23. Photosynthesis from stolen chloroplasts can support sea slug reproductive fitness

Author: Ricardo Calado, Charlotte LeKieffre, Gonçalo Calado, Rosário Domingues, Sónia Cruz, Bruno Jesus, Paulo Cartaxana, Felisa Rey, Stéphane Escrig, Diana Lopes, Anders Meibom, Michael Kühl, Jorge E. Spangenberg, Cédric Hubas, MARE - Centro de Ciências do Mar e do Ambiente, Universidade de Aveiro, Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Muséum national d'Histoire naturelle (MNHN), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Université de Lausanne = University of Lausanne (UNIL), Ecole Polytechnique Fédérale de Lausanne (EPFL), Nantes Université (Nantes Univ), Lusófona University [Lisbon], Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), and University of Copenhagen = Københavns Universitet (UCPH)
Subjects: 0106 biological sciences, Chloroplasts, Gastropoda, Opisthobranchia, elysia-viridis, 01 natural sciences, kleptoplast, fatty acid, reproduction, Sacoglossa, kleptoplast, Environmental Science(all), GONAD, Photosynthesis, Research Articles, General Environmental Science, 0303 health sciences, Agricultural and Biological Sciences(all), Ecology, opisthobranchia, acquisition, ASSOCIATION, General Medicine, kleptoplasts, Sacoglossa, Chloroplast, [SDE]Environmental Sciences, SURVIVAL, FATTY-ACIDS, General Agricultural and Biological Sciences, animal structures, ELYSIA-VIRIDIS, Elysia viridis, Biology, KLEPTOPLASTS, survival, gonad, 010603 evolutionary biology, General Biochemistry, Genetics and Molecular Biology, reproduction, 03 medical and health sciences, Immunology and Microbiology(all), Animals, 14. Life underwater, OPISTHOBRANCHIA, 030304 developmental biology, General Immunology and Microbiology, Reproductive success, ACQUISITION, Biochemistry, Genetics and Molecular Biology(all), Host (biology), fungi, association, fatty-acids, biology.organism_classification, Sea slug, Genetic Fitness, fatty acid
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 ‘snacks’, others advocate that they enhance the overall fitness of sea slugs much more profoundly. Our analysis shows light-dependent incorporation of 13 C and 15 N 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.
Published: 2021
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24. Towards a better understanding of the effects of self-shading on Fucus serratus populations

Author: Cédric Hubas
Subjects: Community and Home Care, biology, Fucus serratus, Ecology, Environmental science, Shading, biology.organism_classification
Published: 2021
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25. Photosynthesis from stolen chloroplasts increases sea slug reproductive fitness

Author: Rosário Domingues, Anders Meibom, Bruno Jesus, Stéphane Escrig, Sónia Cruz, Ricardo Calado, Gonçalo Calado, Paulo Cartaxana, Felisa Rey, Diana Lopes, Michael Kühl, Jorge E. Spangenberg, Cédric Hubas, and Charlotte LeKieffre
Subjects: Chloroplast, animal structures, Algae, biology, Reproductive success, Host (biology), fungi, Zoology, Elysia timida, Photosynthesis, biology.organism_classification, Fecundity, Sea slug
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 ‘snacks’, others advocate that they enhance the overall fitness of sea slugs much more profoundly. Our analysis show 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 suppressing kleptoplast photosynthesis. The present study provides the first thorough experimental evidence 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. Teaser Sea slugs incorporate functional chloroplasts from algae and use products of photosynthesis to maximize reproductive output.
Published: 2021
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26. Environmental heterogeneity drives phytoplankton community assembly patterns in a tropical riverine system

Author: Cédric Hubas and Eric Goberville
Subjects: Community and Home Care, Geography, biology, Caio, Ecology, Phytoplankton, biology.organism_classification, Functional similarity
Abstract: A recommendation of: Caio Graco-Roza, Angel M. Segura, Carla Kruk, Patricia Domingos, Janne Soininen, Marcelo M. Marinho Clumpy coexistence in phytoplankton: The role of functional similarity in community assembly 10.1101/869966
Published: 2021
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27. First Assessment of the Benthic Meiofauna Sensitivity to Low Human-Impacted Mangroves in French Guiana

Author: Gilbert Franck, Claire Michelet, Guillaume Dirberg, Amonda El Houssainy, Isabelle Bihannic, Elisa Baldrighi, Emma Michaud, Baptiste Vivier, Romain Walcker, Cédric Hubas, Cécile Militon, Léa Sylvi, Aurélie Dufour, Justine Receveur, Ronan Jézéquel, Lars-Eric Heimbürger-Boavida, Daniela Zeppilli, Philippe Cuny, Dominique Lamy, Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Muséum national d'Histoire naturelle (MNHN), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Centre de documentation de recherche et d'expérimentations sur les pollutions accidentelles des eaux (Cedre), Cedre, ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), European Project: 1166-39417,FEDER, Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP)
Subjects: 0106 biological sciences, Meiobenthos, nematode, Biodiversité et Ecologie, Meiofauna, Biodiversity, Anthropogenic pressures, Biology, 010603 evolutionary biology, 01 natural sciences, Mangroves, Dominance (ecology), Ecosystem, 14. Life underwater, Trophic level, biodiversity, Nematode, Ecology, 010604 marine biology & hydrobiology, mangroves, Forestry, lcsh:QK900-989, 15. Life on land, South America, natural contamination, 13. Climate action, Benthic zone, meiofauna, Natural contamination, lcsh:Plant ecology, anthropogenic pressures, Mangrove, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bioindicator
Abstract: International audience; Bioindicators assess the mangroves ecological state according to the types of pressures but they differ with the ecosystem’s specificities. We investigated benthic meiofauna diversity and structure within the low human-impacted mangroves in French Guiana (South America) in response to sediment variables with various distances to the main city. Contaminant’s concentrations differed among the stations, but they remained below toxicity guidelines. Meiofauna structure (Foraminifera, Kinorhyncha, Nematoda) however varied accordingly. Nematode’s identification brought details on the sediment’s quality. The opportunistic genus Paraethmolaimus (Jensen, 1994) strongly correlated to the higher concentrations of Hg, Pb. Anoxic sediments were marked by organic enrichment in pesticides, PCB, and mangrove litter products and dominance of two tolerant genus, Terschellingia (de Man, 1888) and Spirinia (Gerlach, 1963). In each of these two stations, we found many Desmodora individuals (de Man, 1889) with the presence of epibionts highlighting the nematodes decreased fitness and defenses. Oxic sediments without contaminants were distinguished by the sensitive genera Pseudocella (Filipjev, 1927) and a higher diversity of trophic groups. Our results suggested a nematodes sensitivity to low contaminants concentrations. Further investigations at different spatio-temporal scales and levels of deterioration, would be necessary to use of this group as bioindicator of the mangroves’ ecological status; Les bioindicateurs évaluent l'état écologique des mangroves en fonction des types de pressions mais ils diffèrent selon les spécificités de l'écosystème. Nous avons étudié la diversité et la structure de la méiofaune benthique dans des mangroves à faible impact humain en Guyane française (Amérique du Sud) en réponse à des variables sédimentaires et à différentes distances de la ville principale. Les concentrations de contaminants différaient selon les stations, mais elles restaient inférieures aux recommandations de toxicité. La structure de la méiofaune (Foraminifera, Kinorhyncha, Nematoda) a cependant varié en conséquence. L'identification des nématodes a apporté des détails sur la qualité des sédiments. Le genre opportuniste Paraethmolaimus (Jensen, 1994) était fortement corrélé aux concentrations plus élevées de Hg, Pb. Les sédiments anoxiques étaient marqués par un enrichissement organique en pesticides, PCB, et produits de la litière de mangrove et par la dominance de deux genres tolérants, Terschellingia (de Man, 1888) et Spirinia (Gerlach, 1963). Dans chacune de ces deux stations, nous avons trouvé de nombreux individus Desmodora (de Man, 1889) avec la présence d'épibiontes mettant en évidence la diminution de la fitness et des capacités de défense des nématodes. Les sédiments oxiques sans contaminants se distinguaient par la présence de genres sensibles Pseudocella (Filipjev, 1927) et une plus grande diversité de groupes trophiques. Nos résultats suggèrent une sensibilité des nématodes à de faibles concentrations de contaminants. Des études supplémentaires à différentes échelles spatio-temporelles et à différents niveaux de détérioration seraient nécessaires pour utiliser ce groupe comme bioindicateur de l'état écologique des mangroves.
Published: 2021
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28. Chlordecone-contaminated epilithic biofilms show increased adsorption capacities

Author: Cédric Hubas, Dominique Monti, Jean-Michel Mortillaro, Sylvie Augagneur, Anne Carbon, Robert Duran, Solange Karama, Tarik Meziane, Patrick Pardon, Théo Risser, Nathalie Tapie, Najet Thiney, Hélène Budzinski, Béatrice Lauga, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Muséum national d'Histoire naturelle (MNHN), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Université des Antilles (Pôle Guadeloupe), Université des Antilles (UA), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Département Performances des systèmes de production et de transformation tropicaux (Cirad-PERSYST), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Université de Pau et des Pays de l'Adour (UPPA), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Earth and Planetary Observation Centre (EPOC), and University of Stirling
Subjects: congenital, hereditary, and neonatal diseases and abnormalities, Insecticides, Environmental Engineering, Lipophilic pigments, Biochimie, Epilithic biofilms, Monosaccharide, Microbial communities, Film comestible, Pollution par l'agriculture, Extracellular polymeric substances, Contamination, T-RFLP, Animals, Environmental Chemistry, Marqueur génétique, Fatty acids, Waste Management and Disposal, Ecosystem, Caribbean, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Monosaccharides, Composition chimique, [SDE.ES]Environmental Sciences/Environmental and Society, Pollution, U50 - Sciences physiques et chimie, respiratory tract diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Chlordecone, Biofilms, Adsorption, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Chlordécone, P02 - Pollution
Abstract: International audience; The rivers of Guadeloupe and Martinique (French West Indies) show high levels of chlordecone (CLD) contamination. This persistent molecule has a dramatic impact on both aquatic ecosystems and human health. In these rivers, epilithic biofilms are the main endogenous primary producers and represent a central food source for fish and crustaceans. Recently, their viscoelastic properties have been shown to be effective in bio-assessing pollution in tropical environments. As these properties are closely related to the biochemical composition of the biofilms, biochemical (fatty acids, pigments, extracellular polymeric substances (EPS) monosaccharides) and molecular markers (T-RFLP fingerprints of bacteria, archaea and eukaryotes) were investigated. Strong links between CLD pollution and both biofilm biochemistry and microbial community composition were found. In particular, high levels of CLD were linked with modified exo-polysaccharides corresponding to carbohydrates with enhanced adsorption and adhesion properties. The observed change probably resulted from a preferential interaction between CLD and sugars and/or a differential microbial secretion of EPS in response to the pollutant. These changes were expected to impact viscoelastic properties of epilithic biofilms highlighting the effect of CLD pollution on biofilm EPS matrix. They also suggested that microorganisms implement a CLD scavenging strategy, providing new insights on the role of EPS in the adaptation of microorganisms to CLD-polluted environments.
Published: 2022
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29. Physical properties of epilithic river biofilm as a new lead to perform pollution bioassessments in overseas territories

Author: Estelle Lefrancois, Alexandra Jestin, Cédric Hubas, Jean-Louis Mansot, Théo Risser, Pascal-Jean Lopez, Hélène Budzinski, Dominique Monti, Laurence Romana, Philippe Keith, Olivier Gros, Béatrice Lauga, Xavier Lourenço, Nathalie Tapie, Alexandre Haouisée, Farid Begarin, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Centre Commun de Caractérisation des Matériaux des Antilles et de la Guyane (C3MAG), Université des Antilles (UA), Groupe de Technologie des Surfaces et Interfaces (GTSI), ECO in-EAU, Fonctionnement agroécologique et performances des systèmes de cultures horticoles (UPR HORTSYS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Université de Pau et des Pays de l'Adour (UPPA), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Pau et des Pays de l'Adour (UPPA), Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Groupe de Technologie des Surfaces et Interfaces [URp2_2] (GTSI), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and ANR-16-IDEX-0002,E2S,E2S(2016)
Subjects: 0106 biological sciences, 0301 basic medicine, Pollution, Science, media_common.quotation_subject, 030106 microbiology, 01 natural sciences, Freshwater ecosystem, Article, Environmental impact, 03 medical and health sciences, Lead (geology), Environmental impact assessment, 14. Life underwater, Environmental quality, media_common, Multidisciplinary, Ecology, 010604 marine biology & hydrobiology, Biofilm, 15. Life on land, Contamination, Tropical ecology, 13. Climate action, [SDE]Environmental Sciences, Medicine, Environmental science
Abstract: International audience; 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. Out of the 11,435 French water bodies analysed for quality compliance according to regulations imposed by European legislation, 10% are located between the tropics and the equator, thousands of kilometres away from European shores 1. In the outermost tropical territories, climatic characteristics often result in highly turbulent tropical streams 2 that support simplified ecosystems with very few primary producers. Due to high river flow, perennial phytoplankton, zooplankton and macroalgae are scarce or missing and the epilithic biofilm deserves here, even more than elsewhere, the comparison with a real productive and contributive "microbial skin" 3. The epilithic biofilm is the only endogenous long-lasting primary producer that grows on submersed river stones and is largely exploited as a food source by all diadromous fish or crustaceans 4,5. In these countries, the simplified food webs and the massive flows of post-larvae and juveniles regularly re-entering the rivers and migrating
Published: 2020
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30. Food sources, digestive efficiency and resource allocation in the sea cucumber Holothuria forskali (Echinodermata: Holothuroidea): Insights from pigments and fatty acids

Author: Hélène Laguerre, Gwen Herault, Cédric Hubas, Théo Bordelet, Frank David, Nadia Ameziane, Aicha Badou, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biotechnologie et Chimie Marine (LBCM), Laboratoire de Biotechnologie et Chimie Marines (LBCM), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Muséum national d'Histoire naturelle (MNHN), and Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, 0303 health sciences, Holothuria forskali, biology, 010604 marine biology & hydrobiology, Aquatic Science, biology.organism_classification, 01 natural sciences, 03 medical and health sciences, Sea cucumber, Botany, [SDE]Environmental Sciences, Resource allocation, 14. Life underwater, 030304 developmental biology
Abstract: International audience; 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 “natural population”‐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 tissues (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 upgrading 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.
Published: 2020
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31. Laminariales host does impact lipid temperature trajectories of the fungal endophyte Paradendryphiella salina (Sutherland.)

Author: Cédric Hubas, Soizic Prado, Tarik Meziane, Marine Vallet, Najet Thiney, Muséum national d'Histoire naturelle (MNHN), Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), and Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN)
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], [SDE.MCG]Environmental Sciences/Global Changes, Kelp, Pharmaceutical Science, Context (language use), Saccharina latissima, 01 natural sciences, fatty acids, Plant use of endophytic fungi in defense, 03 medical and health sciences, Algae, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Drug Discovery, Botany, Pharmacology, Toxicology and Pharmaceutics (miscellaneous), lcsh:QH301-705.5, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Paradendryphiella salina, 0303 health sciences, biology, laminariales, Host (biology), 010604 marine biology & hydrobiology, biology.organism_classification, Laminaria digitata, fungal endophytes, [SDE.ES]Environmental Sciences/Environmental and Society, Salinity, lcsh:Biology (General), [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
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.
Published: 2020
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32. Relationship between bacterial compartment and particulate organic matter (POM) in coastal systems: An assessment using fatty acids and stable isotopes

Author: Sophie Ferreira, Camilla Liénart, Laurence Costes, Pascal Conan, Tarik Meziane, Nicolas Savoye, Eric Maria, Sabrina Bichon, Karine Charlier, Cédric Hubas, Valérie David, Pierrick Barbier, Aurore Gueux, Hervé Derriennic, UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Laboratoire d'Océanographie Microbienne (LOMIC), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], Aquatic Science, Oceanography, French littoral, 01 natural sciences, Mixing models, Organic matter, 14. Life underwater, Fatty acids, POM dynamic, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, chemistry.chemical_classification, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Biomass (ecology), Primary producers, δ13C, Bacteria, 010604 marine biology & hydrobiology, δ15N, 15. Life on land, 6. Clean water, Food web, chemistry, 13. Climate action, Benthic zone, Environmental chemistry, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Surface water
Abstract: International audience; Particulate organic matter (POM) in coastal systems is a mixture of different organic matter (OM) sources originating from land and sea. Among sources, bacterial biomass plays a large role in OM processing and carbon recycling in the ocean and is often neglected as a source in common approaches. The present study proposes to use elemental and isotopic ratio of carbon and nitrogen (C:N, δ13C, δ15N) and fatty acids to investigate the relationship between bacteria and surface water POM composition of three systems with different characteristics (two marine and one estuarine) over an annual cycle. Overall, our results highlight a positive relationship between bacterial contribution and continental degraded or undergoing degradation POM for all the studied systems and an inverse relationship with pelagic primary producers. At multisystem scale, high bacterial contribution is linked to high proportion of refractory terrestrial material characterizing estuarine stations whereas in marine systems, the occurrence of bacteria is mainly linked to river POM. Over the annual cycle, bacterial markers are more abundant during the winter period characterized by larger river and/or benthic POM contribution. This seasonal pattern is mainly driven by changes in river flows and resuspension. This study highlights the importance of bacterial compartment as a component of coastal and estuarine POM. Even though these results remains semi-quantitative, similar studies in other types of systems can help to understand microbial role in OM dynamic and to better estimate bacterial source in carbon budgets and food web studies.
Published: 2020
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33. Trophic niche of the invasive gregarious species Crepidula fornicata , in relation to ontogenic changes

Author: Cédric Hubas, Thibault Androuin, Fabienne Le Grand, Gwendoline Lefebvre, Gauthier Schaal, Stanislas F. Dubois, Antoine Carlier, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Muséum national d'Histoire naturelle (MNHN), and Université de Brest (UBO)
Subjects: 0106 biological sciences, pigments, Zoology, stable isotopes, 010603 evolutionary biology, 01 natural sciences, fatty acids, Sedimentary organic matter, Organic matter, 14. Life underwater, Crepidula, Crepidula fornicata, Trophic level, chemistry.chemical_classification, Biomass (ecology), biology, Primary producers, 010604 marine biology & hydrobiology, ontogenic shift, Bay of Brest, Pelagic zone, biology.organism_classification, trophic niche, chemistry, Benthic zone, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: PCI Recommendation : Trophic niche of the invasive gregarious species Crepidula fornicata, in relation to ontogenic changesThibault Androuin, Stanislas F. Dubois, Cédric Hubas, Gwendoline Lefebvre, Fabienne Le Grand, Gauthier Schaal, Antoine Carlier(2021), bioRxiv, 2020.07.30.229021, ver. 4 peer-reviewed and recommended by Peer Community In Ecology10.1101/2020.07.30.229021; International audience; The slipper limpet 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) suggests 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 discriminated well over the study 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 surface. Over the study 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. 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). However, 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 more likely from ontogenic physiological changes (e.g., differential growth rates, metabolic rate or gametogenesis) rather than diet discrepancies.
Published: 2020
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34. Biofilm monitoring as a tool to assess the efficiency of artificial reefs as substrates: Toward 3D printed reefs

Author: Dominique Lamy, Elisabeth Riera, Cédric Hubas, Patrice Francour, Christophe Goulard, Ecosystèmes Côtiers Marins et Réponses aux Stress (ECOMERS), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Molécules de Communication et Adaptation des Micro-organismes (MCAM), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Environmental Engineering, Bio-indicator, Biodiversity, Management, Monitoring, Policy and Law, 01 natural sciences, Extracellular polymeric substances, 03 medical and health sciences, Artificial reef substrates, 14. Life underwater, Reef, Nature and Landscape Conservation, Trophic level, geography, geography.geographical_feature_category, Ecology, Biofilm, 010604 marine biology & hydrobiology, Substrate (biology), 030104 developmental biology, Habitat destruction, Habitat, Photosynthetic pigments, Environmental science, Artificial reef, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; 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.
Published: 2018
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35. Diel Rhythm Does Not Shape the Vertical Distribution of Bacterial and Archaeal 16S rRNA Transcript Diversity in Intertidal Sediments: a Mesocosm Study

Author: Céline Lavergne, Mylène Hugoni, Hélène Agogué, Cédric Hubas, Christine Dupuy, and Didier Debroas
Subjects: DNA, Bacterial, 0301 basic medicine, Geologic Sediments, Chlorophyll a, Thaumarchaeota, Soil Science, Intertidal zone, Mesocosm, 03 medical and health sciences, chemistry.chemical_compound, RNA, Ribosomal, 16S, 14. Life underwater, Diel vertical migration, Ecosystem, Phylogeny, Ecology, Evolution, Behavior and Systematics, Bacteria, Ecology, biology, Sediment, Biodiversity, Sequence Analysis, DNA, biology.organism_classification, Archaea, DNA, Archaeal, 030104 developmental biology, chemistry, Benthic zone
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.
Published: 2017
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36. Physiological adjustments and transcriptome reprogramming are involved in the acclimation to salinity gradients in diatoms

Author: Pascal J. Lopez, Adrien Bussard, Fanny Coulpier, Evelyne Duvernois-Berthet, Erwan Corre, Gildas Le Corguillé, Pascal Claquin, Cédric Hubas, and Laurent Jourdren
Subjects: 0301 basic medicine, geography, geography.geographical_feature_category, Frustule, Estuary, Biology, biology.organism_classification, Microbiology, Acclimatization, Salinity, Transcriptome, 03 medical and health sciences, 030104 developmental biology, Diatom, Thalassiosira weissflogii, Botany, Seawater, 14. Life underwater, Ecology, Evolution, Behavior and Systematics
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 (LT) cultures. Whole transcriptome analyses revealed a down-regulation of nuclear and plastid encoded genes during the LT response and identified only a few regulated genes that were in common between the ST and LT 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.
Published: 2016
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37. Geographic variation in stable isotopic and fatty acid composition of anguilliform leptocephali and particulate organic matter in the South Pacific

Author: Tsuguo Otake, Mari Kuroki, Katsumi Tsukamoto, Michael J. Miller, Jean-Michel Mortillaro, Cédric Hubas, Tarik Meziane, Alexandre Carpentier, Jun Aoyama, Camilla Liénart, Shun Watanabe, Eric Feunteun, Christine Dupuy, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Station marine Dinard, Centre National de la Recherche Scientifique (CNRS), University of Tokyo (UTokyo), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), and Biodiversité et gestion des territoires EA 7316
Subjects: L51 - Physiologie animale - Nutrition, 0106 biological sciences, Azote, [SDV]Life Sciences [q-bio], Heterotroph, Organisme indicateur, Aquatic Science, Biology, 010603 evolutionary biology, 01 natural sciences, Comportement alimentaire, Matière organique, Autotroph, isotope, Ecology, Evolution, Behavior and Systematics, chemistry.chemical_classification, Ecology, Primary producers, δ13C, Stable isotope ratio, 010604 marine biology & hydrobiology, Fatty acid, δ15N, Acide gras, chemistry, Larve de poisson, Environmental chemistry, M40 - Écologie aquatique, Écologie animale, Composition (visual arts), Alimentation des poissons
Abstract: International audience; 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
Published: 2016
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38. Forces, failles et opportunités de la recherche française en écologie trophique

Author: Clémentine Fritch, Stanislas F. Dubois, Sébastien Lefebvre, Pierre Marmonier, Gérard Lacroix, Marie-Elodie Perga, Cédric Hubas, Cédric Gaucherel, Franck Jabot, Alexandre Bec, Michael Danger, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire d'ingénierie pour les systèmes complexes (UR LISC), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), Laboratoire Chrono-environnement - CNRS - UFC (UMR 6249) (LCE), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut d'écologie et des sciences de l'environnement de Paris (IEES (UMR_7618 / UMR_D_242 / UMR_A_1392 / UM_113) ), Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lille-Université du Littoral Côte d'Opale (ULCO)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - UFC (UMR 6249) (LCE), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Institut National de Recherche en Sciences et Technologies pour l'Environnement et l'Agriculture (IRSTEA), Institut d'Ecologie et des Sciences de l'Environnement de Paris (IEES Paris), Laboratoire d'Océanologie et de Géosciences (LOG), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement (UMR 6249) (LCE), Muséum national d'Histoire naturelle (MNHN), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), and Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN)
Subjects: 0301 basic medicine, Scientific network, General Immunology and Microbiology, Ecology, Trans-ecosystem, [SDV]Life Sciences [q-bio], 030106 microbiology, Population, General Medicine, Community, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, General Agricultural and Biological Sciences, Cleavage
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 “GRET”. The contours of the GRET'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'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., La recherche française en écologie trophique montre des clivages thématiques et géographiques qui ont motivé la création d’un groupement de recherche dédié (GDR GRET), financé par l’Institut national d’écologie et d’environnement du CNRS et l’Inra. Les GDR sont des outils incitatifs visant justement à favoriser la pluridisciplinarité en écologie pour lisser ces hétérogénéités. Néanmoins, la capacité de telles initiatives à atteindre cet objectif dépend nécessairement des causes initiales de clivage. Nous présentons ici les résultats d’un sondage réalisé en 2016 à l’initiative du GRET afin de décrire la communauté française des chercheurs en écologie trophique, de quantifier et caractériser ces clivages et d’identifier leurs causes. Trois césures principales ont été détectées. La première porte sur le manque d’intégration des microbiologistes dans les concepts de l’écologie trophique : les microbes ont virtuellement disparu des concepts trophiques. Le second clivage découle du fait que l’écologie trophique reste une recherche de terrain, un domaine territorial dans lequel les questions de recherche sont intimement dépendantes de l’écosystème d’étude. Enfin, la recherche en écologie trophique est limitée par les frontières de l’écosystème même, avec peu de recherches aux interfaces ou connectant différents types d’écosystèmes. Ces clivages, s’ils limitent l’avancement de la recherche, sont davantage le fait d’héritages culturels que réellement d’enjeux socio-économiques ou de motivations scientifiques. Une comparaison avec la littérature confirme que ces clivages ne sont pas uniquement des particularités de la recherche française, mais font écho aux faiblesses à l’échelle internationale. En ce sens, des initiatives de communication et de mise en place de réseaux tel que le GRET peuvent efficacement contribuer à lisser ces hétérogénéités à l’échelle nationale, en mettant notamment en lumière le bénéfice scientifique à réintégrer les microbes dans les réseaux trophiques, mais également les outils, opportunités et enjeux à conduire des programmes trans- et méta-écosystémiques en écologie trophique. Transformer l’essai demandera néanmoins, à terme, que des programmes de recherches émergent de ce réseau, en dépit du goulet d’étranglement que constitue le financement de la recherche aujourd’hui en France.
Published: 2018
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39. Impairment of the Bacterial Biofilm Stability by Triclosan

Author: Sabine Ulrike Gerbersdorf, Helen V. Lubarsky, F. Ricciardi, Cédric Hubas, David M. Paterson, Sebastian Behrens, University of St Andrews. School of Biology, University of St Andrews. Scottish Oceans Institute, University of St Andrews. St Andrews Sustainability Institute, University of St Andrews. Sediment Ecology Research Group, and University of St Andrews. Marine Alliance for Science & Technology Scotland
Subjects: Q Science, Geologic Sediments, Applied Microbiology, Microorganism, Marine and Aquatic Sciences, Bacterial growth, Toxicology, Bacterial cell structure, Bacterial films, Microbial ecology, chemistry.chemical_compound, Engineering, Freshwater Ecology, Multidisciplinary, Ecology, biology, Microbial Growth and Development, Biodiversity, Pollution, Chemistry, Environmental chemistry, Medicine, Stability, Ecosystem Functioning, Research Article, Freshwater Environments, Pollutants, Environmental Engineering, Ecological Metrics, Science, Toxic Agents, Carbohydrates, Marine Biology, Microbiology, Ecosystems, Microbial Ecology, Molecular Genetics, Extracellular polymeric substance, Bacterial Proteins, Cell Adhesion, Genetics, Environmental Chemistry, Seawater, Biology, Ecosystem, Bacteria, Biofilm, Species Diversity, biology.organism_classification, Triclosan, Ecologia microbiana, Scotland, chemistry, Biofilms, Fresh water -- Pollution, Ecosystem Engineering, Earth Sciences, Population Genetics, Environmental Sciences, Aigua dolça -- Contaminació, Developmental Biology, Ecological Environments
Abstract: The accumulation of the widely-used antibacterial and antifungal compound triclosan (TCS) in freshwaters raises concerns about the impact of this harmful chemical on the biofilms that are the dominant life style of microorganisms in aquatic systems. However, investigations to-date rarely go beyond effects at the cellular, physiological or morphological level. The present paper focuses on bacterial biofilms addressing the possible chemical impairment of their functionality, while also examining their substratum stabilization potential as one example of an important ecosystem service. The development of a bacterial assemblage of natural composition – isolated from sediments of the Eden Estuary (Scotland, UK) – on non-cohesive glass beads (
Published: 2018

40. Microphytobenthic Biofilms: Composition and Interactions

Author: Claire Passarelli, David M. Paterson, Cédric Hubas, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Muséum national d'Histoire naturelle (MNHN), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), University of Essex, Sediment Ecology Research Group, and University of St Andrews [Scotland]
Subjects: 0106 biological sciences, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, 030306 microbiology, Ecology, Chemistry, 010604 marine biology & hydrobiology, Microbial interaction, Microorganism, Biofilm, biochemical phenomena, metabolism, and nutrition, 01 natural sciences, 03 medical and health sciences, Extracellular polymeric substance, Ecosystem, 14. Life underwater
Abstract: International audience; 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.
Published: 2018
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41. Mudflat Ecosystem Engineers and Services

Author: Cédric Hubas, David M. Paterson, Claire Passarelli, University of Essex, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), University of St Andrews [Scotland], and Sediment Ecology Research Group
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0106 biological sciences, Abiotic component, Ecology, 010604 marine biology & hydrobiology, 15. Life on land, 010603 evolutionary biology, 01 natural sciences, Ecosystem engineer, Ecosystem services, Geography, Habitat, 13. Climate action, Benthic zone, Abundance (ecology), Sustainability, Ecosystem, 14. Life underwater
Abstract: International audience; 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.
Published: 2018
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42. Spatio-temporal variations in the composition of organic matter in surface sediments of a mangrove receiving shrimp farm effluents (New Caledonia)

Author: Jonathan Deborde, Cyril Marchand, Cédric Hubas, Adélaïde Aschenbroich, Tarik Meziane, Hervé Rybarczyk, Nathalie Molnar, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de recherche pour le développement [IRD] : UR206, Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), and Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Geologic Sediments, Environmental Engineering, Aquaculture, Wastewater, 010501 environmental sciences, 01 natural sciences, Shrimp farming, New Caledonia, Crustacea, Animals, Environmental Chemistry, Water Pollutants, Organic matter, 14. Life underwater, Fatty acids, Mangrove, Waste Management and Disposal, Effluent, Unsaturated fatty acid, Stable isotopes, 0105 earth and related environmental sciences, chemistry.chemical_classification, Ecology, ACL, 010604 marine biology & hydrobiology, Water Pollution, fungi, Sediment, δ15N, Eutrophication, 15. Life on land, Pollution, chemistry, Benthic zone, Environmental chemistry, Chlorophyll-a, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Environmental Monitoring
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 (delta C-13 and delta N-15), 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 18:1 omega 9 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 FM, 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.
Published: 2015
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43. Seasonal variations of the composition of microbial biofilms in sandy tidal flats: Focus of fatty acids, pigments and exopolymers

Author: Tarik Meziane, Bruno Jesus, Mickael Ruivo, Claire Passarelli, Najet Thiney, Cédric Hubas, Christian Jeanthon, Dominique Boeuf, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Muséum national d'Histoire naturelle (MNHN), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), ECOlogy of MArine Plankton (ECOMAP), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Des Substances et Organismes de la Mer - UR 2160 (ISOMER), Nantes Université - UFR des Sciences Pharmaceutiques et Biologiques (Nantes Univ - UFR Pharmacie), Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ), Universidade de Lisboa = University of Lisbon (ULISBOA), MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Mer, molécules et santé EA 2160 (MMS), Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN)-Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN), and Universidade de Lisboa (ULISBOA)
Subjects: chemistry.chemical_classification, Ecology, pigments, Microorganism, biogenic structures, Biofilm, Fatty acid, Context (language use), Aquatic Science, Biology, Oceanography, fatty acids, 6. Clean water, monosaccharide composition, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Extracellular polymeric substance, chemistry, 13. Climate action, Environmental chemistry, Monosaccharide, Ecosystem, 14. Life underwater, Microbial mat, biofilms, EPS
Abstract: International audience; 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.
Published: 2015
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44. The impact of suspended oyster farming on nitrogen cycling and nitrous oxide production in a sub-tropical Australian estuary

Author: Dirk V. Erler, Daniele Nizzoli, Tarik Meziane, William W. Bennet, Cédric Hubas, Angus J. P. Ferguson, David T. Welsh, Southern Cross University (SCU), Griffith University [Brisbane], Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Parma = Università degli studi di Parma [Parme, Italie], and New South Wales Office of Environment and Heritage
Subjects: 0106 biological sciences, Oyster, Sydney rock oyster, Denitrification, 010504 meteorology & atmospheric sciences, Oyster farming, Aquatic Science, Oceanography, 01 natural sciences, chemistry.chemical_compound, Nitrate, biology.animal, 14. Life underwater, Nitrogen cycle, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, biology, Ecology, 010604 marine biology & hydrobiology, biology.organism_classification, chemistry, Anammox, Environmental chemistry, Environmental science, Nitrification
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 ± 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 ± 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.
Published: 2017
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45. Caractérisation des substances polymériques extracellulaires (EPS) de biofilms de diatomées benthiques marines

Author: Daniel, Steven G., Cédric Hubas, Hubert Bonnefond, Sophie Sablé, Olivier Bernard, Martin Laviale, Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Muséum national d'Histoire naturelle (MNHN), Station de Biologie Marine de Concarneau, Direction générale déléguée à la Recherche, à l’Expertise, à la Valorisation et à l’Enseignement-Formation (DGD.REVE), Muséum national d'Histoire naturelle (MNHN)-Muséum national d'Histoire naturelle (MNHN), Biological control of artificial ecosystems (BIOCORE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Villefranche-sur-mer (OOVM), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract: National audience
Published: 2016

46. The fate of C4 and C3 macrophyte carbon in central Amazon floodplain waters: Insights from a batch experiment

Author: Cédric Hubas, Luciana O. Vidal, P. Albéric, Gwenaël Abril, Marc F. Benedetti, Najet Thiney, Claire Passarelli, Tarik Meziane, Marcela A.P. Pérez, Patricia Moreira-Turcq, Jean-Michel Mortillaro, Luis Felipe Artigas, Direction régionale à Madagascar (Dgdrs-Dre), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Universidade Federal Fluminense [Rio de Janeiro] (UFF), Institut des Sciences de la Terre d'Orléans - UMR7327 (ISTO), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Biogéosystèmes Continentaux - UMR7327, PSL Research University (PSL)-PSL Research University (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Université de Lille-Université du Littoral Côte d'Opale-Centre National de la Recherche Scientifique (CNRS), Institut de Physique du Globe de Paris (IPGP), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS), Institut de recherche pour le développement (IRD [Burkina Faso]), Laboratório de Ecologia Aquática, Universidade Federal de Juiz de Fora (UFJF), CNPq (National Council for Scientific and Technological Development – Brazil, Universal Program grant number 477655/2010-6), it was conducted within an international cooperation agreement between the CNPq (Brazil) and the IRD (Institute for Research and Development – France), and under the auspices of the Environmental Research Observatory Hydrology and Geochemistry of the Amazon Basin (HYBAM), supported by the INSU and the IRD, ANR-08-BLAN-0221,CARBAMA,CARBon biogeochemistry and atmospheric exchanges in the AMAzon river system(2008), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Centre National de la Recherche Scientifique (CNRS)-Université d'Orléans (UO)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Muséum national d'Histoire naturelle (MNHN), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-Observatoire des Sciences de l'Univers en région Centre (OSUC), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord]), Université du Littoral Côte d'Opale (ULCO), Institut de Physique du Globe de Paris (IPG Paris), Université du Littoral Côte d'Opale-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Mécanismes et Transfert en Géologie (LMTG), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), and Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, F40 - Écologie végétale, F60 - Physiologie et biochimie végétale, [SDV]Life Sciences [q-bio], Heterotroph, Aquatic Science, 01 natural sciences, fatty acids, Degradation, Total inorganic carbon, stables isotopes, Aquatic plant, Organic matter, Ecosystem, Central amazon, Fatty acids, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Central Amazon, degradation, chemistry.chemical_classification, Total organic carbon, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, 010604 marine biology & hydrobiology, Floodplains, Mineralization (soil science), 15. Life on land, Macrophyte, macrophytes, Stables isotopes, Macrophytes, chemistry, floodplains, 13. Climate action, Environmental chemistry, M40 - Écologie aquatique, Environmental science
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 C-4 macrophytes generally produce larger biomasses than C-3 macrophytes, food webs in the central Amazon floodplains appear dominantly based on a C-3 carbon source. In order to investigate the respective fate and degradation patterns of C-4 and C-3 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 C-3 and C-4 macrophyte, representative of in situ densities occurring in central Amazon floodplains. In the C-4 Paspalum repens treatments, organic (POC, DOC) and inorganic carbon (DIC) got rapidly enriched in C-13, whereas in the C-3 Salvinia auriculata treatments, POC and DOC showed little change in concentration and isotopic composition, and DIC got depleted in C-13. 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 C-3 S. auriculata and control treatments, an observation attributed to the lower C-3 biomass encountered in the field, to a slower degradation rate of C-3 compared to C-4 compounds, and to similar isotopic compositions for river POC and DOC, and C-3 compounds. The C-13 enrichments of POC, DOC, and DIC from P. repens treatments were attributed to an enhanced bacterially-mediated hydrolysis and mineralization of C-4 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 C-4 aquatic plants, as a large source of almost entirely biodegradable organic matter available for heterotrophic activity and CO2 outgassing to the atmosphere.
Published: 2016
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47. Physiological adjustments and transcriptome reprogramming are involved in the acclimation to salinity gradients in diatoms

Author: Adrien, Bussard, Erwan, Corre, Cédric, Hubas, Evelyne, Duvernois-Berthet, Gildas, Le Corguillé, Laurent, Jourdren, Fanny, Coulpier, Pascal, Claquin, and Pascal Jean, Lopez
Subjects: Diatoms, Salinity, Silicon, Acclimatization, Down-Regulation, Seawater, Photosynthesis, Estuaries, Transcriptome, Carbon
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 (LT) cultures. Whole transcriptome analyses revealed a down-regulation of nuclear and plastid encoded genes during the LT response and identified only a few regulated genes that were in common between the ST and LT 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.
Published: 2016

48. Meiofauna distribution in a mangrove forest exposed to shrimp farm effluents (New Caledonia)

Author: Cédric Hubas, Tarik Meziane, Jonathan Deborde, L. Della Patrona, Cyril Marchand, N. Molnar, Lagons, Ecosystèmes et Aquaculture Durable [Nouméa] (LEAD), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de recherche pour le développement [IRD] : UR206-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Ifremer - Nouvelle-Calédonie, Institut de Recherche pour le Développement (IRD), Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), and Muséum national d'Histoire naturelle (MNHN)
Subjects: 0106 biological sciences, Aquatic Organisms, Meiobenthos, Meiofauna, Aquaculture, 010501 environmental sciences, Aquatic Science, Biology, Wastewater, Oceanography, 01 natural sciences, Shrimp farming, Environmental status, New Caledonia, 14. Life underwater, Mangrove, Effluent, 0105 earth and related environmental sciences, Ecology, 010604 marine biology & hydrobiology, General Medicine, biology.organism_classification, Pollution, Fishery, Taxon, Avicennia marina, Wetlands, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Environmental Monitoring
Abstract: International audience; 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.
Published: 2016
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49. Surface adhesion of microphytobenthic biofilms is enhanced under Hediste diversicolor (O.F. Müller) trophic pressure

Author: Tarik Meziane, Claire Passarelli, Julie Grange, Audrey Nicolas Segui, and Cédric Hubas
Subjects: Abiotic component, Ecology, Exopolymer, fungi, Sediment, Context (language use), Aquatic Science, Biology, biology.organism_classification, Microbial population biology, Benthic zone, Hediste diversicolor, Microcosm, Ecology, Evolution, Behavior and Systematics
Abstract: In soft-bottom tidal flats, sediment stability is one of the crucial parameters modulating the abundance and composition of benthic assemblages. It is dependent on a wide range of variables, both abiotic and biotic. Investigating how these variables and their interactions influence sediment stability is therefore essential to understand how benthic assemblages are distributed in their environment. In this context, we designed a microcosm study to examine how microorganisms and macrofauna interact to alter sediment stability. We cultured a natural microbial community, enriched with diatoms, both alone and together with the common ragworm Hediste diversicolor , and monitored their effects on photosynthetic biomasses, bacterial abundances, exopolymer secretions and sediment stability. We also assessed the consumption of biofilm by worms using fatty acid biomarkers. Our results demonstrate that even if H. diversicolor fed on diatoms, they stimulated biofilm development, in terms of photosynthetic biomass and exopolymer production. Also, sediment cohesiveness was enhanced when both diatoms and H. diversicolor were cultured together; this result was unexpected since macrofauna, through consumption of microorganisms and modification of sediment properties, is often considered to have a destabilising effect on sediment. Predicting the effect of macrofauna on microphytobenthic biofilms and their associated influence of sediment stability is therefore not straightforward. Similar experiments including different types of organisms or more complex assemblages might help to further characterise the effect of biota on sediment stability.
Published: 2012
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50. Impacts of biogenic structures on benthic assemblages: microbes, meiofauna, macrofauna and related ecosystem functions

Author: Cédric Hubas, Frédéric Olivier, David M. Paterson, and Claire Passarelli
Subjects: Ecology, biology, Water flow, Meiobenthos, fungi, Intertidal zone, Aquatic Science, biology.organism_classification, Ecosystem engineer, Ecosystem services, Oceanography, Diatom, Benthic zone, Ecosystem, Ecology, Evolution, Behavior and Systematics
Abstract: Species that modify their surroundings are known as ecosystem engineers. For example, patches of polychaete tubes enhance soft-bottom intertidal habitat complexity, modify- ing water flow, promoting sediment accretion and affecting nutrient fluxes at the water-sediment interface. Understanding how such structures affect the benthic ecosystem's functioning requires the assessment of their influence on all benthic components and how the related ecosystem serv- ices may be modified. We performed an in situ experimental study, involving the use of artificial mimics of polychaete tubes, to investigate the purely physical impacts of the structures without the complexity of worm activity. Benthic chambers of different mimic densities were used, and their effect on the recolonisation of defaunated natural sandy sediments by microorganisms, meio- fauna and macrofauna was monitored. We also measured air-sediment CO2 fluxes and sediment stability as they constitute crucial ecosystem services provided by benthic habitats. We showed that the biogenic structures stimulated the development of diatom biofilms (microphytobenthos) and their associated extracellular polymeric substances (EPS). Impacts of tubes on meiofaunal and macrofaunal assemblages were significant; in most cases, species and groups were more abun- dant in treatments with few or no tubes. In response to the tube density increase, the whole system tended towards heterotrophy and higher sediment stability, probably as a consequence of the development of the diatom biofilm. Biogenic structures are, therefore, of critical importance for soft-bottom intertidal communities in terms of both structure and function.
Published: 2012
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