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36 results on '"Militon, Cécile"'

6. GoArrays: highly dynamic and efficient microarray probe design

Author

Rimour, Sébastien, Hill, David, Militon, Cécile, and Peyret, Pierre

Subjects
Quantitative Biology - Quantitative Methods
Abstract

MOTIVATION: The use of oligonucleotide microarray technology requires a very detailed attention to the design of specific probes spotted on the solid phase. These problems are far from being commonplace since they refer to complex physicochemical constraints. Whereas there are more and more publicly available programs for microarray oligonucleotide design, most of them use the same algorithm or criteria to design oligos, with only little variation. RESULTS: We show that classical approaches used in oligo design software may be inefficient under certain experimental conditions, especially when dealing with complex target mixtures. Indeed, our biological model is a human obligate parasite, the microsporidia Encephalitozoon cuniculi. Targets that are extracted from biological samples are composed of a mixture of pathogen transcripts and host cell transcripts. We propose a new approach to design oligonucleotides which combines good specificity with a potentially high sensitivity. This approach is original in the biological point of view as well as in the algorithmic point of view. We also present an experimental validation of this new strategy by comparing results obtained with standard oligos and with our composite oligos. A specific E.cuniculi microarray will overcome the difficulty to discriminate the parasite mRNAs from the host cell mRNAs demonstrating the power of the microarray approach to elucidate the lifestyle of an intracellular pathogen using mix mRNAs.

Published
2008
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7. Spatial Patterns of Mangrove Nematode Diversity between the Atlantic-Caribbean East Pacific and the Indo-West Pacific

Author

Spedicato, Adriana, primary, Zeppilli, Daniela, additional, Thouzeau, Gérard, additional, Cuny, Philippe, additional, Militon, Cécile, additional, Sylvi, Léa, additional, Hubas, Cédric, additional, Dirberg, Guillaume, additional, Jézéquel, Ronan, additional, Barrière, Guerric, additional, Michel, Loïc, additional, Bezerra, Tânia Nara, additional, and Michaud, Emma, additional

Published
2023
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8. Effective degradation of organophosphate ester flame retardants and plasticizers in coastal sediments under high urban pressure

Author

Castro-Jimenez, Javier, Cuny, Philippe, Militon, Cécile, Sylvi, Lea, Royer, F, Papillon, L, Sempere, Richard, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut méditerranéen d'océanologie (MIO), and 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)

Subjects
[SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Multidisciplinary, Biodegradation, Environmental, Plasticizers, [SDE]Environmental Sciences, Esters, Organophosphates, Flame Retardants
Abstract

Empirical evidence of the effective degradation at environmentally relevant conditions of organophosphate esters (OPEs) flame retardants and plasticizers in coastal sediments from an impacted area in the NW Mediterranean Sea is provided. Half-lives varied from 23.3 to 77.0 (abiotic conditions) and from 16.8 to 46.8 days (biotic conditions), depending on the compound, highlighting the relevant role of microbial assemblages enhancing OPE degradation. After an immediate significant reduction of the bacterial abundance due to OPE addition to the sediment at the very beginning of the experiment, the observed biodegradation was associated to a general stimulation of the growth of the bacterial community during a first period, but without a marked change of the structure of the community. However, OPE contamination induced a decrease on the diversity of the bacterial community in the coastal sediment, noticeable after 14 days of incubation. It is likely that on one side the contamination had favoured the growth of some bacterial groups maybe involved in the biodegradation of these compounds but, on the other side, had also impacted some sensitive bacteria. The estimated half-lives fill a data gap concerning OPE degradation rates in marine sediments and will be valuable data for the refinement of OPE chemical risk assessment in marine environments, particularly on impacted sites.

Published
2022
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12. NEW INSIGHTS INTO MICROBIAL WAX ESTER BIOSYNTHESIS, NATURAL OCCURRENCE AND ADAPTIVE ROLE

Author

Grossi, Vincent, Antheaume, Ingrid, Ariztegui, Daniel, Borrel, Guillaume, Cravo-Laureau, Cristiana, Cuny, Philippe, Hugoni, Mylène, Militon, Cécile, Sala, David, Sylvi, Lea, Thomas, Camille, Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), Institut Pasteur [Paris] (IP), 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), 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), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), and GROSSI, Vincent

Subjects
[SDE] Environmental Sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, [SDU.STU.GC] Sciences of the Universe [physics]/Earth Sciences/Geochemistry, [SDE]Environmental Sciences, [SDV.EE.ECO] Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDU.ENVI] Sciences of the Universe [physics]/Continental interfaces, environment
Abstract

International audience

Published
2021

16. BathyBot - a Deep-sea Crawler to See the Unseen in the NW Mediterranean Sea

Author

Martini, Séverine, Gojak, Carl, Arnaubec, Aurelien, Bernardet, Karim, Bocquet, Olivier, Chevaldonné, P., Ciausu, Viorel, Durrieu de Madron, Xavier, Le Direach, Laurence, Grenz, Christian, Lamare, Patrick, Lefevre, Dominique, Mahiouz, Karim, Matabos, Marjolaine, Nerini. David, Picheral, Laura, Piasco, Romain, Sarrazin, J., Thomsen, Laurenz, Tamburini, Cristian, Aguzzi, Jacopo, Barnes-Davin, Laury, Bertin, Vincent, Bombled, Bruno, Coyle, P., Cuny, Philippe, Garel, Marc, Rouanet, Elodie, Hafidi, Zouhir, Laus, Celine, Le Bris, Nadine, Marini, Simone, Militon, Cécile, Pérez, Thierry, Picheral, Marc, Rabouille, Christophe, Thibault, Delphine, European Commission, and Centre National de la Recherche Scientifique (France)

Abstract

Ocean Sciences Meeting (OSM), 16-21 February 2020, San Diego, CA, USA.- 1 page, 3 figures, The deep sea remains one of the less known environment on Earth and is characterized by high pressure, low availability of organic matter and absence of light. While there are still numerous discoveries concerning the diversity and adaptations of deep-sea organisms to their environement, this ecosystem is under an increasing anthropogenic pressure such as climate-related stressors (warming, acidification and deoxygenation), deep-sea fishing, human pollution (microplastics, POP), oil and gas extraction and could face new threats from emerging industries (e.g. mineral mining). How these changes will affect biodiversity and ecosystem functioning is one question of major importance for the future. In the darkness of the oceans, several organisms have the capability to emit light: called bioluminescence. Recent studies quantified that as much as 75% of pelagic and about 40% of benthic organisms are known to be bioluminescent. In this framework, we present a new deep-sea crawler, BathyBot, to be dedicated to the long-term exploration of deep-sea ecosystems allowing biological and-geochemical surveys. BathyBot will be deployed in 2020 in the Mediterranean Sea, at the MEUST-NUMerEnv/KM3NeT site, to strength the ecological-based monitoring capability of the European Multidisciplinary Seafloor and water column Observatory (EMSO ERIC) network. BathyBot will be able to explore an area of about 15 000 m2 at a depth of 2500m and will be devoted to 1) observe and monitor the dynamics of deep-sea pelagic and benthic organisms, 2) better define the occurrence and functions of bioluminescence in situ (increasing the dataset of bioluminescence records), 3) explore relationships between deep-sea organisms, biogeochemical (carbon content, oxygen concentrations) and environmental variables (temperature, salinity, current) in the context of global changes and their effects on the deep ocean, and 4) investigate benthic biogeochemical processes through the use of oxygen microprofiling in sediment porewaters, This work is funded by UE FEDER NUMerEnv project (number: 1166-39417, 2017), CNRS-INSU Moyens Mi-Lourd 2019 and VICAT-Tangram-MIO project

Published
2020

17. Oil Spill response in mangroves: why a specific Ecosystem-based Management is required?

Author

CUNY, Philippe, Jézéquel, Ronan, Michaud, Emma, SYLVI, Lea, Militon, Cécile, 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), Centre de documentation de recherche et d'expérimentations sur les pollutions accidentelles des eaux (Cedre), Cedre, 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), Michaud, Emma, and 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)

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.MCG] Environmental Sciences/Global Changes, [CHIM.ANAL] Chemical Sciences/Analytical chemistry, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDE.MCG]Environmental Sciences/Global Changes, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, [SDU.ENVI] Sciences of the Universe [physics]/Continental interfaces, environment, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

18. First Assessment of the Benthic Meiofauna Sensitivity to Low Human-Impacted Mangroves in French Guiana

Author

Michelet, Claire, Zeppilli, Daniela, Hubas, Cédric, Baldrighi, Elisa, Cuny, Philippe, Dirberg, Guillaume, Militon, Cécile, Walcker, Romain, Lamy, Dominique, Jézéquel, Ronan, Receveur, Justine, Gilbert, Franck, Houssainy, Amonda El, Dufour, Aurélie, Heimbürger-boavida, Lars-eric, Bihannic, Isabelle, Sylvi, Léa, Vivier, Baptiste, Michaud, Emma, Michelet, Claire, Zeppilli, Daniela, Hubas, Cédric, Baldrighi, Elisa, Cuny, Philippe, Dirberg, Guillaume, Militon, Cécile, Walcker, Romain, Lamy, Dominique, Jézéquel, Ronan, Receveur, Justine, Gilbert, Franck, Houssainy, Amonda El, Dufour, Aurélie, Heimbürger-boavida, Lars-eric, Bihannic, Isabelle, Sylvi, Léa, Vivier, Baptiste, and Michaud, Emma

Abstract

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.

Published
2021
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20. Seawater copper content controls biofilm bioaccumulation and microbial community on microplastics

Author

Fiard, Maud, CUNY, Philippe, Sylvi, Léa, Hubas, Cédric, Jézéquel, Ronan, Lamy, Dominique, Walcker, Romain, El Houssainy, Amonda, Heimbürger-Boavida, Lars-Eric, Robinet, Tony, Bihannic, Isabelle, Gilbert, Franck, Michaud, Emma, Dirberg, Guillaume, Militon, Cécile, Departments of Physics, Molecular and Cellular Biology, and College of Optical Sciences, University of Arizona, Tucson, Departments of Physics, Molecular and Cellular Biology, and College of Optical Sciences, 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 Matériaux Polymères Interfaces Environnement Marin - EA 4323 (MAPIEM), Université de Toulon (UTLN), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), and 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)

Subjects
Environmental Engineering, Biofilm, Microbiota, Microplastics, Bioaccumulation, Pollution, Bioconcentration, Microbial community composition, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Biofilms, Environmental Chemistry, Seawater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Plastics, Waste Management and Disposal, Copper, Water Pollutants, Chemical
Abstract

International audience; The adsorption of trace metals on microplastics (MPs) is affected by the presence of surficial biofilms but their interactions are poorly understood. Here, we present the influence of Cu levels in real seawater (Toulon Bay, NW Mediterranean Sea) on microbial communities and Cu content of the resulting biofilms grown during incubation experiments on high density polyethylene. Two sets of incubation experiments were run with seawater supplied with MPs, sampled in two sites with contrasting Cu levels: Pt12 (most contaminated site) and Pt41P (less contaminated site). For each incubation experiment, 5 treatments were considered differing in Cu concentrations, ranging between 30 and 400 nM and between 6 and 60 nM, for Pt12 and Pt41p, respectively. A control experiment (filtered at 0.2 μm) was run in parallel for each incubation experiment. We observed that, at the time scale of the incubation period, both prokaryotic and eukaryotic richness and diversity were higher in the biofilms formed from the most contaminated site. In addition, we showed that Cu levels are shaping biofilm communities, evidencing co-occurrence patterns between prokaryotes and eukaryotes with diatoms playing a central role. These differences in biofilm formation were reflected in the amount of bioaccumulated Cu per dry weight of MPs, exhibiting higher values in the most contaminated site. Within this site, the increase of Cu seawater content enhanced its bioaccumulation onto MPs until reaching saturation. This study strongly suggests a striking link between seawater copper content, biofilm community shaping and the resulting Cu bioaccumulation onto MPs.

Published
2022
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21. First Assessment of the Benthic Meiofauna Sensitivity to Low Human-Impacted Mangroves in French Guiana

Author

Michelet, Claire, primary, Zeppilli, Daniela, additional, Hubas, Cédric, additional, Baldrighi, Elisa, additional, Cuny, Philippe, additional, Dirberg, Guillaume, additional, Militon, Cécile, additional, Walcker, Romain, additional, Lamy, Dominique, additional, Jézéquel, Ronan, additional, Receveur, Justine, additional, Gilbert, Franck, additional, Houssainy, Amonda El, additional, Dufour, Aurélie, additional, Heimbürger-Boavida, Lars-Eric, additional, Bihannic, Isabelle, additional, Sylvi, Léa, additional, Vivier, Baptiste, additional, and Michaud, Emma, additional

Published
2021
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23. BathyBot - a Deep-sea Crawler to See the Unseen in the NW Mediterranean Sea

Author

European Commission, Centre National de la Recherche Scientifique (France), Martini, Séverine, Gojak, Carl, Arnaubec, Aurelien, Bernardet, Karim, Bocquet, Olivier, Chevaldonné, P., Ciausu, Viorel, Durrieu de Madron, Xavier, Le Direach, Laurence, Grenz, Christian, Lamare, Patrick, Lefevre, Dominique, Mahiouz, Karim, Matabos, Marjolaine, Nerini. David, Picheral, Laura, Piasco, Romain, Sarrazin, J., Thomsen, Laurenz, Tamburini, Cristian, Aguzzi, Jacopo, Barnes-Davin, Laury, Bertin, Vincent, Bombled, Bruno, Coyle, P., Cuny, Philippe, Garel, Marc, Rouanet, Elodie, Hafidi, Zouhir, Laus, Celine, Le Bris, Nadine, Marini, Simone, Militon, Cécile, Pérez, Thierry, Picheral, Marc, Rabouille, Christophe, Thibault, Delphine, European Commission, Centre National de la Recherche Scientifique (France), Martini, Séverine, Gojak, Carl, Arnaubec, Aurelien, Bernardet, Karim, Bocquet, Olivier, Chevaldonné, P., Ciausu, Viorel, Durrieu de Madron, Xavier, Le Direach, Laurence, Grenz, Christian, Lamare, Patrick, Lefevre, Dominique, Mahiouz, Karim, Matabos, Marjolaine, Nerini. David, Picheral, Laura, Piasco, Romain, Sarrazin, J., Thomsen, Laurenz, Tamburini, Cristian, Aguzzi, Jacopo, Barnes-Davin, Laury, Bertin, Vincent, Bombled, Bruno, Coyle, P., Cuny, Philippe, Garel, Marc, Rouanet, Elodie, Hafidi, Zouhir, Laus, Celine, Le Bris, Nadine, Marini, Simone, Militon, Cécile, Pérez, Thierry, Picheral, Marc, Rabouille, Christophe, and Thibault, Delphine

Abstract

The deep sea remains one of the less known environment on Earth and is characterized by high pressure, low availability of organic matter and absence of light. While there are still numerous discoveries concerning the diversity and adaptations of deep-sea organisms to their environement, this ecosystem is under an increasing anthropogenic pressure such as climate-related stressors (warming, acidification and deoxygenation), deep-sea fishing, human pollution (microplastics, POP), oil and gas extraction and could face new threats from emerging industries (e.g. mineral mining). How these changes will affect biodiversity and ecosystem functioning is one question of major importance for the future. In the darkness of the oceans, several organisms have the capability to emit light: called bioluminescence. Recent studies quantified that as much as 75% of pelagic and about 40% of benthic organisms are known to be bioluminescent. In this framework, we present a new deep-sea crawler, BathyBot, to be dedicated to the long-term exploration of deep-sea ecosystems allowing biological and-geochemical surveys. BathyBot will be deployed in 2020 in the Mediterranean Sea, at the MEUST-NUMerEnv/KM3NeT site, to strength the ecological-based monitoring capability of the European Multidisciplinary Seafloor and water column Observatory (EMSO ERIC) network. BathyBot will be able to explore an area of about 15 000 m2 at a depth of 2500m and will be devoted to 1) observe and monitor the dynamics of deep-sea pelagic and benthic organisms, 2) better define the occurrence and functions of bioluminescence in situ (increasing the dataset of bioluminescence records), 3) explore relationships between deep-sea organisms, biogeochemical (carbon content, oxygen concentrations) and environmental variables (temperature, salinity, current) in the context of global changes and their effects on the deep ocean, and 4) investigate benthic biogeochemical processes through the use of oxygen microprofiling in se

Published
2020

25. Assessment of oil weathering and impact in mangrove ecosystem: PRISME Experiment.

Author

Jézéquel, Ronan, primary, Duboscq, Karine, additional, Sylvi, Léa, additional, Michaud, Emma, additional, Ferriz, Lise Millera, additional, Roic, Enora, additional, Duran, Robert, additional, Cravo-laureau, Cristiana, additional, Michotey, Valérie, additional, Bonin, Patricia, additional, Gilbert, Franck, additional, Tedetti, Marc, additional, Militon, Cécile, additional, and Cuny, Philippe, additional

Published
2017
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26. Metatranscriptomes of oil-contaminated marine coastal sediment affected by oil addition and/or by the bioturbating activity of the marine polychaete Hediste diversicolor: Who are the microbial players?

Author

Militon, Cécile, primary, Atkinson, Alexandre, additional, Michotey, Valérie, additional, Jeziorski, Céline, additional, Cravo-Laureau, Cristiana, additional, Duran, Robert, additional, Bonin, Patricia, additional, and Cuny, Philippe, additional

Published
2016
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27. Bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil

Author

Militon , Cécile, Boucher , Delphine, Vachelard , Cédric, Perchet , Geoffrey, BARRA , Vincent, Troquet , Julien, Peyretaillade , Eric, Peyret , Pierre, Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes ( LIMOS ), Centre National de la Recherche Scientifique ( CNRS ) -Sigma CLERMONT ( Sigma CLERMONT ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ), Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes ( LIMOS ), Sigma CLERMONT ( Sigma CLERMONT ) -Université Clermont Auvergne ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Conception, Ingénierie et Développement de l'Aliment et du Médicament ( CIDAM ), Université d'Auvergne - Clermont-Ferrand I ( UdA ), Laboratoire Microorganismes : Génome et Environnement ( LMGE ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Centre National de la Recherche Scientifique ( CNRS ), Biopôle Clermont-Limagne, and Biobasic Environnement

Subjects
[ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, [ INFO.INFO-TS ] Computer Science [cs]/Signal and Image Processing, Bacterial diversity, bioremediation, 165rRNA gene, aliphatic hydrocarbons, ComputingMilieux_MISCELLANEOUS, [ INFO.INFO-LG ] Computer Science [cs]/Machine Learning [cs.LG]
Abstract

International audience; The microbial community response during the oxygen biostimulation process of aged oil-polluted soils is poorly documented and there is no reference for the long-term monitoring of the unsaturated zone. To assess the potential effect of air supply on hydrocarbon fate and microbial community structure, two treatments (0 and 0.056 mol h⁻¹ molar flow rate of oxygen) were performed in fixed bed reactors containing oil-polluted soil. Microbial activity was monitored continuously over 2 years throughout the oxygen biostimulation process. Microbial community structure before and after treatment for 12 and 24 months was determined using a dual rRNA/rRNA gene approach, allowing us to characterize bacteria that were presumably metabolically active and therefore responsible for the functionality of the community in this polluted soil. Clone library analysis revealed that the microbial community contained many rare phylotypes. These have never been observed in other studied ecosystems. The bacterial community shifted from Gammaproteobacteria to Actinobacteria during the treatment. Without aeration, the samples were dominated by a phylotype linked to the Streptomyces. Members belonging to eight dominant phylotypes were well adapted to the aeration process. Aeration stimulated an Actinobacteria phylotype that might be involved in restoring the ecosystem studied. Phylogenetic analyses suggested that this phylotype is a novel, deep-branching member of the Actinobacteria related to the well-studied genus Acidimicrobium.

Published
2010
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29. Use of dispersant in mudflat oil-contaminated sediment: behavior and effects of dispersed oil on micro- and macrobenthos

Author

Cuny, Philippe, primary, Gilbert, Franck, additional, Militon, Cécile, additional, Stora, Georges, additional, Bonin, Patricia, additional, Michotey, Valérie, additional, Guasco, Sophie, additional, Duboscq, Karine, additional, Cagnon, Christine, additional, Jézéquel, Ronan, additional, Cravo-Laureau, Cristiana, additional, and Duran, Robert, additional

Published
2015
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31. Oil spill effects on macrofaunal communities and bioturbation of pristine marine sediments (Caleta Valdés, Patagonia, Argentina): experimental evidence of low resistance capacities of benthic systems without history of pollution

Author

Ferrando, Agustina, primary, Gonzalez, Emilia, additional, Franco, Marcos, additional, Commendatore, Marta, additional, Nievas, Marina, additional, Militon, Cécile, additional, Stora, Georges, additional, Gilbert, Franck, additional, Esteves, José Luis, additional, and Cuny, Philippe, additional

Published
2015
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32. Caractérisation des communautés procaryotiques impliquées dans la bioremédiation d'un sol pollué par des hydrocarbures et développement d'outils d'analyse à haut débit

Author

Militon, Cécile, Meyer, Camille, Laboratoire Microorganismes : Génome et Environnement ( LMGE ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Centre National de la Recherche Scientifique ( CNRS ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ), Université Blaise Pascal - Clermont-Ferrand II, Université d'Auvergne - Clermont-Ferrand I, Pierre Peyret, Laboratoire Microorganismes : Génome et Environnement (LMGE), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)

Subjects
biopuces, Procaryotes, [ SDV.MP.PRO ] Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, [SDV.MP.PRO] Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology
Abstract

Environmental ecosystems are sensitive to damage from human activities and there is an increasing need to develop better methods for removing pollutants from soils. The removal of pollutants or their transformation to less toxic products by bioremediation is a less invasive and expensive process than classical decontamination. However, the use and optimization of bioremediation treatments requires knowledge on the microbial communities directly and indirectly involved in the degradation of the pollutants. Therefore, after the creation of a synthesis describing the microbial diversity and the available tools for the isolation and the identification of microorganisms, we have studied the structure and the dynamic of the bacterial communities during the bioremediation of an aliphatic hydrocarbon-polluted soil. Beyond the characterization of a bacterial "core-set" present throughout the decontamination process, we have identified several phylotypes potentially involved in degradation. In order to globally monitor these bacterial communities, we also have developed a probe design software (PhylArray) generating efficient and explorative probes for high-throughput molecular tools: the DNA microarrays., La bioremédiation est une réelle alternative aux techniques invasives de réhabilitation des sols pollués par des hydrocarbures. Cependant, la mise en place et l'optimisation de tels procédés nécessitent une meilleure connaissance des communautés microbiennes impliquées dans la biodégradation de ces polluants. Ainsi, nous avons étudié la structure et la dynamique des communautés bactériennes au cours d'un procédé de biostimulation d'un sol pollué aux hydrocarbures aliphatiques. Outre la caractérisation d' un core set bactérien présent tout au long du procédé, cette étude nous a permis d'identifier des phylotypes potentiellement impliqués dans la biodégradation de ces polluants. Enfin nous nous sommes attachés à mettre au point des outils moléculaires à haut débit, afin d'étudier plus globalement ces communautés environnementales, et ce par le développement d'un logiciel de sélection de sondes sensibles, spécifiques et exploratoires pour biopuces phylogénétiques (PhylArray)

Published
2007

34. Impact of Oil on Bacterial Community Structure in Bioturbated Sediments

Author

Stauffert, Magalie, primary, Cravo-Laureau, Cristiana, additional, Jézéquel, Ronan, additional, Barantal, Sandra, additional, Cuny, Philippe, additional, Gilbert, Franck, additional, Cagnon, Christine, additional, Militon, Cécile, additional, Amouroux, David, additional, Mahdaoui, Fatima, additional, Bouyssiere, Brice, additional, Stora, Georges, additional, Merlin, François-Xavier, additional, and Duran, Robert, additional

Published
2013
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36. Bacterial community changes during bioremediation of aliphatic hydrocarbon-contaminated soil.

Author

Militon C, Boucher D, Vachelard C, Perchet G, Barra V, Troquet J, Peyretaillade E, and Peyret P

Subjects
Actinobacteria classification, Actinobacteria genetics, Biodegradation, Environmental, Bioreactors, DNA, Bacterial genetics, Gammaproteobacteria classification, Gammaproteobacteria genetics, Oxygen metabolism, Phylogeny, Pilot Projects, RNA, Ribosomal, 16S genetics, Soil analysis, Actinobacteria isolation & purification, Gammaproteobacteria isolation & purification, Hydrocarbons metabolism, Soil Microbiology, Soil Pollutants metabolism
Abstract

The microbial community response during the oxygen biostimulation process of aged oil-polluted soils is poorly documented and there is no reference for the long-term monitoring of the unsaturated zone. To assess the potential effect of air supply on hydrocarbon fate and microbial community structure, two treatments (0 and 0.056 mol h⁻¹ molar flow rate of oxygen) were performed in fixed bed reactors containing oil-polluted soil. Microbial activity was monitored continuously over 2 years throughout the oxygen biostimulation process. Microbial community structure before and after treatment for 12 and 24 months was determined using a dual rRNA/rRNA gene approach, allowing us to characterize bacteria that were presumably metabolically active and therefore responsible for the functionality of the community in this polluted soil. Clone library analysis revealed that the microbial community contained many rare phylotypes. These have never been observed in other studied ecosystems. The bacterial community shifted from Gammaproteobacteria to Actinobacteria during the treatment. Without aeration, the samples were dominated by a phylotype linked to the Streptomyces. Members belonging to eight dominant phylotypes were well adapted to the aeration process. Aeration stimulated an Actinobacteria phylotype that might be involved in restoring the ecosystem studied. Phylogenetic analyses suggested that this phylotype is a novel, deep-branching member of the Actinobacteria related to the well-studied genus Acidimicrobium., (FEMS Microbiology Ecology © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original French government works.)

Published
2010
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