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127 results on '"Patricia Bonin"'

1. Cellular Damage of Bacteria Attached to Senescent Phytoplankton Cells as a Result of the Transfer of Photochemically Produced Singlet Oxygen: A Review

Author: Jean-François Rontani and Patricia Bonin
Subjects: attached bacteria, phytodetritus, oxidative damage, singlet oxygen transfer, solar irradiance, mineral matrices, Biology (General), QH301-705.5
Abstract: Several studies set out to explain the presence of high proportions of photooxidation products of cis-vaccenic acid (generally considered to be of bacterial origin) in marine environments. These studies show that these oxidation products result from the transfer of singlet oxygen from senescent phytoplankton cells to the bacteria attached to them in response to irradiation by sunlight. This paper summarizes and reviews the key findings of these studies, i.e., the demonstration of the process at work and the effect of different parameters (intensity of solar irradiance, presence of bacterial carotenoids, and presence of polar matrices such as silica, carbonate, and exopolymeric substances around phytoplankton cells) on this transfer. A large part of this review looks at how this type of alteration of bacteria can affect the preservation of algal material in the marine environment, especially in polar regions where conditions drive increased transfer of singlet oxygen from sympagic algae to bacteria.
Published: 2023
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2. Identification of enriched hyperthermophilic microbial communities from a deep-sea hydrothermal vent chimney under electrolithoautotrophic culture conditions

Author: Guillaume Pillot, Oulfat Amin Ali, Sylvain Davidson, Laetitia Shintu, Anne Godfroy, Yannick Combet-Blanc, Patricia Bonin, and Pierre-Pol Liebgott
Subjects: Medicine, Science
Abstract: Abstract Deep-sea hydrothermal vents are extreme and complex ecosystems based on a trophic chain. We are still unsure of the identities of the first colonizers of these environments and their metabolism, but they are thought to be (hyper)thermophilic autotrophs. Here we investigate whether the electric potential observed across hydrothermal chimneys could serve as an energy source for these first colonizers. Experiments were performed in a two-chamber microbial electrochemical system inoculated with deep-sea hydrothermal chimney samples, with a cathode as sole electron donor, CO2 as sole carbon source, and nitrate, sulfate, or oxygen as electron acceptors. After a few days of culturing, all three experiments showed growth of electrotrophic biofilms consuming the electrons (directly or indirectly) and producing organic compounds including acetate, glycerol, and pyruvate. Within the biofilms, the only known autotroph species retrieved were members of Archaeoglobales. Various heterotrophic phyla also grew through trophic interactions, with Thermococcales growing in all three experiments as well as other bacterial groups specific to each electron acceptor. This electrotrophic metabolism as energy source driving initial microbial colonization of conductive hydrothermal chimneys is discussed.
Published: 2021
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3. Dry-Wet Cycles Affect Nitrous Oxide Emissions Across Aquatic-Terrestrial Interfaces: A Mesocosms Study

Author: Renata Pinto, Gabriele Weigelhofer, Matthias Pucher, Rebecca Clare Hood-Nowotny, Patricia Bonin, António Guerreiro Brito, and Thomas Hein
Subjects: N2O, nitrification, denitrification, drying-rewetting, sediments, floodplain, Chemistry, QD1-999, Engineering geology. Rock mechanics. Soil mechanics. Underground construction, TA703-712
Abstract: Aquatic-terrestrial interfaces may act as biogeochemical hotspots for greenhouse gas emissions, especially when exposed to frequent transitions between wet and dry phases. The study aimed to analyze the dynamics of nitrogen (N) processing along an inundation gradient from floodplain soils to river sediments and identify environmental factors affecting net nitrous oxide (N2O) production from different microbial sources. Intact soil and sediment cores were subject to two consecutive drying-rewetting cycles in laboratory experiments. The 15N isotope pairing technique was used to quantify N2O emissions sourced from denitrification and nitrification. We observed enhanced N2O emissions from both nitrification and denitrification following drying events. Sites exposed to frequent drying-rewetting cycles appear less affected by drying than hydrologically more stable habitats. Fluxes from nitrification were related to the organic matter content, while fluxes from denitrification were controlled by dissolved organic matter quality changes during the drying-rewetting cycles. This study shows the potential link between carbon metabolism and N2O production, combining the effect of drying-rewetting cycles.
Published: 2022
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4. Similar Methanogenic Shift but Divergent Syntrophic Partners in Anaerobic Digesters Exposed to Direct versus Successive Ammonium Additions

Author: Julie Hardy, Patricia Bonin, Adele Lazuka, Estelle Gonidec, Sophie Guasco, Corinne Valette, Sébastien Lacroix, and Léa Cabrol
Subjects: acetate, syntrophic, methanogen disturbance, adaptation, acclimation, ammonia, Microbiology, QR1-502
Abstract: ABSTRACT During anaerobic digestion (AD) of protein-rich wastewater, ammonium (NH4+) is released by amino acid degradation. High NH4+ concentrations disturb the AD microbiome balance, leading to process impairments. The sensitivity of the AD microbiome to NH4+ and the inhibition threshold depend on multiple parameters, especially the previous microbial acclimation to ammonium stress. However, little is known about the effect of different NH4+ acclimation strategies on the differential expression of key active microbial taxa. Here, we applied NH4+ inputs of increasing intensity (from 1.7 to 15.2 g N-NH4+ liters−1) in batch assays fed with synthetic wastewater, according to two different strategies: (i) direct independent inputs at a unique target concentration and (ii) successive inputs in a stepwise manner. In both strategies, along the NH4+ gradient, the active methanogens shifted from acetoclastic Methanosaeta to Methanosarcina and eventually hydrogenotrophic Methanoculleus. Despite shorter latency times, the successive input modality led to lower methane production rate, lower soluble chemical oxygen demand (sCOD) removal efficiency, and lower half maximal inhibitory concentration, together with higher volatile fatty acid (VFA) accumulation, compared to the independent input modality. These differential performances were associated with a drastically distinct succession pattern of the active bacterial partners in both experiments. In particular, the direct exposure modality was characterized by a progressive enrichment of VFA producers (mainly Tepidimicrobium) and syntrophic VFA oxidizers (mainly Syntrophaceticus) with increasing NH4+ concentration, while the successive exposure modality was characterized by a more dynamic succession of VFA producers (mainly Clostridium, Sporanaerobacter, Terrisporobacter) and syntrophic VFA oxidizers (mainly Tepidanaerobacter, Syntrophomonas). These results bring relevant insights for improved process management through inoculum adaptation, bioaugmentation, or community-driven optimization. IMPORTANCE Anaerobic digestion (AD) is an attractive biotechnological process for wastewater bioremediation and bioenergy production in the form of methane-rich biogas. However, AD can be inhibited by ammonium generated by protein-rich effluent, commonly found in agro-industrial activities. Insights in the microbial community composition and identification of AD key players are crucial for anticipating process impairments in response to ammonium stress. They can also help in defining an optimal microbiome adapted to high ammonium levels. Here, we compared two strategies for acclimation of AD microbiome to increasing ammonium concentration to better understand the effect of this stress on the methanogens and their bacterial partners. Our results suggest that long-term cumulative exposure to ammonia disrupted the AD microbiome more strongly than direct (independent) ammonium additions. We identified bioindicators with different NH4+ tolerance capacity among VFA producers and syntrophic VFA oxidizers.
Published: 2021
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5. Evolution of Thermophilic Microbial Communities from a Deep-Sea Hydrothermal Chimney under Electrolithoautotrophic Conditions with Nitrate

Author: Guillaume Pillot, Oulfat Amin Ali, Sylvain Davidson, Laetitia Shintu, Yannick Combet-Blanc, Anne Godfroy, Patricia Bonin, and Pierre-Pol Liebgott
Subjects: microbial electrochemical systems, electroautotrophy, thermophily, deep-sea hydrothermal vent, nitrate, Biology (General), QH301-705.5
Abstract: Recent studies have shown the presence of an abiotic electrical current across the walls of deep-sea hydrothermal chimneys, allowing the growth of electroautotrophic microbial communities. To understand the role of the different phylogenetic groups and metabolisms involved, this study focused on electrotrophic enrichment with nitrate as electron acceptor. The biofilm density, community composition, production of organic compounds, and electrical consumption were monitored by FISH confocal microscopy, qPCR, metabarcoding, NMR, and potentiostat measurements. A statistical analysis by PCA showed the correlation between the different parameters (qPCR, organic compounds, and electron acceptors) in three distinct temporal phases. In our conditions, the Archaeoglobales have been shown to play a key role in the development of the community as the first colonizers on the cathode and the first producers of organic compounds, which are then used as an organic source by heterotrophs. Finally, through subcultures of the community, we showed the development of a greater biodiversity over time. This observed phenomenon could explain the biodiversity development in hydrothermal contexts, where energy sources are transient and unstable.
Published: 2021
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6. Increasing Hydrostatic Pressure Impacts the Prokaryotic Diversity during Emiliania huxleyi Aggregates Degradation

Author: Christian Tamburini, Marc Garel, Aude Barani, Dominique Boeuf, Patricia Bonin, Nagib Bhairy, Sophie Guasco, Stéphanie Jacquet, Frédéric A. C. Le Moigne, Christos Panagiotopoulos, Virginie Riou, Sandrine Veloso, Chiara Santinelli, and Fabrice Armougom
Subjects: biological carbon pump, carbon cycle, mesopelagic, mineral ballast, coccolithophorid, Emiliania huxleyi, Hydraulic engineering, TC1-978, Water supply for domestic and industrial purposes, TD201-500
Abstract: In the dark ocean, the balance between the heterotrophic carbon demand and the supply of sinking carbon through the biological carbon pump remains poorly constrained. In situ tracking of the dynamics of microbial degradation processes occurring on the gravitational sinking particles is still challenging. Our particle sinking simulator system (PASS) intends to mimic as closely as possible the in situ variations in pressure and temperature experienced by gravitational sinking particles. Here, we used the PASS to simultaneously track geochemical and microbial changes that occurred during the sinking through the mesopelagic zone of laboratory-grown Emiliania huxleyi aggregates amended by a natural microbial community sampled at 105 m depth in the North Atlantic Ocean. The impact of pressure on the prokaryotic degradation of POC and dissolution of E. huxleyi-derived calcite was not marked compared to atmospheric pressure. In contrast, using global O2 consumption monitored in real-time inside the high-pressure bottles using planar optodes via a sapphire window, a reduction of respiration rate was recorded in surface-originated community assemblages under increasing pressure conditions. Moreover, using a 16S rRNA metabarcoding survey, we demonstrated a drastic difference in transcriptionally active prokaryotes associated with particles, incubated either at atmospheric pressure or under linearly increasing hydrostatic pressure conditions. The increase in hydrostatic pressure reduced both the phylogenetic diversity and the species richness. The incubation at atmospheric pressure, however, promoted an opportunistic community of “fast” degraders from the surface (Saccharospirillaceae, Hyphomonadaceae, and Pseudoalteromonadaceae), known to be associated with surface phytoplankton blooms. In contrast, the incubation under increasing pressure condition incubations revealed an increase in the particle colonizer families Flavobacteriaceae and Rhodobacteraceae, and also Colwelliaceae, which are known to be adapted to high hydrostatic pressure. Altogether, our results underline the need to perform biodegradation experiments of particles in conditions that mimic pressure and temperature encountered during their sinking along the water column to be ecologically relevant.
Published: 2021
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7. Pressure-Retaining Sampler and High-Pressure Systems to Study Deep-Sea Microbes Under in situ Conditions

Author: Marc Garel, Patricia Bonin, Séverine Martini, Sophie Guasco, Marie Roumagnac, Nagib Bhairy, Fabrice Armougom, and Christian Tamburini
Subjects: pressure-retaining sampler, deep sea, in situ sampling, prokaryotic activities, prokaryotic diversity, Microbiology, QR1-502
Abstract: The pelagic realm of the dark ocean is characterized by high hydrostatic pressure, low temperature, high-inorganic nutrients, and low organic carbon concentrations. Measurements of metabolic activities of bathypelagic bacteria are often underestimated due to the technological limitations in recovering samples and maintaining them under in situ environmental conditions. Moreover, most of the pressure-retaining samplers, developed by a number of different labs, able to maintain seawater samples at in situ pressure during recovery have remained at the prototype stage, and therefore not available to the scientific community. In this paper, we will describe a ready-to-use pressure-retaining sampler, which can be adapted to use on a CTD-carousel sampler. As well as being able to recover samples under in situ high pressure (up to 60 MPa) we propose a sample processing in equi-pressure mode. Using a piloted pressure generator, we present how to perform sub-sampling and transfer of samples in equi-pressure mode to obtain replicates and perform hyperbaric experiments safely and efficiently (with
Published: 2019
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8. Identification of enriched hyperthermophilic microbial communities from a deep-sea hydrothermal vent chimney under electrolithoautotrophic culture conditions

Author: Pierre-Pol Liebgott, Yannick Combet-Blanc, Sylvain Davidson, Patricia Bonin, Anne Godfroy, Oulfat Amin, Laetitia Shintu, Guillaume Pillot, 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), Institut des Sciences Moléculaires de Marseille (ISM2), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: 0303 health sciences, 030306 microbiology, Ecosystem ecology, Science, Biodiversity, Deep sea, Article, Hydrothermal circulation, 03 medical and health sciences, chemistry.chemical_compound, chemistry, Nitrate, [SDU]Sciences of the Universe [physics], 13. Climate action, Environmental chemistry, Medicine, Chimney, Autotroph, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Sulfate, Energy source, 030304 developmental biology, Hydrothermal vent
Abstract: Deep-sea hydrothermal vents are extreme and complex ecosystems based on a trophic chain. We are still unsure of the identities of the first colonizers of these environments and their metabolism, but they are thought to be (hyper)thermophilic autotrophs. Here we investigate whether the electric potential observed across hydrothermal chimneys could serve as an energy source for these first colonizers. Experiments were performed in a two-chamber microbial electrochemical system inoculated with deep-sea hydrothermal chimney samples, with a cathode as sole electron donor, CO2 as sole carbon source, and nitrate, sulfate, or oxygen as electron acceptors. After a few days of culture, all three experiments showed growth of electrotrophic biofilms consuming the electrons (directly or indirectly) and producing organic compounds including acetate, glycerol, and pyruvate. Within the biofilms, the only known autotroph species retrieved were members of Archaeoglobales. Various heterotrophic phyla also grew through trophic interactions, with Thermococcales growing in all three experiments as well as other bacterial groups specific to each electron acceptor. This electrotrophic metabolism as energy source driving initial microbial colonization of conductive hydrothermal chimneys is discussed.
Published: 2021

9. The role of coupled DNRA-Anammox during nitrate removal in a highly saline lake

Author: Patricia Bonin, Thomas Hein, Juan José Gómez-Alday, Wolfgang Wanek, Nicolas Valiente, Judith Prommer, Franz Jirsa, 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)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), 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: 0106 biological sciences, Pollution, inorganic chemicals, Environmental Engineering, Denitrification, 010504 meteorology & atmospheric sciences, Nitrogen, media_common.quotation_subject, Nitrous Oxide, chemistry.chemical_element, 01 natural sciences, Mesocosm, chemistry.chemical_compound, Nitrate, Ammonium Compounds, Environmental Chemistry, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Waste Management and Disposal, Ecosystem, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, media_common, Nitrates, Chemistry, 010604 marine biology & hydrobiology, Aquatic ecosystem, Nitrous oxide, 6. Clean water, Lakes, 13. Climate action, Anammox, Environmental chemistry, [SDE]Environmental Sciences, Oxidation-Reduction
Abstract: Nitrate (NO3-) removal from aquatic ecosystems involves several microbially mediated processes, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and anaerobic ammonium oxidation (anammox), controlled by slight changes in environmental gradients. In addition, some of these processes (i.e. denitrification) may involve the production of undesirable compounds such as nitrous oxide (N2O), an important greenhouse gas. Saline lakes are prone to the accumulation of anthropogenic contaminants, making them highly vulnerable environments to NO3- pollution. The aim of this paper was to investigate the effect of light and oxygen on the different NO3- removal pathways under highly saline conditions. For this purpose, mesocosm experiments were performed using lacustrine, undisturbed, organic-rich sediments from the Petrola Lake (Spain), a highly saline waterbody subject to anthropogenic NO3- pollution. The revised 15N-isotope pairing technique (15N-IPT) was used to determine NO3- sink processes. Our results demonstrate for the first time the coexistence of denitrification, DNRA, and anammox processes in a highly saline lake, and how their contribution was determined by environmental conditions (oxygen and light). DNRA, and especially denitrification to N2O, were the dominant nitrogen (N) removal pathways when oxygen and/or light were present (up to 82%). In contrast, anoxia and darkness promoted NO3- reduction by DNRA (52%), combined with N loss by anammox (28%). Our results highlight the role of coupled DNRA-anammox, which has not yet been investigated in lacustrine sediments. We conclude that anoxia and darkness favored DNRA and anammox processes over denitrification and therefore to restrict N2O emissions to the atmosphere.
Published: 2022

10. Evolution of Thermophilic Microbial Communities from a Deep-Sea Hydrothermal Chimney under Electrolithoautotrophic Conditions with Nitrate

Author: Liebgott, Guillaume Pillot, Oulfat Amin Ali, Sylvain Davidson, Laetitia Shintu, Yannick Combet-Blanc, Anne Godfroy, Patricia Bonin, and Pierre-Pol
Subjects: microbial electrochemical systems, electroautotrophy, thermophily, deep-sea hydrothermal vent, nitrate
Abstract: Recent studies have shown the presence of an abiotic electrical current across the walls of deep-sea hydrothermal chimneys, allowing the growth of electroautotrophic microbial communities. To understand the role of the different phylogenetic groups and metabolisms involved, this study focused on electrotrophic enrichment with nitrate as electron acceptor. The biofilm density, community composition, production of organic compounds, and electrical consumption were monitored by FISH confocal microscopy, qPCR, metabarcoding, NMR, and potentiostat measurements. A statistical analysis by PCA showed the correlation between the different parameters (qPCR, organic compounds, and electron acceptors) in three distinct temporal phases. In our conditions, the Archaeoglobales have been shown to play a key role in the development of the community as the first colonizers on the cathode and the first producers of organic compounds, which are then used as an organic source by heterotrophs. Finally, through subcultures of the community, we showed the development of a greater biodiversity over time. This observed phenomenon could explain the biodiversity development in hydrothermal contexts, where energy sources are transient and unstable.
Published: 2021
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11. Thriving of hyperthermophilic microbial communities from a deep-sea sulfidic hydrothermal chimney under electrolithoautotrophic conditions with nitrate as electron acceptor

Author: Yannick Combet-Blanc, Guillaume Pillot, Pierre-Pol Liebgott, Sylvain Davidson, Patricia Bonin, Tanet L, Anne Godfroy, Laetitia Shintu, 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), MEDITERRANEAN INSTITUTE OF OCEANOGRAPHY MARSEILLE FRA, Partenaires IRSTEA, and Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)
Subjects: Abiotic component, 0303 health sciences, biology, 030306 microbiology, Chemistry, Heterotroph, Context (language use), biology.organism_classification, Deep sea, Hydrothermal circulation, Thermococcales, 03 medical and health sciences, chemistry.chemical_compound, Nitrate, Environmental chemistry, [SDE]Environmental Sciences, Energy source, 030304 developmental biology
Abstract: Recent studies have shown the presence of an abiotic electrical current across the walls of deep-sea hydrothermal chimneys, allowing the growth of electroautotrophic microbial communities. To understand the role of the different phylogenetic groups and metabolisms involved, this study focused on an electrotrophic enrichment, with nitrate as electron acceptor. The biofilm density, the community composition, the organic products released, and the electrical consumption were monitored by FISH confocal microscopy, qPCR, Metabarcoding, MNR and potentiostat measurements. A statistic analysis by PCA showed the correlation between the different parameters in 3 distinct temporal phases. The Archaeoglobales have been shown to play a key role in the development of the community, as first colonizers and producing pyruvate, therefor used as organic source for heterotrophs. Some Thermococcales showed the ability to perform electrofermentation of this pyruvate into acetate and H2. Finally, through subcultures of the community, we showed the development of a larger biodiversity over time. This observed phenomenon could explain the biodiversity development in hydrothermal context where energy sources are transient and unstable.
Published: 2021

12. Use of Stress Signals of Their Attached Bacteria to Monitor Sympagic Algae Preservation in Canadian Arctic Sediments

Author: Amiraux, Rémi, primary, Patricia, Bonin, additional, Christopher, Burot, additional, and Jean-François, Rontani, additional
Published: 2021
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13. Similar Methanogenic Shift but Divergent Syntrophic Partners in Anaerobic Digesters Exposed to Direct versus Successive Ammonium Additions

Author: Estelle Gonidec, Léa Cabrol, Sébastien Lacroix, Adele Lazuka, Corinne Valette, Patricia Bonin, Julie Hardy, Sophie Guasco, 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), Veolia Environnement (FRANCE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), MEDITERRANEAN INSTITUTE OF OCEANOGRAPHY MARSEILLE FRA, Partenaires IRSTEA, and Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)
Subjects: Physiology, Acclimatization, volatile fatty acids (VFA), adaptation, Wastewater, acclimation, 010501 environmental sciences, ammonia, 01 natural sciences, chemistry.chemical_compound, Bioreactors, Ammonium Compounds, Food science, Amino Acids, disturbance, 2. Zero hunger, 0303 health sciences, Ecology, biology, Chemistry, methane, Microbiota, Chemical oxygen demand, QR1-502, 6. Clean water, stress adaptation, Biodegradation, Environmental, Infectious Diseases, [SDE]Environmental Sciences, Methanoculleus, Research Article, Microbiology (medical), Bioaugmentation, perturbation, Microbiology, Methanosaeta, Bacteria, Anaerobic, 03 medical and health sciences, Ammonia, Genetics, Ammonium, stepwise, 0105 earth and related environmental sciences, General Immunology and Microbiology, 030306 microbiology, Cell Biology, Methanosarcina, biology.organism_classification, syntrophs, Anaerobic digestion, microbial diversity, syntrophic acetate oxidation (SAO), Methanomicrobiaceae, methanogen disturbance, acetate, syntrophic
Abstract: During anaerobic digestion (AD) of protein-rich wastewater, ammonium (NH4+) is released by amino acid degradation. High NH4+ concentrations disturb the AD microbiome balance, leading to process impairments. The sensitivity of the AD microbiome to NH4+ and the inhibition threshold depend on multiple parameters, especially the previous microbial acclimation to ammonium stress. However, little is known about the effect of different NH4+ acclimation strategies on the differential expression of key active microbial taxa. Here, we applied NH4+ inputs of increasing intensity (from 1.7 to 15.2 g N-NH4+ liters−1) in batch assays fed with synthetic wastewater, according to two different strategies: (i) direct independent inputs at a unique target concentration and (ii) successive inputs in a stepwise manner. In both strategies, along the NH4+ gradient, the active methanogens shifted from acetoclastic Methanosaeta to Methanosarcina and eventually hydrogenotrophic Methanoculleus. Despite shorter latency times, the successive input modality led to lower methane production rate, lower soluble chemical oxygen demand (sCOD) removal efficiency, and lower half maximal inhibitory concentration, together with higher volatile fatty acid (VFA) accumulation, compared to the independent input modality. These differential performances were associated with a drastically distinct succession pattern of the active bacterial partners in both experiments. In particular, the direct exposure modality was characterized by a progressive enrichment of VFA producers (mainly Tepidimicrobium) and syntrophic VFA oxidizers (mainly Syntrophaceticus) with increasing NH4+ concentration, while the successive exposure modality was characterized by a more dynamic succession of VFA producers (mainly Clostridium, Sporanaerobacter, Terrisporobacter) and syntrophic VFA oxidizers (mainly Tepidanaerobacter, Syntrophomonas). These results bring relevant insights for improved process management through inoculum adaptation, bioaugmentation, or community-driven optimization. IMPORTANCE Anaerobic digestion (AD) is an attractive biotechnological process for wastewater bioremediation and bioenergy production in the form of methane-rich biogas. However, AD can be inhibited by ammonium generated by protein-rich effluent, commonly found in agro-industrial activities. Insights in the microbial community composition and identification of AD key players are crucial for anticipating process impairments in response to ammonium stress. They can also help in defining an optimal microbiome adapted to high ammonium levels. Here, we compared two strategies for acclimation of AD microbiome to increasing ammonium concentration to better understand the effect of this stress on the methanogens and their bacterial partners. Our results suggest that long-term cumulative exposure to ammonia disrupted the AD microbiome more strongly than direct (independent) ammonium additions. We identified bioindicators with different NH4+ tolerance capacity among VFA producers and syntrophic VFA oxidizers.
Published: 2021

14. Benthic oxygen dynamics and implication for the maintenance of chronic hypoxia and ecosystem degradation in the Berre lagoon (France)

Author: Bastien Lamarque, Patricia Bonin, Pascal Mirleau, Olivier Radakovitch, Sylvain Rigaud, Bruno Deflandre, Samuel Meulé, Antoine Grémare, Márcio Murilo Barboza Tenório, Marie-Ange Cordier, Nicolas Mayot, Ludovic Pascal, Lara Pozzato, Vincent Faure, Baptiste Voltz, Florian Cesbron, Valérie Michotey, Christian Grenz, Alicia Romero-Ramirez, Détection, évaluation, gestion des risques CHROniques et éMErgents (CHROME) / Université de Nîmes (CHROME), Université de Nîmes (UNIMES), 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), 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 Universitaire des Sciences Appliquées de Cherbourg (LUSAC), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Institut national des sciences et techniques de la mer (INTECHMER), Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), 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), Groupement d'intérêt public pour la réhabilitation de l'étang de Berre (GIPREB), GIPREB, Universidade Federal do Rio de Janeiro (UFRJ), 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), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Laboratoire de recherche sur les transferts des radionucléides dans les écosystèmes aquatiques (IRSN/PSE-ENV/SRTE/LRTA), Service de recherche sur les transferts et les effets des radionucléides sur les écosystèmes (IRSN/PSE-ENV/SRTE), and Institut de Radioprotection et de Sûreté Nucléaire (IRSN)-Institut de Radioprotection et de Sûreté Nucléaire (IRSN)
Subjects: 0106 biological sciences, Biogeochemical cycle, 010504 meteorology & atmospheric sciences, Aquatic Science, Oceanography, Coastal hypoxia, 01 natural sciences, Water column, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Sediment–water interface, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Ecosystem, 14. Life underwater, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 010604 marine biology & hydrobiology, fungi, Biogeochemistry, Hypoxia (environmental), Sediment, 15. Life on land, Benthic habitat quality, Oxygen, 13. Climate action, Benthic zone, Sediment-water interface, [SDE]Environmental Sciences, Environmental science, Berre lagoon, geographic locations
Abstract: International audience; Chronic hypoxia and anoxia have strong impacts on coastal aquatic ecosystems worldwide. Such situations are essentially driven by high benthic oxygen (O2) demand resulting from organic matter mineralization in surface sediment and amplified by a low mixing of the water column. However, the benthic O2 demand may greatly vary according to the O2 availability, sediment biogeochemical properties, and bioturbation by macrobenthic fauna. Here we examined how the sediment O2 demand vary in response to seasonal and long-term (pluri-decadal) hypoxia in the Berre lagoon, a coastal ecosystem impacted by chronic hypoxia events since ca 60 years. Oxygen penetration depth, diffusive and total O2 fluxes were measured in situ using a microelectrode autonomous profiler and benthic chamber deployments at three sites impacted by quite-permanent (PA), seasonal (PI) and occasional (PO) hypoxia in August 2016. Those measurements were seasonally repeated at site PI between August 2015 and August 2016. Additional physical and chemical characteristics were also measured in surface sediment. Sediment profile images analysis combined to measures of benthic macrofaunal communities characteristics were determined in order to estimate the quality of the benthic ecosystem. The highest benthic O2 demand was observed after seasonal anoxia in relation to the important accumulation of reduced chemical species in surface sediment. Interestingly, both pluri-decadal hypoxia and normoxia produced relatively high benthic O2 demand related to a higher accumulation of organic matter and to the presence of reduced chemical species at site dominated by hypoxia, and to the presence of fresher organic matter and active bioturbating macrofaunal communities in normoxic site. The low benthic O2 demand at site seasonally impacted by hypoxia was explained by the degraded state of the macrofaunal community and by the lower accumulation of reduced chemical species. The occurrence of hypoxia and anoxia situations in the Berre lagoon was predicted from the competition between kinetics of benthic O2 demand and water column reoxygenation events induced by strong wind. The good correspondence between the measured and predicted hypoxia/anoxia occurrence clearly indicates that the chronic deoxygenation events in the Berre lagoon, and the associated degraded state of the benthic ecosystem are driven jointly by the benthic O2 demand and the intensity and duration of the water column stratification.
Published: 2021

15. Ecosystem maturity modulates greenhouse gases fluxes from artificial lakes

Author: Julien Cucherousset, Jean-Marc Baudoin, Fanny Colas, Patricia Bonin, Rémy Lassus, Léa Cabrol, Martin Daufresne, 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), Pôle Écla - écosystèmes lacustres (ECLA), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Office français de la biodiversité (OFB), 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), Institute of Ecology and Biodiversity and Department of Ecological Sciences, Facultad de Ciencias, Universidad de Chile, Risques, Ecosystèmes, Vulnérabilité, Environnement, Résilience (RECOVER), Aix Marseille Université (AMU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Équipe 3 - Écologie, Évolution, Écosystemes Souterrains (E3S), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Environmental Engineering, 010504 meteorology & atmospheric sciences, Gravel pit, [SDE.MCG]Environmental Sciences/Global Changes, Gas fluxes, Artificial lakes, 010501 environmental sciences, 01 natural sciences, Carbon cycle, Temperate climate, Environmental Chemistry, Ecosystem, Waste Management and Disposal, Ecosystem metabolism, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Maturity (geology), [SDE.IE]Environmental Sciences/Environmental Engineering, Ecology, Lake ecosystem, 15. Life on land, Eutrophication, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Pollution, 6. Clean water, 13. Climate action, Greenhouse gas, C cycling, [SDE]Environmental Sciences, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Lentic ecosystems play a major role in the global carbon cycling but the understanding of the environmental determinants of lake metabolism is still limited, notably in small artificial lakes. Here the effects of environmental conditions on lake metabolism and CO2 and CH4 emissions were quantified in 11 small artificial gravel pit lakes covering a gradient of ecosystem maturity, ranging from young oligotrophic to older, hypereutrophic lakes. The diffusive fluxes of CO2 and CH4 ranged from −30.10 to 37.78 mmol m−2 d−1 and from 3.05 to 25.45 mmol m−2 d−1 across gravel pit lakes, respectively. Nutrients and chlorophyll a concentrations were negatively correlated with CO2 concentrations and emissions but positively correlated with CH4 concentrations and emissions from lakes. These findings indicate that, as they mature, gravel pit lakes switch from heterotrophic to autotrophic-based metabolism and hence turn into CO2-sinks. In contrast, the emission of CH4 increased along the maturity gradient. As a result, eutrophication occurring during ecosystem maturity increased net emissions in terms of climate impact (CO2 equivalent) due to the higher contribution of CH4 emissions. Overall, mean CO2equivalent emission was 7.9 g m−2 d−1, a value 3.7 and 4.7 times higher than values previously reported in temperate lakes and reservoirs, respectively. While previous studies reported that lakes represent emitters of C to the atmosphere, this study highlights that eutrophication may reverse lake contribution to global C budgets. However, this finding is to be balanced with the fact that eutrophication also increased CH4 emissions and hence, enhanced the potential impact of these ecosystems on climate. Implementing mitigation strategies for maintaining intermediate levels of maturity is therefore needed to limit the impacts of small artificial waterbodies on climate. This could be facilitated by their small size and should be planned at the earliest stages of artificial lake construction.
Published: 2021

16. Bacterial diversity and lipid biomarkers in sea ice and sinking particulate organic material during the melt season in the Canadian Arctic

Author: Fabrice Armougom, Eléonore Frouin, Lise Artigue, Patricia Bonin, Marcel Babin, Rémi Amiraux, Jean-François Rontani, 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)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Takuvik Joint International Laboratory ULAVAL-CNRS, Centre National de la Recherche Scientifique (CNRS)-Université Laval [Québec] (ULaval), 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), Université Laval [Québec] (ULaval)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Takuvik International Research Laboratory, and Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Atmospheric Science, geography, Environmental Engineering, geography.geographical_feature_category, Ecology, Geology, 010501 environmental sciences, Particulates, Geotechnical Engineering and Engineering Geology, Oceanography, 01 natural sciences, 03 medical and health sciences, 030104 developmental biology, Arctic, 13. Climate action, [SDE]Environmental Sciences, Sea ice, Environmental science, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Lipid biomarkers, 0105 earth and related environmental sciences
Abstract: International audience; The estimation of important carbon fluxes in a changing Arctic environment remains a challenge, one that could benefit from the development of biomarkers that distinguish between sympagic (ice-associated) and pelagic organic material. Products of 10S-DOX-like lipoxygenase and fatty acid cis-trans isomerase (CTI) activity of bacteria attached to sympagic particulate organic matter (POM) were proposed previously as potential biomarkers of the contribution of sympagic biota to carbon fluxes to the seafloor. To date, neither the bacteria involved in such enzymatic activities nor the detection of these potential biomarkers at their presumed source (i.e., sea ice) has been investigated. Here, we determined and compared the diversity of prokaryotic communities (based on operational taxonomic units) attached to sea ice POM and under-ice sinking particles during an early stage of ice melt (brine drainage) in Baffin Bay (Canadian Arctic). Based on a time series of biodiversity analyses and the quantification of lipid tracers of these two bacterial enzymatic activities, we suggest that CTI-active bacteria, exposed to hypersaline stress, are attached to algal POM just above bottom sea ice and released into the water column following brine drainage. In contrast, bacteria attached to sinking particles and exhibiting 10S-DOX-like lipoxygenase activity are suggested to come from the bottommost layer of sea ice, where they may play a role in the detoxification of algae-produce free fatty acids. These results provide a refined view of the potential use of products of CTI activity as specific biomarkers of sympagic organic matter.
Published: 2021

17. Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning

Author: Patricia Bonin, Rémy Guyoneaud, Johanne Aubé, Pavel Senin, Olivier Pringault, Christophe Klopp, Céline Jeziorski, Olivier Bouchez, Marisol Goñi-Urriza, 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), Los Alamos National Laboratory (LANL), 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)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme Bio-Informatique - Génotoul, Institut National de la Recherche Agronomique (INRA), ANR-11-BSV7-0014,FUNHYMAT,Structure et fonctionnement de tapis microbiens contaminés avec des hydrocarbures(2011), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Ecosystèmes lagunaires : organisation biologique et fonctionnement (ECOLAG), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Département Génétique Animale (DEPT GA), GeT PlaGe, Genotoul, Unité de Biométrie et Intelligence Artificielle (UBIA), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), 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), GeT PlaGe, Genotoul (GeT PlaGe), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), and Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0301 basic medicine, BACTERIAL, GENES, Environmental remediation, 030106 microbiology, Soil Science, Polycyclic aromatic hydrocarbon, BIODEGRADATION, Oceanospirillales, diversity, BIOREMEDIATION, functioning, 03 medical and health sciences, Microbial ecology, Microbial mats, Alteromonadales, Microbial mat, Functioning, Ecology, Evolution, Behavior and Systematics, metatranscriptomic, chemistry.chemical_classification, Diversity, metagenomics, Bacteria, Ecology, biology, COMMUNITY RESPONSE, ARCHAEAL, microbial mats, DEGRADATION, Contamination, biology.organism_classification, OIL, Hydrocarbons, 030104 developmental biology, Metabolism, chemistry, 13. Climate action, Metagenomics, Environmental chemistry, [SDE]Environmental Sciences, Metagenome, Metatranscriptomic, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Transcriptome, metabolism, Water Pollutants, Chemical
Abstract: International audience; Photosynthetic microbial mats are stable, self-supported communities. Due to their coastal localization, these mats are frequently exposed to hydrocarbon contamination and are able to grow on it. To decipher how this contamination disturbs the functioning of microbial mats, we compared two mats: a contaminated mat exposed to chronic petroleum contamination and a reference mat. The taxonomic and metabolic structures of the mats in spring and fall were determined using metagenomic and metatranscriptomic approaches. Extremely high contamination disturbed the seasonal variations of the mat. ABC transporters, two-component systems, and type IV secretion system-related genes were overabundant in the contaminated mats. Xenobiotic degradation metabolism was minor in the metagenomes of both mats, and only the expression of genes involved in polycyclic aromatic hydrocarbon degradation was higher in the contaminated mat. Interestingly, the expression rates of genes involved in hydrocarbon activation decreased during the 1-year study period, concomitant with the decrease in easily degradable hydrocarbons, suggesting a transient effect of hydrocarbon contamination. Alteromonadales and Oceanospirillales hydrocarbonoclastic bacteria appeared to be key in hydrocarbon remediation in the contaminated mat. Overall, the contaminated microbial mat was able to cope with hydrocarbon contamination and displayed an adaptive functioning that modified seasonal behaviour.
Published: 2020

18. Oxygen and light determine the pathways of nitrate reduction in a highly saline lake

Author: Patricia Bonin, Thomas Hein, Wolfgang Wanek, Juan José Gómez-Alday, Franz Jirsa, Nicolas Valiente, University of Oslo (UiO), University of Vienna [Vienna], University of Johannesburg [South Africa] (UJ), Interuniversity Center for Aquatic Ecosystem Research, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), 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), Universidad de Castilla-La Mancha = University of Castilla-La Mancha (UCLM), PhD grant (BES-2012-052256) and project CICYT-CGL2017-87216-C4-2-R from the Spanish government, the SBPLY/17/180501/000296 project from the Castilla–La Mancha regional government, and funds for a Research Visit to Vienna (UCLM), University of Johannesburg (UJ), University of Natural Resources and Life Sciences (BOKU), and Universidad de Castilla-La Mancha (UCLM)
Subjects: inorganic chemicals, Pollution, Denitrification, [SDE.MCG]Environmental Sciences/Global Changes, Aquatic ecosystem, media_common.quotation_subject, Hypersaline lake, 6. Clean water, Mesocosm, chemistry.chemical_compound, Nitrate, chemistry, 13. Climate action, Anammox, Environmental chemistry, Ecosystem, media_common
Abstract: Nitrate (NO3−) removal from aquatic ecosystems involves several microbially mediated processes including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and anaerobic ammonium oxidation (anammox) regulated by slight changes in environmental gradients. Saline lakes are prone to the accumulation of anthropogenic contaminants, making them highly vulnerable environments to NO3− pollution. We investigated nitrate removal pathways in mesocosm experiments using lacustrine, undisturbed, organic-rich sediments from Pétrola Lake (Spain), a highly saline waterbody subject to anthropogenic NO3− pollution. We used the revised 15N-isotope pairing technique (15N-IPT) to determine NO3− sink processes. Our results demonstrate the coexistence of denitrification, DNRA, and anammox processes, and their contribution was determined by environmental conditions (oxygen and light). DNRA and N2O-denitrification were the dominant nitrogen (N) removal pathways when oxygen and/or light were present (up to 82 %). In contrast, anoxia and darkness promoted NO3− reduction by DNRA (52 %) and N loss by anammox (28 %). Our results highlight the role of coupled DNRA-anammox, as yet has never been investigated in hypersaline lake ecosystems. We conclude that anoxia and darkness favored DNRA and anammox processes over denitrification and therefore reduce N2O emissions to the atmosphere.
Published: 2020

19. Supplementary material to 'Oxygen and light determine the pathways of nitrate reduction in a highly saline lake'

Author: Nicolás Valiente, Franz Jirsa, Thomas Hein, Wolfgang Wanek, Patricia Bonin, and Juan José Gómez-Alday
Published: 2020

20. Stress factors resulting from the Arctic vernal sea-ice melt

Author: Patricia Bonin, Rémi Amiraux, Sophie Guasco, Frédéric Vaultier, Marcel Babin, Christopher Burot, Jean-François Rontani, Guillaume Massé, 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 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), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Takuvik International Research Laboratory, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), Variabilité de l'Océan et de la Glace de mer (VOG), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)
Subjects: 0106 biological sciences, Atmospheric Science, Environmental Engineering, 010504 meteorology & atmospheric sciences, Oceanography, 01 natural sciences, Stress (mechanics), Algae, Sea ice, 14. Life underwater, 0105 earth and related environmental sciences, geography, geography.geographical_feature_category, Ecology, biology, Chemistry, 010604 marine biology & hydrobiology, Geology, Geotechnical Engineering and Engineering Geology, biology.organism_classification, The arctic, Salinity, 13. Climate action, [SDE]Environmental Sciences, human activities
Abstract: International audience; During sea-ice melt in the Arctic, primary production by sympagic (sea-ice) algae can be exported efficiently to the seabed if sinking rates are rapid and activities of associated heterotrophic bacteria are limited. Salinity stress due to melting ice has been suggested to account for such low bacterial activity. We further tested this hypothesis by analyzing samples of sea ice and sinking particles collected from May 18 to June 29, 2016, in western Baffin Bay as part of the Green Edge project. We applied a method not previously used in polar regions—quantitative PCR coupled to the propidium monoazide DNA-binding method—to evaluate the viability of bacteria associated with sympagic and sinking algae. We also measured cis-trans isomerase activity, known to indicate rapid bacterial response to salinity stress in culture studies, as well as free fatty acids known to be produced by algae as bactericidal compounds. The viability of sympagic-associated bacteria was strong in May (only approximately 10% mortality of total bacteria) and weaker in June (average mortality of 43%; maximum of 75%), with instances of elevated mortality in sinking particle samples across the time series (up to 72%). Short-term stress reflected by cis-trans isomerase activity was observed only in samples of sinking particles collected early in the time series. Following snow melt, however, and saturating levels of photosynthetically active radiation in June, we observed enhanced ice-algal production of bactericidal compounds (free palmitoleic acid; up to 4.8 mg L–1). We thus suggest that protection of sinking sympagic material from bacterial degradation early in a melt season results from low bacterial activity due to salinity stress, while later in the season, algal production of bactericidal compounds induces bacterial mortality. A succession of bacterial stressors during Arctic ice melt helps to explain the efficient export of sea-ice algal material to the seabed.
Published: 2020

21. Salinity shifts in marine sediment: Importance of number of fluctuation rather than their intensities on bacterial denitrifying community

Author: Patricia Bonin, Imen Zaghmouri, Fabrice Armougom, Valérie Michotey, Sophie Guasco, 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: Salinity fluctuations, 0106 biological sciences, 0301 basic medicine, Microcosm, Geologic Sediments, Salinity, salinity fluctuations, Denitrification, [SDE.MCG]Environmental Sciences/Global Changes, Resistance, Aquatic Science, Oceanography, 01 natural sciences, resistance, 03 medical and health sciences, Denitrifying bacteria, Abundance (ecology), Pseudomonas, Community shift, 14. Life underwater, community shift, denitrification, Bacteria, Resistance (ecology), Ecology, 010604 marine biology & hydrobiology, Sediment, Pollution, microcosm, High resistance, 030104 developmental biology, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; The sensitivity of denitrifying community to salinity fluctuations was studied in microcosms filled with marine coastal sediments subjected to different salinity disturbances over time (sediment under frequent salinity changes vs sediment with "stable" salinity pattern). Upon short-term salinity shift, denitrification rate and denitrifiers abundance showed high resistance whatever the sediment origin is. Denitrifying community adapted to frequent salinity changes showed high resistance when salinity increases, with a dynamic nosZ relative expression level. Marine sediment denitrifying community, characterized by more stable pattern, was less resistant when salinity decreases. However, after two successive variations of salinity, it shifted toward the characteristic community of fluctuating conditions, with larger proportion of Pseudomonas-nosZ, exhibiting an increase of nosZ relative expression level. The impact of long-term salinity variation upon bacterial community was confirmed at ribosomal level with a higher percentage of Pseudomonas and lower proportion of nosZII clade genera.
Published: 2018

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

Author: Valérie Michotey, Patricia Bonin, Emma Michaud, Léa Sylvi, Robert Duran, Marc Tedetti, Enora Roic, Cécile Militon, Lise Millera Ferriz, Ronan Jézéquel, Cristiana Cravo-Laureau, Franck Gilbert, Philippe Cuny, Karine Duboscq, Centre de documentation de recherche et d'expérimentations sur les pollutions accidentelles des eaux (Cedre), Cedre, 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 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 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), 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), and Université de Toulouse (UT)
Subjects: 0301 basic medicine, Ecology, [SDE.MCG]Environmental Sciences/Global Changes, Weathering, 15. Life on land, 010501 environmental sciences, [SDE.ES]Environmental Sciences/Environmental and Society, 01 natural sciences, 03 medical and health sciences, 030104 developmental biology, 13. Climate action, Environmental science, Marine ecosystem, 14. Life underwater, Mangrove, Mangrove ecosystem, Oil pollution, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract: 2017-410 Mangroves are among the most sensitive marine ecosystems to oil pollution due both to the sensitivity of mangroves species and to the high persistence of hydrocarbons in these environments. Despite their ecological and socio-economic value, the potential effects of an oil spill on French Guiana mangroves remain so far unknown. Yet, there is an increasing transboundary risk of oil spill due to Brazilian offshore oil exploitation (in mid-April 2013, there were 122 offshore drilling rigs in Brazil, including 29 under construction – Brazilian Amapá region located in the French Guiana border area is thought to become an important world oil production area in the coming years). The aim of the PRISME project was to assess the natural degradation of oil in mangrove sediment as well as its impact on benthic communities (micro, meio and macrobenthos): a one-month in situ experiment was conducted in the young French Guianese mangrove (around 3 years old) at the mouth of the Sinnamary estuary. The experimental units consisted in eight plastic cores (Ø : 10 cm ; height: 30 cm) manually introduced within sediments. A thin layer of oiled sediment (2 cm, 20 000 ppm) was applied on four cores while the remaining four cores were considered as control (no oil addition). Three cores were additionally sampled at the beginning of the experiment as initial control sediments. After one month in situ, the eight cores were collected and sliced on site into different sedimentary layers aliquots for later analyses (hydrocarbons, bacterial, meio, macrofauna fauna diversity, bioturbation, biogeochemical parameters). Samples were sent to the different laboratories involved in this multidisciplinary project. Results and knowledge gained from this experimental work were used to develop an approach for assessing coastal vulnerability for oil spills preparedness in mangroves.
Published: 2017

23. Enhanced biotic degradation of terrestrial POM in an estuarine salinity gradient: interactive effects of organic matter pools and changes of bacterial communities

Author: Mairie-Aimée Galeron, Jean-François Rontani, Sophie Guasco, Patricia Bonin, Anne-Hélène Prime, Laboratoire de psychologie sociale et de psychologie cognitive (LAPSCO), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)
Subjects: chemistry.chemical_classification, geography, geography.geographical_feature_category, [SDV]Life Sciences [q-bio], Estuary, 15. Life on land, Aquatic Science, Biodegradation, Salinity, Interactive effects, chemistry, Terrestrial organic matter, 13. Climate action, Environmental chemistry, [SDE]Environmental Sciences, Degradation (geology), Environmental science, Organic matter, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

24. Pressure-Retaining Sampler and High-Pressure Systems to Study Deep-Sea Microbes Under in situ Conditions

Author: Christian Tamburini, Fabrice Armougom, Marie Roumagnac, Nagib Bhairy, Patricia Bonin, Marc Garel, Sophie Guasco, Séverine Martini, 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 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), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: In situ, Microbiology (medical), Hydrostatic pressure, lcsh:QR1-502, chemistry.chemical_element, prokaryotic diversity, Oxygen, Deep sea, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Mediterranean sea, prokaryotic activities, 14. Life underwater, Incubation, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, 0303 health sciences, Atmospheric pressure, 030306 microbiology, [SDE.IE]Environmental Sciences/Environmental Engineering, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, chemistry, 13. Climate action, deep sea, Environmental chemistry, pressure-retaining sampler, Environmental science, Seawater, in situ sampling, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: The pelagic realm of the dark ocean is characterized by high hydrostatic pressure, low temperature, high-inorganic nutrients, and low organic carbon concentrations. Measurements of metabolic activities of bathypelagic bacteria are often underestimated due to the technological limitations in recovering samples and maintaining them under in situ environmental conditions. Moreover, most of the pressure-retaining samplers, developed by a number of different labs, able to maintain seawater samples at in situ pressure during recovery have remained at the prototype stage, and therefore not available to the scientific community. In this paper, we will describe a ready-to-use pressure-retaining sampler, which can be adapted to use on a CTD-carousel sampler. As well as being able to recover samples under in situ high pressure (up to 60 MPa) we propose a sample processing in equi-pressure mode. Using a piloted pressure generator, we present how to perform sub-sampling and transfer of samples in equi-pressure mode to obtain replicates and perform hyperbaric experiments safely and efficiently (with
Published: 2019
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25. Pressure-Retaining Sampler and High-Pressure Systems to Study Deep-Sea Microbes Under

Author: Marc, Garel, Patricia, Bonin, Séverine, Martini, Sophie, Guasco, Marie, Roumagnac, Nagib, Bhairy, Fabrice, Armougom, and Christian, Tamburini
Subjects: deep sea, prokaryotic activities, pressure-retaining sampler, Methods, in situ sampling, prokaryotic diversity, Microbiology
Abstract: The pelagic realm of the dark ocean is characterized by high hydrostatic pressure, low temperature, high-inorganic nutrients, and low organic carbon concentrations. Measurements of metabolic activities of bathypelagic bacteria are often underestimated due to the technological limitations in recovering samples and maintaining them under in situ environmental conditions. Moreover, most of the pressure-retaining samplers, developed by a number of different labs, able to maintain seawater samples at in situ pressure during recovery have remained at the prototype stage, and therefore not available to the scientific community. In this paper, we will describe a ready-to-use pressure-retaining sampler, which can be adapted to use on a CTD-carousel sampler. As well as being able to recover samples under in situ high pressure (up to 60 MPa) we propose a sample processing in equi-pressure mode. Using a piloted pressure generator, we present how to perform sub-sampling and transfer of samples in equi-pressure mode to obtain replicates and perform hyperbaric experiments safely and efficiently (with
Published: 2018

26. Denitrification activity in mangrove sediments varies with associated vegetation

Author: P.A. LokaBharathi, Maria-Judith Gonsalves, Sheryl Oliveira Fernandes, Pinky Dutta, Patricia Bonin, 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: 0106 biological sciences, Environmental Engineering, Denitrification, [SDE.MCG]Environmental Sciences/Global Changes, Intertidal zone, 010501 environmental sciences, Management, Monitoring, Policy and Law, 01 natural sciences, Dominance (ecology), 14. Life underwater, 0105 earth and related environmental sciences, Nature and Landscape Conservation, Rhizophora mucronata, biology, [SDE.IE]Environmental Sciences/Environmental Engineering, Ecology, 010604 marine biology & hydrobiology, Sediment, 15. Life on land, Plant litter, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, 13. Climate action, Avicennia marina, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Mangrove
Abstract: International audience; To test the hypothesis that mangrove vegetation associated sediment characteristics could influence an ecologically important function such as denitrification, a study was carried out at the Divar mangrove ecosystem in Goa, India. The composition of intertidal mangroves was assessed based on which the down-core (0-10 cm) variation in environmental variables and denitrification activity (DNT) associated with dominant vegetation types was examined. Our observations revealed a distinct zonation pattern of mangroves with the dominance of Rhizophora mucronata (RM) in the lower intertidal zone followed by Avicennia marina (AM) in the mid region. Acanthus ilicifolius (AI) was restricted to the upper intertidal zone (UIZ) which was characterized by relatively lower sediment temperatures, higher porewater salinity and intense reducing conditions. A zonation pattern in occurrence of DNT was also observed. Denitrification activity generally decreased with depth and increased in intensity from the seaward to the landward side. Maximum DNT of 4.06 +/- 0.44 nmol N2O g(-1) h(-1) was recorded in the surficial AI sediments followed by AM and RM sediments. Surface plant litter content also increased from the lower to UIZ. A negative relationship of NH4+ and total organic carbon content (n=15, r=-0.388, p
Published: 2016

27. The nature of the electron acceptor (MnIV/NO3) triggers the differential expression of genes associated with stress and ammonium limitation responses in Shewanella algae C6G3

Author: Patricia Bonin, Chantal Iobbi-Nivol, Valérie Michotey, Fabrice Armougom, Nicolas Fernandez-Nunez, Jean Imbert, Aurélie Bergon, Béatrice Loriod, Axel Aigle, Sophie Guasco, 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), Theories and Approaches of Genomic Complexity (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Bioénergétique et Ingénierie des Protéines (BIP ), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Shewanella, 030106 microbiology, Asparagine synthetase, Manganese-oxide, Shewanella algae, Electrons, Microbiology, Cofactor, Electron Transport, 03 medical and health sciences, chemistry.chemical_compound, Bacterial Proteins, nitrate, Glutamine synthetase, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Ammonium Compounds, Genetics, Ammonium, Nitrite, manganese oxide, Molecular Biology, Peroxidase, chemistry.chemical_classification, Nitrates, biology, Chemistry, catalase, nitrogen limitation, Oxides, nitrogen-limitation, Gene Expression Regulation, Bacterial, biology.organism_classification, Catalase, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Amino acid, 030104 developmental biology, Biochemistry, Manganese Compounds, biology.protein, catalase 30, transcriptome
Abstract: Shewanella algae C6G3 can dissimilatively reduce nitrate into ammonium and manganese oxide (MnIV) into MnII. It has the unusual ability to anaerobically produce nitrite from ammonium in the presence of MnIV. To gain insight into their metabolic capabilities, global mRNA expression patterns were investigated by RNA-seq and qRT-PCR in cells growing with lactate and ammonium as carbon and nitrogen sources, and with either MnIV or nitrate as electron acceptors. Genes exhibiting higher expression levels in the presence of MnIV belonged to functional categories of carbohydrate, coenzyme, lipid metabolisms and inorganic ion transport. The comparative transcriptomic pattern between MnIV and NO3 revealed that the strain presented an ammonium limitation status with MnIV, despite the presence of a non-limiting concentration of ammonium under both culture conditions. In addition, in the presence of MnIV, ntrB/nrtC regulators, ammonium channel, nitrogen regulatory protein P-II, glutamine synthetase and asparagine synthetase glutamine-dependent genes were over-represented. Under the nitrate condition, the expression of genes involved in the synthesis of several amino acids was increased. Finally, the expression level of genes associated with the general stress response was also amplified in both conditions and among them, katE, a putative catalase/peroxidase present on several Shewanella genomes, was highly expressed with a median value relatively higher in the MnIV condition.
Published: 2018

28. Evolutionary Success of Prokaryotes

Author: Anne Godfroy, Philippe Normand, Karine Alain, Patricia Bonin, Bernard Ollivier, Nathalie Pradel, Jean-Claude Bertrand, Institut Pythéas (OSU PYTHEAS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-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), 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 de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bertrand, J.C. (ed.), Normand, P. (ed.), Ollivier, Bernard (ed.), Sime-Ngando, T. (ed.), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Laboratoire d'océanographie et de biogéochimie (LOB), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Département informatique (INFO), and Institut Mines-Télécom [Paris] (IMT)-Télécom Bretagne-Université européenne de Bretagne - European University of Brittany (UEB)
Subjects: 0303 health sciences, 03 medical and health sciences, Race (biology), Red queen, 030306 microbiology, Ecology, [SDV]Life Sciences [q-bio], [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biology, ComputingMilieux_MISCELLANEOUS, Organism, 030304 developmental biology
Abstract: How can the evolutionary success of prokaryotes be explained ? How did they manage to survive conditions that have fluctuated, with drastic events over 3.5 billion years ? Which significant metabolisms and mechanisms have appeared over the course of evolution that have permitted them to survive the most inhospitable conditions from the physicochemical point of view ? In a 'Red Queen Race', prokaryotes have always run sufficiently fast to adapt to constraints imposed by the environment and the other living species with which they have established interactions. If the criterion retained to define the level of evolution of an organism is its capacity to survive and to yield the largest number of offsprings, prokaryotes must be considered highly evolved organisms.
Published: 2018

29. Monitoring photo-oxidative and salinity-induced bacterial stress in the Canadian Arctic using specific lipid tracers

Author: Frédéric Vaultier, Rémi Amiraux, Michel Gosselin, Simon T. Belt, Virginie Galindo, Patricia Bonin, Jean-François Rontani, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Département d'Océanographie, Université du Québec à Rimouski (UQAR), Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Université du Québec A Rimouski ( UQAR ), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Biogeochemistry Research Centre (BGC), Plymouth University, University of Manitoba [Winnipeg], Institut des Sciences de la MER de Rimouski (ISMER), 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: 0106 biological sciences, 0301 basic medicine, [SDE.MCG]Environmental Sciences/Global Changes, Oceanography, 01 natural sciences, 03 medical and health sciences, Extracellular polymeric substance, Water column, Algae, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Phytoplankton, Sea ice, Environmental Chemistry, Organic matter, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, Water Science and Technology, chemistry.chemical_classification, geography, geography.geographical_feature_category, biology, 010604 marine biology & hydrobiology, General Chemistry, biology.organism_classification, Salinity, [ SDE.MCG ] Environmental Sciences/Global Changes, 030104 developmental biology, chemistry, Arctic, 13. Climate action, [SDE]Environmental Sciences, [ CHIM.ANAL ] Chemical Sciences/Analytical chemistry
Abstract: We determined, and compared, the abiotic stress state of algae and their attached bacterial communities following their release into the water column during the Arctic sea ice melt season using specific lipid markers that are characteristic of type II photo-oxidation processes, together with those associated with cis-trans isomerase and 10 S -DOX-like lipoxygenase activity, which are indicative of salinity stress. More specifically, parent lipids and some of their oxidation products were quantified in sinking particles (from sediment traps) collected from the Beaufort Sea, Resolute Passage and the Davis Strait (Canadian Arctic) in 2009, 2012 and 2015, respectively. Our data show that salinity- and light-induced bacterial stress processes are temporally decoupled, with the former occurring at the beginning of ice melting and the latter observed during the final stages of ice melt and in subsequent open waters. The salinity-induced bacterial stress seen during the early stages of ice melting contrasts the healthy state of sea ice algae under the same hypersaline conditions. As sea ice melt progresses, brine channels become hyposaline, thus reducing the bacterial salinity stress, while ice algae become susceptible to photodegradation by singlet oxygen ( 1 O 2 ), despite relatively low temperatures and irradiance. However, the presence of high amounts of extracellular polymeric substances (EPS) encapsulating the algae likely prevents the diffusion of 1 O 2 to the attached bacteria. Photo-oxidative stress is enhanced further in open waters due to the low amounts of EPS. The lower amounts of active bacteria in the Arctic compared to temperate or tropical regions is thus attributed to the combined action of efficient salinity stress in spring and photo-oxidative stress in summer. Outcomes from this study also imply that surface sediments from the Canadian Arctic contain relatively high quantities of sea ice-derived organic matter that has undergone a strong degree of salinity-induced stress.
Published: 2017

30. Physiological and transcriptional approaches reveal connection between nitrogen and manganese cycles in Shewanella algae C6G3

Author: Vincent Méjean, Patricia Bonin, Axel Aigle, Chantal Iobbi-Nivol, Valérie Michotey, 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), Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), and Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)
Subjects: 0301 basic medicine, Shewanella, Nitrite Reductases, Transcription, Genetic, Nitrogen, [SDV]Life Sciences [q-bio], 030106 microbiology, chemistry.chemical_element, Electrons, Shewanella algae, Manganese, Nitrate Reductase, Article, 03 medical and health sciences, chemistry.chemical_compound, Nitrate, Ammonium, Anaerobiosis, Nitrite, Nitrites, chemistry.chemical_classification, Nitrates, Multidisciplinary, biology, Cell Membrane, Gene Expression Regulation, Bacterial, Electron acceptor, biology.organism_classification, Nitrite reductase, Kinetics, 030104 developmental biology, Biochemistry, chemistry, Genes, Bacterial, Cytochromes
Abstract: To explain anaerobic nitrite/nitrate production at the expense of ammonium mediated by manganese oxide (Mn(IV)) in sediment, nitrate and manganese respirations were investigated in a strain (Shewanella algae C6G3) presenting these features. In contrast to S. oneidensis MR-1, a biotic transitory nitrite accumulation at the expense of ammonium was observed in S. algae during anaerobic growth with Mn(IV) under condition of limiting electron acceptor, concomitantly, with a higher electron donor stoichiometry than expected. This low and reproducible transitory accumulation is the result of production and consumption since the strain is able to dissimilative reduce nitrate into ammonium. Nitrite production in Mn(IV) condition is strengthened by comparative expression of the nitrate/nitrite reductase genes (napA, nrfA, nrfA-2), and rates of the nitrate/nitrite reductase activities under Mn(IV), nitrate or fumarate conditions. Compared with S. oneidensis MR-1, S. algae contains additional genes that encode nitrate and nitrite reductases (napA-α and nrfA-2) and an Outer Membrane Cytochrome (OMC)(mtrH). Different patterns of expression of the OMC genes (omcA, mtrF, mtrH and mtrC) were observed depending on the electron acceptor and growth phase. Only gene mtrF-2 (SO1659 homolog) was specifically expressed under the Mn(IV) condition. Nitrate and Mn(IV) respirations seem connected at the physiological and transcriptional levels.
Published: 2017

31. Biotic and abiotic degradation of marine and terrestrial higher plant material in intertidal surface sediments from Arcachon Bay (France): A lipid approach

Author: Jean-François Rontani, Patricia Bonin, and Frédéric Vaultier
Subjects: Fragmentation (reproduction), Autoxidation, biology, Bacterial degradation, Intertidal zone, General Chemistry, Oceanography, biology.organism_classification, Seagrass, Botany, Environmental Chemistry, Degradation (geology), Zostera, Bay, Geology, Water Science and Technology
Abstract: The lipid content of muddy and sandy surface sediments from Arcachon Bay (France) was investigated. A very intense autoxidation and bacterial degradation of sitosterol (mainly arising in this zone from terrestrial higher plants or seagrasses) was observed. In order to explain this unexpected very strong degradation, the lipid contents of senescent leaves of terrestrial higher plants and Zostera noltii (the dominant seagrass in Arcachon Bay) were examined. Lipids and notably sterols appeared to be strongly affected by photooxidative processes in Z. noltii , but not in terrestrial higher plants. On the basis of: (i) the very high efficiency of photooxidation processes in detached leaves of seagrasses and (ii) the very good preservation of hydroperoxides in this material, the intense autoxidation of sitosterol observed was attributed to a strong contribution of highly photooxidized senescent leaves of Z. noltii to these sediments. Due to the presence of metal ions able to induce oxido-reduction reactions with one electron transfer, photochemically-produced hydroperoxides could be cleaved homolytically inducing then free radical oxidation processes in seagrass debris within the oxic layer of sediments. It was hypothesized that the intense bacterial degradation of sitosterol also observed result from solar light-induced fragmentation of leaves of Z. noltii .
Published: 2014

32. Denitrification activity is closely linked to the total ambient Fe concentration in mangrove sediments of Goa, India

Author: Patricia Bonin, P.A. LokaBharathi, Valérie Michotey, Maria-Judith Gonsalves, Sheryl Oliveira Fernandes, 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: 0106 biological sciences, Denitrification, [SDE.MCG]Environmental Sciences/Global Changes, chemistry.chemical_element, Aquatic Science, Oceanography, Monsoon, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Nitrate, Respiration, medicine, 14. Life underwater, Hydrology, 0303 health sciences, 030306 microbiology, 010604 marine biology & hydrobiology, Seasonality, medicine.disease, [SDE.ES]Environmental Sciences/Environmental and Society, Nitrogen, chemistry, Benthic zone, Environmental chemistry, Mangrove, denitrification denitrifiers iron mangroves nitrogen sediments
Abstract: Denitrification activity (DNT) and associated environmental parameters were examined in two mangrove ecosystems of Goa, India- the relatively pristine Tuvem and the anthropogenically influenced Divar. Sampling was carried out at every 2 cm interval within the 0-10 cm depth range to determine (i) seasonal (pre-monsoon, monsoon and post-monsoon) down-core variation in DNT (ii) assess the environmental factors influencing the DNT and (iii) to build predictive models for benthic DNT. Denitrification generally decreased with depth and showed marked seasonal variation at both the locations (p < 0.001, df = 2). Denitrification peaked during the pre-monsoon occurring at a rate of up to 21.00 ± 12.84 nmol N2O g -1 h -1 within 0-4 cm at both the locations. Further, DNT at pre-monsoon was significantly influenced by Fe content at Tuvem (n = 15, r = -0.660, p < 0.01) and Divar (r = -0.631, p < 0.01) suggesting Fe-mediated nitrate respiration. The influence of other limiting substrates like NO3 - and NO2 - was most important during the monsoon and post-monsoon especially at Divar. The multiple regression models developed could predict 67-98% of the observed variability in DNT through the seasons. About 6-9 environmental variables were required to fairly predict DNT in these sediments with the complexity governing DNT decreasing from pre-monsoon to post-monsoon. Our results reveal that seasonal dynamics of DNT in tropical mangrove sediments are closely linked to the total Fe at the prevailing ambient concentration in both the systems.
Published: 2013

33. 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: Alexandre Atkinson, Céline Jeziorski, Patricia Bonin, Cécile Militon, Valérie Michotey, Robert Duran, Cristiana Cravo-Laureau, Philippe Cuny, Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -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)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Equipe Environnement et Microbiologie (EEM ), 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)-Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), French National Agency (ANR) under the DHYVA project [ANR 2006 SEST 09], French National Agency (ANR) under DECAPAGE project [ANR 2011 CESA 006 01], ANR-06-SEST-0009,DHYVA,Dégradation d'HYdrocarbures dans les VAsières (DHYVA) : Rôle des mécanismes bactériens et effet de la bioturbation dans la biodisponibilité des polluants organiques(2006), ANR-11-CESA-0006,DECAPAGE,Caractérisation des capacités de dégradation de communautés bactériennes de sédiments marins : adaptation, processus métaboliques et influence des régimes d'oxygénation(2011), 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), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), GeT PlaGe, Genotoul, Institut National de la Recherche Agronomique (INRA), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)-Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD)
Subjects: 0301 basic medicine, Geologic Sediments, Hydrocarbon, Microorganism, [ SDV.BBM.BM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, 010501 environmental sciences, Aquatic Science, 01 natural sciences, 03 medical and health sciences, Microbial community, Genetics, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Animals, Petroleum Pollution, 14. Life underwater, Marine sediment, 0105 earth and related environmental sciences, Polychaete, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Oxygen regimes, biology, Bacteria, Ecology, fungi, Sediment, Polychaeta, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Contamination, biology.organism_classification, 030104 developmental biology, Microbial population biology, 13. Climate action, Benthic zone, Hediste diversicolor, Metagenome, France, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Metatranscriptomic, Bioturbation, Transcriptome, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: In coastal marine sediment, oxygen fluctuations induced by bioturbating activities are widespread and exert a great influence, not only on the structure and diversity of the microbenthic communities, but also on their activities. Thus, the activity of benthic organisms can have a significant influence on the degradation of hydrocarbons (HC) and can favor the development of hydrocarbonoclastic microorganisms in contaminated marine sediments. Here, we have generated metatranscriptomic data from coastal marine sediments affected by oil addition and/or by the reworking activity of the marine polychaete Hediste diversicolor to gain insights into the active microbial groups involved in the response to oil addition under the oxygen-fluctuating conditions. The preliminary results suggest that the macrofauna promote the diversity of active aerobic hydrocarbonoclastic bacteria in marine sediments, even if its influence cannot be strongly observed at the microbial community expression profiles level.
Published: 2016

34. The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats

Author: Rémy Guyoneaud, Christophe Klopp, Noëlle Bru, Olivier Bouchez, Bruno Deflandre, Marisol Goñi-Urriza, Johanne Aubé, Pavel Senin, Patricia Bonin, Edurne Biritxinaga-Etchart, Olivier Pringault, Los Alamos National Laboratory (LANL), Ecologie des systèmes marins côtiers (Ecosym), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), 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)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Laboratoire de Mathématiques et de leurs Applications [Pau] (LMAP), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Institut des sciences analytiques et de physico-chimie pour l'environnement et les materiaux (IPREM), 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), Environnements et Paléoenvironnements OCéaniques (EPOC), 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), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), French National Research Agency (ANR FUNHYMAT) [ANR11 BSV7 014 01], Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: Biogeochemical functioning, 0301 basic medicine, Cyanobacteria, Biogeochemical cycle, Microbial Consortia, 030106 microbiology, Aquatic Science, Oceanography, Photosynthesis, 03 medical and health sciences, RNA, Ribosomal, 16S, Microbial mats, medicine, Microbial mat, Diversity, Bacteria, biology, Ecology, Seasonality, Contamination, medicine.disease, biology.organism_classification, Hydrocarbonoclastic bacteria, Pollution, Hydrocarbons, 030104 developmental biology, Microbial population biology, 13. Climate action, [SDE]Environmental Sciences, France, Seasons, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Sulfur, Water Pollutants, Chemical
Abstract: International audience; Photosynthetic microbial mats are metabolically structured systems driven by solar light. They are ubiquitous and can grow in hydrocarbon-polluted sites. Our aim is to determine the impact of chronic hydrocarbon contamination on the structure, activity, and functioning of a microbial mat. We compared it to an uncontaminated mat harboring similar geochemical characteristics. The mats were sampled in spring and fall for 2 years. Seasonal variations were observed for the reference mat: sulfur cycle-related bacteria dominated spring samples, while Cyanobacteria dominated in autumn. The contaminated mat showed minor seasonal variation; a progressive increase of Cyanobacteria was noticed, indicating a perturbation of the classical seasonal behavior. Hydrocarbon content was the main factor explaining the differences in the microbial community structure; however, hydrocarbonoclastic bacteria were among rare or transient Operational Taxonomic Units (OTUs) in the contaminated mat. We suggest that in long-term contaminated systems, hydrocarbonoclastic bacteria cannot be considered a sentinel of contamination
Published: 2016

35. Bacteria as part of bioluminescence emission at the deep ANTARES station (North-Western Mediterranean Sea) during a one-year survey

Author: Sophie Guasco, Valérie Michotey, Patricia Bonin, Séverine Martini, Laurie Casalot, Marc Garel, Christian Tamburini, 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)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), 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: 0301 basic medicine, 030106 microbiology, Aquatic Science, Biology, Oceanography, Prokaryotic activities, 03 medical and health sciences, Nutrient, Mediterranean sea, Dissolved organic carbon, Mediterranean Sea, Bioluminescence, 14. Life underwater, ANTARES, In situ observatory, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Bioluminescent bacteria, Photobacterium, biology.organism_classification, Salinity, 030104 developmental biology, Light emission, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Bioluminescent bacteria have been studied during a one-year survey in 2011 at the deep ANTARES site (Northwestern Mediterranean Sea, 2000 m depth). The neutrino underwater telescope ANTARES, located at this station, has been used to record the bioluminescence at the same depth. Together with these data, environmental variables (potential temperature, salinity, nutrients, dissolved organic carbon and oxygen) have been characterized in water samples. The year 2011 was characterized by relatively stable conditions, as revealed by minor variability in the monitored oceanographic variables, by low bioluminescence and low current speed. This suggests weak eukaryote participation and mainly non-stimulated light emission. Hence, no processes of dense water have affected the ANTARES station during this survey. Abundance of bioluminescent bacteria belonging to Photobacterium genus, measured by qPCR of the luxF gene, ranged from 1.4 x 10(2) to 7.2 x 10(2) genes mL(-1). Their effective activity was confirmed through mRNA luxF quantification. Our results reveal that bioluminescent bacteria appeared more active than the total counterpart of bacteria, suggesting an ecological benefit of this feature such as favoring interaction with macro-organisms. Moreover, these results show that part of the bioluminescence, recorded at 2000 m depth over one year, could be due to bioluminescent bacteria in stable hydrological conditions. (C) 2016 Elsevier Ltd. All rights reserved.
Published: 2016

36. Coupling of bacterial nitrification with denitrification and anammox supports N removal in intertidal sediments (Arcachon Bay, France)

Author: Valérie Michotey, Cedric Javanaud, Sophie Guasco, Sheryl Oliveira Fernandes, Patricia Bonin, Pierre Anschutz, 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), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
Subjects: 0301 basic medicine, Denitrification, Nitrogen, 030106 microbiology, Aquatic Science, Oceanography, Sediments, 03 medical and health sciences, Anammox, Diversity, biology, Chemistry, Sediment, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biology.organism_classification, Nitrification, 030104 developmental biology, Benthic zone, Scalindua, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Eutrophication, Bay, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Microbial activity measurements and molecular approaches were combined to study temporal variation in nitrogen (N) removal mechanisms from muddy and sandy intertidal sediments (Arcachon Bay, France). Stable isotopes ((NH4+)-N-15/(NO3-)-N-15) were used to measure oxidation of NH4+ to NO3-/NO2- and its subsequent reduction to N-2 via denitrification and/or anammox. We found that denitrification mainly fuelled N loss in both sediment types. However in sandy sediments, anammox accounted for relatively higher N-2 production (45%). Nitrification-denitrification (D-n) and nitrification-anammox coupling was observed particularly in muddy sediments. Temporal variations in prokaryotic abundance (Bacteria, Archaea) and of functional groups responsible for nitrification and denitrification were studied by qPCR and for anammoxifiers by cloning. Bacterial density in both sediment types varied between 10(7-8) equivalent cell per g(-1) dry weight sediment and were overall more abundant in muddy sediments. Archaeal equivalent cell varied between 0.5 and 6.5% of the total prokaryotes, with extreme values observed in muddy sediment during October and January respectively. Denitrifiers were 1-2 orders higher than ammonium oxidizers and archeal nitrifiers appeared insignificant compared to betaproteobacterial counterpart. Furthermore, nitrifiers exhibited greater fluctuations in sandy sediments compared to muddy ones. Anammoxifiers were mainly restricted to the "Candidatus Scalindua" group, and were detected in both sediment types and all sampling periods providing an indirect proof on the occurrence of anammox. In muddy sediments, N-2 production presented overall higher rate over sandy sediments and exhibited the same trend as nitrifier abundance. This finding suggests a central role of bacterially-mediated benthic nitrification in supporting dissimilatory processes through generation of NO3-/NO2 and preventing eutrophication in this mesotidal lagoon
Published: 2016

37. Fatty acid composition of bacterial strains associated with living cells of the haptophyte Emiliania huxleyi

Author: Jean-François Rontani, Sophie Guasco, Nathalie Zabeti, John K. Volkman, Patricia Bonin, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Marine and Atmospheric Research, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, chemistry.chemical_classification, 0303 health sciences, Degree of unsaturation, biology, 030306 microbiology, Vaccenic acid, Fatty acid, biology.organism_classification, Cell wall, Haptophyte, 03 medical and health sciences, chemistry.chemical_compound, chemistry, Biochemistry, Biosynthesis, Geochemistry and Petrology, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, Bacteria, 030304 developmental biology, Emiliania huxleyi
Abstract: A number of bacterial strains previously isolated from living cells of the marine haptophyte Emiliania huxleyi and identified from their 16S r-DNA profiles as Dietzia maris sp. S1, Stappia sp. AG2, Nocardioides sp. S3, Sphingomonas sp. AG6, Oceanicaulis alexandrii sp. AG4, O. alexandrii sp. AG7 and Micrococcus sp. AG10 were cultured for examination of their fatty acid (FA) compositions. The total fatty acid (TFA) contents of the different strains ranged from 0.3% to 4% dry wt., which suggests that the use of a single value when converting FA content to estimates of bacterial biomass may have a significant error. A variety of FA distributions was observed, illustrating the diverse patterns in bacteria from marine ecosystems. Some species showed a dominance of saturated and monounsaturated straight chain FAs, while in others iso - and anteiso -branched FAs were the major constituents. The specificity and possible modes of biosynthesis of the unusual constituents, 11-methyloctadec-12-enoic and 10,13-epoxy-11-methyloctadeca-10,12-enoic acids, found in some species, are discussed. Deuterium labelling allowed us to demonstrate that these two compounds arise from the methionine-mediated methylation of cis -vaccenic acid, which supports the previously proposed role of this monounsaturated FA as the precursor of bacterial furan FAs. The strain Sphingomonas sp. AG6 contains C 14 –C 16 2-hydroxy acids (strongly dominated by 2-hydroxytetradecanoic acid), which are components of sphingolipid structures linked to sphingosine by amide bonds. 3-Hydroxyacids ranging from C 11 to C 18 were detected in Stappia sp. AG2, O. alexandrii sp. AG4, O. alexandrii sp. AG7 and Micrococcus sp. AG10. These are classical components of cell wall lipopolysaccharides. C 32 –C 37 mycolic acids exhibiting an unusually high degree of unsaturation and dominance of odd numbered main chains (>78% of the FAs had a C 21 main chain) were detected in the strain D. maris sp. S1. The data provide further examples of the close association of different types of bacteria with geochemically important algal species.
Published: 2010

38. Caldinitratiruptor microaerophilus, gen. nov., sp. nov. isolated from a French hot spring (Chaudes-Aigues, Massif Central): a novel cultivated facultative microaerophilic anaerobic thermophile pertaining to the Symbiobacterium branch within the Firmicutes

Author: Valérie Michotey, Vanessa Barsotti, Bernard Ollivier, Manon Joseph, Jean-Luc Cayol, Marie-Laure Fardeau, Patricia Bonin, Sophie Guasco, Laboratoire de Microbiologie IRD ( ESIL GMBA ), Université de Provence - Aix-Marseille 1, Extremophiles - IFR BAIM ( UR 101 ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Laboratoire de Microbiologie IRD (ESIL GMBA), Extremophiles - IFR BAIM (UR 101), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, Geologic Sediments, Hot Temperature, Firmicutes, Biology, Polymerase Chain Reaction, Microbiology, Hot Springs, Evolution, Molecular, Bacteria, Anaerobic, 03 medical and health sciences, Caldinitratiruptor microaerophilus, Thermophilic, Hot spring, Microaerophile, Nitrate-reduction, Ecosystem, Phylogeny, ComputingMilieux_MISCELLANEOUS, Microaerophilic, 030304 developmental biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Base Composition, 0303 health sciences, Strain (chemistry), 030306 microbiology, Thermophile, Temperature, Hot Spring, Sequence Analysis, DNA, General Medicine, Symbiobacterium thermophilum, Hydrogen-Ion Concentration, Ribosomal RNA, biology.organism_classification, Microscopy, Electron, Phenotype, Biochemistry, Molecular Medicine, Fermentation, France, Bacteria
Abstract: A novel facultative microaerophilic nitrate-reducing bacterium designated CA62N(T) was isolated from a thermal spring in France. Cells were non-motile rods (2-3 x 0.2 mum) and showed low cytoplasmic density when observed under a phase-contrast microscope. Strain CA62N(T) grew at temperatures between 50 and 75 degrees C (optimum 65 degrees C) and at a pH between 6.3 and 7.9 (optimum 7.0). NaCl was not required for growth but was tolerated up to 10 gl(-1). Sulfate, thiosulfate, elemental sulfur, sulfite, and nitrite were not used as electron acceptors. Nitrate was reduced to nitrite. Strain CA62N(T) used lactate, pyruvate, glucose, mannose, fructose, and casamino acids and some amino acids as electron donors only in the presence of nitrate as electron acceptor. None of these substrates was fermented. The main end-products of glucose oxidation were acetate, CO(2), and traces of H(2). The G + C content of the genomic DNA was 70.3 mol% (HPLC techniques). Phylogenetic analysis of the small-subunit (SSU) ribosomal RNA (rRNA) gene sequence indicated that strain CA62N(T) was affiliated to the Symbiobacterium branch within the Firmicutes and had Symbiobacterium thermophilum and "S. toebii" as its closest phylogenetic relatives. On the basis of phylogenetical and physiological characteristics, strain CA62N(T) is proposed to be the type strain for the novel species in the novel genus, Caldinitratiruptor microaerophilus gen. nov., sp. nov. (DSM 22660, JCM 16183).
Published: 2010

39. Nitrogen fluxes from marine sediments: quantification of the associated co-occurring bacterial processes

Author: Valérie Michotey, Laura Minjeaud, Patricia Bonin, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Denitrification, chemistry.chemical_element, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Anammox, Environmental Chemistry, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Earth-Surface Processes, Water Science and Technology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, denitrification, nitrous oxide, Isotope, 010604 marine biology & hydrobiology, Sediment, Nitrous oxide, isotope pairing method, simulation, Substrate (marine biology), Nitrogen, nitrification, Oceanography, chemistry, Environmental chemistry, Environmental science, Nitrification
Abstract: Different models for calculate on of di-nitrogen fluxes using 15NO3 tracers were tested for their congruence with experimental data obtained with marine sediment samples. The co-occurence of nitrification as source of substrate and the simultaneous N2 production from denitrification and/or Anammox were taken into account as well as nitrous oxide production in the total denitrification rate. The results highlighted that isotope technique provides a powerful tool to evaluate, in the same experimental set up, the rates of total N2 fluxes: denitrification and/or Anammox if it is carefully applied and its limitations, mainly the range of 15NO3 inputs are adapted to the studied samples and the linearity of the kinetics of the products checked.
Published: 2008

40. Incompatibilité ABO et greffe allogénique de cellules souches hématopoïétiques à l’ère des conditionnements non myéloablatifs

Author: M. Rodet, Patricia Bonin, Cécile Pautas, Sébastien Maury, Catherine Cordonnier, M. Kuentz, Yosr Hicheri, C. Boccaccio, F. Noizat-Pirenne, and J.-V. Malfuson
Subjects: congenital, hereditary, and neonatal diseases and abnormalities, business.industry, medicine.medical_treatment, Biochemistry (medical), Clinical Biochemistry, Pure red cell aplasia, Hematology, Hematopoietic stem cell transplantation, medicine.disease, biological factors, Hemolysis, Transplantation, Regimen, hemic and lymphatic diseases, Transfusion requirement, parasitic diseases, Immunology, Medicine, Stem cell, Aplastic anemia, business
Abstract: ABO incompatibility is not a barrier for allogeneic hematopoietic stem cell transplantation but is associated with specific complications. Major ABO incompatibility is associated with delayed erythroid engraftment, increased transfusion requirement and cases of pure red cell aplasia. Minor ABO incompatibility may be responsible for acute haemolytic reactions in the first months following transplantation. The widely used non myeloablative conditioning regimens might modify the management of ABO incompatibility. They could favour pure red cell aplasia development in the setting of major ABO mismatch since they are associated with a prolonged persistence of host anti-donor isohemagglutinins after allogeneic hematopoietic stem cell transplantation. In the setting of minor ABO incompatibility, the use of peripheral blood stem cells and the nature of graft-versus-host disease prophylaxis regimen may have an impact on the incidence of haemolytic reactions. In that review, the clinical and therapeutic aspects of ABO incompatibility are studied, especially regarding the impact of the conditioning regimen intensity.
Published: 2007

41. Impact of nonmyeloablative conditioning regimens on the occurrence of pure red cell aplasia after ABO-incompatible allogeneic haematopoietic stem cell transplantation

Author: Sébastien Maury, Cécile Pautas, M. Kuentz, Catherine Cordonnier, Patricia Bonin, J.-V. Malfuson, R. B. Amor, M. Rodet, C. Boccaccio, and F. Noizat-Pirenne
Subjects: Adult, Male, Transplantation Conditioning, medicine.medical_treatment, Delayed Graft Function, Graft vs Host Disease, Pure red cell aplasia, Red-Cell Aplasia, Pure, ABO Blood-Group System, Conditioning regimen, hemic and lymphatic diseases, ABO blood group system, medicine, Humans, Transplantation, Homologous, business.industry, Hematopoietic Stem Cell Transplantation, Blood cells transfusion, Immunosuppression, Hematology, General Medicine, Middle Aged, medicine.disease, Transplantation, Haematopoiesis, Hemagglutinins, surgical procedures, operative, Immunology, Female, Stem cell, business
Abstract: Background and Objectives In the setting of major ABO-incompatible allogeneic haematopoietic stem cell transplantation (HSCT), pure red cell aplasia (PRCA) is linked to the persistence of host residual plasma cells secreting antidonor isohaemagglutinins (HA) after transplantation. There are conflicting results regarding the impact of the intensity of conditioning regimen on the occurrence of PRCA after major ABO-mismatched HSCT. Material and Methods To address this question, we compared two cases occurring after nonmyeloablative (NMA) and myeloablative (MA) HSCT and reviewed previous cases reported in the NMA setting. Results and Conclusions We observed a delayed disappearance of antidonor HAs in the NMA setting, associated to a more prolonged period of red blood cells transfusion dependence than in the MA setting. In our case as in several others, the disappearance of antidonor HAs and resolution of PRCA were observed after reinforcement of the graft-versus-host effect (i.e. immunosuppression removal or donor leukocytes infusion).
Published: 2007

42. Microbial ecology of hydrocarbon-polluted coastal sediments

Author: Cristiana Cravo-Laureau, Robert Duran, Philippe Cuny, Patricia Bonin, Equipe Environnement et Microbiologie (EEM ), 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)-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)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), MEB, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), ANR-11-CESA-0006,DECAPAGE,Caractérisation des capacités de dégradation de communautés bactériennes de sédiments marins : adaptation, processus métaboliques et influence des régimes d'oxygénation(2011), 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), 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)-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), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)-Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Health, Toxicology and Mutagenesis, 010501 environmental sciences, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Microbial ecology, 11. Sustainability, Environmental Chemistry, Marine ecosystem, Ecosystem, 14. Life underwater, Microbial mat, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, 0303 health sciences, geography, geography.geographical_feature_category, 030306 microbiology, Ecology, Estuary, General Medicine, 15. Life on land, Pollution, 6. Clean water, chemistry, 13. Climate action, Salt marsh, Environmental science, Petroleum, Mangrove, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Coastal shorelines suffer a variety of pollution injuries from both sides, from the sea, predominantly by crude oil from shipping and offshore mining, and from the land, principally through agricultural practices, urban wastewaters, and industrial activities. As a result, multi-pollution hot spots are found along shorelines, especially in estuaries and harbors. Microbial communities have evolved to adapt their metabolism to the presence of multi-contaminants (Duran et al. 2008; Gillan et al. 2005; Iannelli et al. 2012; Kaci et al. 2014; SabadiniSantos et al. 2014; Wang and Tam 2012). However, hydrocarbon compounds and crude oil-derived products are the most abundant pollutants, the more spectacular source being oil spill as illustrated by the recent catastrophe of Deepwater Horizon in 2010, the largest oil spill so far observed (Atlas and Hazen 2011). Although they are frequently found at unacceptably high concentrations, hydrocarbons are natural compounds, and thus, most of them can be biodegraded by the collective catabolic diversity of microorganisms (Duran and Goni Urriza 2010; Head et al. 2006; Leahy and Colwell 1990; Miralles et al. 2007; Paisse et al. 2011; Paisse et al. 2010), particularly demonstrated in coastal marine ecosystems such as salt marshes with microbial mat structures (Bordenave et al. 2004a; Bordenave et al. 2008; Bordenave et al. 2007; Bordenave et al. 2004b), mangroves (Brito et al. 2009; Brito et al. 2006) and estuaries (Chronopoulou et al. 2013; Coulon et al. 2012). However, coastal marine sediments constitute particular ecosystems submitted to fluctuating oxygenation and redox conditions from the tidal cycles and burrowing activities of the macrofauna that in turn drive microbial degradation processes (Cravo-Laureau and Duran 2014). The biodegradation of hydrocarbon compounds in such oxic/anoxic oscillating environments still remains poorly understood (Cravo-Laureau et al. 2011; Cuny et al. 2011; Vitte et al. 2013; Vitte et al. 2011). The understanding of the particular microbes involved, their ecology, their genetic and enzymatic capacities, their interactions, as well as their functioning in the changing redox conditions, is crucial for the implementation of efficient bioremediation strategies (Goni-Urriza et al. 2013; McGenity 2014). The DECAPAGE project (ANR CESA-2011-006 01; http://ipremeem.univ-pau.fr/live/DECAPAGE), funded by the French National Agency for Research (ANR), was precisely devoted to understand the adaptation mechanisms driving the reorganization of bacterial communities in response to petroleum in coastal sediments. In this special issue, the scientists involved in the DECAPAGE project present their contribution for understanding the microbial ecology in hydrocarbon-polluted mudflat sediments. The special issue also includes articles from scientists involved in other projects and programs in order to enlarge the topic to diverse ecosystems, to different biological organization levels from microbial and macrobenthic communities to bacterial populations, and addressing remediation strategies as well. Thus, the 15 articles compiled in this special issue explore diverse facets of the microbial ecology of hydrocarbon-polluted coastal sediments. The article of Acosta-Gonzalez et al. (2015) reviews the impact of the Prestige oil spill, an accident that occurred in 2002 at the Responsible editor: Philippe Garrigues
Published: 2015

43. Dynamic of bacterial communities attached to lightened phytodetritus

Author: Jean-François Rontani, Patricia Bonin, Vincent Méjean, Frédéric Vaultier, Cécile Jourlin-Castelli, Rémi Amiraux, Morgan Petit, Valérie Michotey, Sophie Guasco, Joshua Armitano, CE, 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), MEB, 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)-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), Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
Subjects: Shewanella, Light, Health, Toxicology and Mutagenesis, [ SDV.BBM.BM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Radiation Tolerance, Bacterial Adhesion, Microbiology, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Environmental Chemistry, Shewanella oneidensis, Carotenoid, Emiliania huxleyi, chemistry.chemical_classification, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Microbial Viability, Photolysis, biology, Singlet Oxygen, Roseovarius, Chemotaxis, fungi, Phytodetritus, Haptophyta, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, Roseobacter, biology.organism_classification, Pollution, chemistry, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bacteria, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; The effects of singlet oxygen ((1)O2) transfer to bacteria attached on phytodetritus were investigated under laboratory-controlled conditions. For this purpose, a nonaxenic culture of Emiliania huxleyi in late stationary phase was studied for bacterial viability. Our results indicated that only 9 ± 3 % of attached bacteria were alive compared to 46 ± 23 % for free bacteria in the E. huxleyi culture. Apparently, under conditions of low irradiance (36 W m(-2)), during the culture, the cumulative dose received (22,000 kJ m(-2)) was sufficiently important to induce an efficient (1)O2 transfer to attached bacteria during the senescence of E. huxleyi cells. At this stage, attached bacteria appeared to be dominated by pigmented bacteria (Maribacter, Roseobacter, Roseovarius), which should resist to (1)O2 stress probably due to their high contents of carotenoids. After subsequent irradiation of the culture until fully photodegradation of chlorophyll, DGGE analyses showed that the diversity of bacteria attached to E. huxleyi cells is modified by light. Photooxidative alterations of bacteria were confirmed by the increasing amounts of cis-vaccenic photoproducts (bacterial marker) per bacteria observed during irradiation time. Interestingly, preliminary chemotaxis experiments showed that Shewanella oneidensis considered here as a model of motile bacteria was attracted by phytodetritus producing or not (1)O2. This lack of repulsive effects could explain the high mortality rate of bacteria measured on E. huxleyi cells.
Published: 2015

44. Draft-genome sequence of Shewanella algae strain C6G3

Author: Patricia Bonin, Axel Aigle, Valérie Michotey, 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), MEB, 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)-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), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
Subjects: Whole genome sequencing, Shewanella algae, Shewanella, Strain (chemistry), biology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Ribosomal RNA, biology.organism_classification, Genome, Microbiology, Short Genome Report, Dissimilative reduction of nitrite into ammonium, Shewanella oneidensis, Nitrate reduction, Botany, Genetics, Metal-oxide reduction, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Gene, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Shewanella algae strain C6G3, isolated from the 2 uppermost centimeters of muddy sediment of Arcachon Bay (SW Atlantic French coast, sampled in October 2007) has the capability to use a large panel of terminal electron acceptors under anaerobic condition, such as nitrate, nitrite and metal-oxide, and presents a great metabolic versatility. Here, we present the non-contiguous draft-genome sequence of Shewanella algae C6G3, which consists of a 4,879,425 bp. The chromosome contains 5792 predicted genes. In total, the genome consists of 24 rRNA genes, 86 tRNA genes and 5660 genes assigned as protein-coding genes. Electronic supplementary material The online version of this article (doi:10.1186/s40793-015-0022-0) contains supplementary material, which is available to authorized users.
Published: 2015

45. Ecological significance of Synergistetes in the biological treatment of tuna cooking wastewater by an anaerobic sequencing batch reactor

Author: Moktar Hamdi, Marie-Laure Fardeau, Cécile Militon, Olfa Hamdi, Patricia Bonin, Valérie Michotey, Bernard Ollivier, Hassib Bouallagui, Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), MEB, Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -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)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), 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), 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)-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: Protein-rich effluent, Microbial diversity, Health, Toxicology and Mutagenesis, Sequencing batch reactor, [ SDV.BBM.BM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, 010501 environmental sciences, Biology, Wastewater, 01 natural sciences, Water Purification, Industrial wastewater treatment, 03 medical and health sciences, Bioreactors, Biogas, Anaerobic digestion, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Environmental Chemistry, Animals, Cooking, 030304 developmental biology, 0105 earth and related environmental sciences, 0303 health sciences, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Waste management, Bacteria, Tuna, Chemical oxygen demand, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, biology.organism_classification, Pulp and paper industry, Pollution, 6. Clean water, Biodegradation, Environmental, Synergistetes, Sewage treatment, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Tuna effluent, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Lab-scale 2L-anaerobic sequencing batch reactor was operated under mesothermic conditions. The degradation of protein-rich organic matter was determined by chemical oxygen demand, biogas production, and protein-removal activity over the operation. The structure of the microbial community was determined by qPCR and next-generation sequencing on 16S rRNA genes. At the steady state, a very efficient removal of protein (92 %) was observed. Our results demonstrate a decrease of archaeal and bacterial abundance over time. Members of the phylum Synergistetes, with a peculiar emphasis for those pertaining to families Dethiosulfovibrionaceae and Aminiphilaceae, are of major ecological significance regarding the treatment of this industrial wastewater. The prominent role to be played by members of the phylum Synergistetes regarding protein and/or amino acid degradation is discussed.
Published: 2015

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

Author: Patricia Bonin, Sophie Guasco, Cécile Militon, Valérie Michotey, Ronan Jézéquel, Robert Duran, Cristiana Cravo-Laureau, Franck Gilbert, Philippe Cuny, Christine Cagnon, Karine Duboscq, Georges Stora, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), MEB, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Equipe Environnement et Microbiologie (EEM ), 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)-Centre National de la Recherche Scientifique (CNRS)-Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), 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), Université de Pau et des Pays de l'Adour (UPPA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-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 ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), 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), 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)-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), and Université de Toulouse (UT)
Subjects: Geologic Sediments, Health, Toxicology and Mutagenesis, Detergents, Biomass, Dispersant, Oil pollution, [ SDV.BBM.BM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Mesocosm, chemistry.chemical_compound, Bioremediation, RNA, Ribosomal, 16S, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Environmental Chemistry, Petroleum Pollution, 14. Life underwater, Organic Chemicals, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Mudflat sediments, Bacteria, Environmental engineering, Sediment, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, Pollution, Mesocosms, Hydrocarbons, RNA, Bacterial, Biodegradation, Environmental, Petroleum, chemistry, 13. Climate action, Benthic zone, Environmental chemistry, Environmental science, Macrofauna, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bioturbation, Polymorphism, Restriction Fragment Length, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; The present study aimed to examine whether the use of dispersant would be suitable for favoring the hydrocarbon degradation in coastal marine sediments without impacting negatively micro- and macrobenthic organisms. Mudflat sediments, maintained during 286 days in mesocosms designed to simulate natural conditions, were contaminated or not with Ural blend crude oil (REBCO) and treated or not with third-generation dispersant (Finasol OSR52). While the dispersant did not lead to an increase of hydrocarbon biodegradation, its use enables an attenuation of more than 55 % of the sediment concentration of total petroleum hydrocarbons (TPH). Canonical correspondence analysis (CCA) correlating T-RFLP patterns with the hydrocarbon content and bacterial abundance indicated weak differences between the different treatments except for the mesocosm treated with oil and dispersant for which a higher bacterial biomass was observed. The use of the dispersant did not significantly decrease the macrobenthic species richness or macroorganisms' densities in uncontaminated or contaminated conditions. However, even if the structure of the macrobenthic communities was not affected, when used in combination with oil, biological sediment reworking coefficient was negatively impacted. Although the use of the dispersant may be worth considering in order to accelerate the attenuation of hydrocarbon-contaminated mudflat sediments, long-term effects on functional aspects of the benthic system such as bioturbation and bacterial activity should be carefully studied before.
Published: 2015

47. Effect of physical sediments reworking on hydrocarbon degradation and bacterial community structure in marine coastal sediments

Author: Patricia Bonin, Cécile Militon, Cristiana Cravo-Laureau, Christine Cagnon, Franck Gilbert, Robert Duran, Philippe Cuny, Karine Dubosc, Valérie Michotey, Ronan Jézéquel, Claire Gassie, Justine Abella, Fanny Terrisse, Equipe Environnement et Microbiologie (EEM ), 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)-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)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), MEB, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre de documentation de recherche et d'expérimentations sur les pollutions accidentelles des eaux (Cedre), Cedre, 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), ANR-11-CESA-0006,DECAPAGE,Caractérisation des capacités de dégradation de communautés bactériennes de sédiments marins : adaptation, processus métaboliques et influence des régimes d'oxygénation(2011), Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS)-Université de Pau et des Pays de l'Adour (UPPA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-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-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), 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), 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)-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), and Université de Toulouse (UT)
Subjects: DNA, Bacterial, Geologic Sediments, Co-occurrence network, Health, Toxicology and Mutagenesis, Phytane, Oil pollution, Ecological succession, [ SDV.BBM.BM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, 010501 environmental sciences, Polymerase Chain Reaction, 01 natural sciences, Mesocosm, 03 medical and health sciences, chemistry.chemical_compound, Bioremediation, T-RFLP, RNA, Ribosomal, 16S, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Environmental Chemistry, 14. Life underwater, Phylogeny, 030304 developmental biology, 0105 earth and related environmental sciences, 0303 health sciences, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Bacteria, Ecology, Community structure, Sediment, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Sequence Analysis, DNA, General Medicine, Pollution, Mesocosms, Hydrocarbons, Terminal restriction fragment length polymorphism, Biodegradation, Environmental, Petroleum, chemistry, Benthic zone, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Polymorphism, Restriction Fragment Length, Water Pollutants, Chemical, Harrowing, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; The present study aimed to examine whether the physical reworking of sediments by harrowing would be suitable for favouring the hydrocarbon degradation in coastal marine sediments. Mudflat sediments were maintained in mesocosms under conditions as closer as possible to those prevailing in natural environments with tidal cycles. Sediments were contaminated with Ural blend crude oil, and in half of them, harrowing treatment was applied in order to mimic physical reworking of surface sediments. Hydrocarbon distribution within the sediment and its removal was followed during 286 days. The harrowing treatment allowed hydrocarbon compounds to penetrate the first 6 cm of the sediments, and biodegradation indexes (such as n-C18/phytane) indicated that biodegradation started 90 days before that observed in untreated control mesocosms. However, the harrowing treatment had a severe impact on benthic organisms reducing drastically the macrofaunal abundance and diversity. In the harrowing-treated mesocosms, the bacterial abundance, determined by 16S rRNA gene Q-PCR, was slightly increased; and terminal restriction fragment length polymorphism (T-RFLP) analyses of 16S rRNA genes showed distinct and specific bacterial community structure. Co-occurrence network and canonical correspondence analyses (CCA) based on T-RFLP data indicated the main correlations between bacterial operational taxonomic units (OTUs) as well as the associations between OTUs and hydrocarbon compound contents further supported by clustered correlation (ClusCor) analysis. The analyses highlighted the OTUs constituting the network structural bases involved in hydrocarbon degradation. Negative correlations indicated the possible shifts in bacterial communities that occurred during the ecological succession.
Published: 2015

48. Molecular and biochemical characterization of mannitol-1-phosphate dehydrogenase from the model brown alga Ectocarpus sp

Author: Anaïs Guibert, Agnès Groisillier, Alice Raimbault, Catherine Boyen, Thierry Tonon, Patricia Bonin, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Station biologique de Roscoff [Roscoff] (SBR), and 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)
Subjects: Ectocarpus sp, Recombinant protein, Molecular Sequence Data, Brown algae, Dehydrogenase, Plant Science, Horticulture, Phaeophyta, Biochemistry, Sequence Analysis, Protein, Catalytic Domain, medicine, [CHIM]Chemical Sciences, Amino Acid Sequence, Sugar alcohol, Molecular Biology, Phylogeny, chemistry.chemical_classification, biology, Mannitol-1-phosphate dehydrogenase, General Medicine, Ectocarpus, biology.organism_classification, Enzyme assay, Recombinant Proteins, Metabolic pathway, Kinetics, Enzyme, chemistry, biology.protein, Mannitol cycle, Mannitol, medicine.drug, Sugar Alcohol Dehydrogenases
Abstract: International audience; The sugar alcohol mannitol is important in the food, pharmaceutical, medical and chemical industries. It is one of the most commonly occurring polyols in nature, with the exception of Archaea and animals. It has a range of physiological roles, including as carbon storage, compatible solute, and osmolyte. Mannitol is present in large amounts in brown algae, where its synthesis involved two steps: a mannitol-1-phosphate dehydrogenase (M1PDH) catalyzes a reversible reaction between fructose-6-phosphate (F6P) and mannitol-1-phosphate (M1P) (EC 1.1.1.17), and a mannitol-1-phosphatase hydrolyzes M1P to mannitol (EC 3.1.3.22). Analysis of the model brown alga Ectocarpus sp. genome provided three candidate genes for M1PDH activities. We report here the sequence analysis of Ectocarpus M1PDHs (EsM1PDHs), and the biochemical characterization of the recombinant catalytic domain of EsM1PDH1 (EsM1PDH1cat). Ectocarpus M1PDHs are representatives of a new type of modular M1PDHs among the polyol-specific long-chain dehydrogenases/reductases (PSLDRs). The N-terminal domain of EsM1PDH1 was not necessary for enzymatic activity. Determination of kinetic parameters indicated that EsM1PDH1cat displayed higher catalytic efficiency for F6P reduction compared to M1P oxidation. Both activities were influenced by NaCl concentration and inhibited by the thioreactive compound pHMB. These observations were completed by measurement of endogenous M1PDH activity and of EsM1PDH gene expression during one diurnal cycle. No significant changes in enzyme activity were monitored between day and night, although transcription of two out of three genes was altered, suggesting different levels of regulation for this key metabolic pathway in brown algal physiology.
Published: 2015

49. Aminobacterium thunnarium sp. nov., a mesophilic, amino acid-degrading bacterium isolated from an anaerobic sludge digester, pertaining to the phylum Synergistetes

Author: Moktar Hamdi, Marie-Laure Fardeau, Patricia Bonin, Anne Postec, Wajdi Ben Hania, Hassib Bouallagui, Bernard Ollivier, Olfa Hamdi, 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 d'Ecologie et de Technologie Microbiennes (LETMi), and Institut National des Sciences Appliquées et de Technologie - Carthage (INSAT Carthage)
Subjects: DNA, Bacterial, Tunisia, Molecular Sequence Data, Gram-Positive Bacteria, Microbiology, Bacteria, Anaerobic, 03 medical and health sciences, Valine, RNA, Ribosomal, 16S, Yeast extract, Amino Acids, Phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Alanine, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Base Composition, 0303 health sciences, Sewage, biology, Strain (chemistry), 030306 microbiology, Fatty Acids, Sequence Analysis, DNA, General Medicine, biology.organism_classification, 6. Clean water, Biochemistry, Fermentation, Ketoglutaric Acids, Isoleucine, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bacteria, Mesophile
Abstract: A new Gram-staining-positive, non-sporulating, mesophilic, amino acid-degrading anaerobic bacterium, designated strain OTA 102T, was isolated from an anaerobic sequencing batch reactor treating wastewater from cooking tuna. The cells were curved rods (0.6–2.5×0.5 µm) and occurred singly or in pairs. The strain was motile by means of one lateral flagellum. Strain OTA 102T grew at temperatures between 30 and 45 °C (optimum 40 °C), between pH 6.0 and 8.4 (optimum pH 7.2) and NaCl concentrations between 1 and 5 % (optimum 2 %, w/v). Strain OTA 102T required yeast extract for growth. Serine, threonine, glycine, cysteine, citrate, fumarate, α-ketoglutarate and pyruvate were fermented. When co-cultured with Methanobacterium formicicum as the hydrogen scavenger, strain OTA 102T oxidized alanine, valine, leucine, isoleucine, aspartate, tyrosine, methionine, histidine and asparagine. The genomic DNA G+C content of strain OTA 102T was 41.7 mol%. The main fatty acid was iso-C15 : 0. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain OTA 102T was related to Aminobacterium colombiense and Aminobacterium mobile (95.5 and 95.2 % similarity, respectively), of the phylum Synergistetes . On the basis of phylogenetic, genetic and physiological characteristics, strain OTA 102T is proposed to represent a novel species of the genus Aminobacterium , Aminobacterium thunnarium sp. nov. The type strain is OTA 102T ( = DSM 27500T = JCM 19320T).
Published: 2015

50. Substrates specialization in lipid compounds and hydrocarbons of Marinobacter genus

Author: Christophe Vieira, Patricia Bonin, Oscar Lima, Corina P. D. Brussaard, Philippe Cuny, Valérie Michotey, Régis Grimaud, Cécile Militon, Sophie Guasco, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), MEB, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie Moléculaire, IBEAS, EA 3525, Université de Pau et des Pays de l'Adour (UPPA), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Royal Netherlands Institute for Sea Research (NIOZ), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Aquatic Microbiology (IBED, FNWI), 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), 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)-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), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie ( MIO ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU ) -Université de Toulon ( UTLN ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Ecologie Moléculaire ( IBEAS ), Université de Pau et des Pays de l'Adour ( UPPA ), Ecosystèmes, biodiversité, évolution [Rennes] ( ECOBIO ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -INEE-Observatoire des Sciences de l'Univers de Rennes ( OSUR ) -Centre National de la Recherche Scientifique ( CNRS ), and Royal Netherlands Institute for Sea Research ( NIOZ )
Subjects: Geologic Sediments, Hydrocarbon, Health, Toxicology and Mutagenesis, Marinobacter pelagius, [ SDV.BBM.BM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Biology, Marinobacter adhaerens, medicine.disease_cause, Marinobacter flavimaris, Marinobacter xestospongiae, 03 medical and health sciences, Quantification, Marinobacter, Botany, [ SDV.EE.IEO ] Life Sciences [q-bio]/Ecology, environment/Symbiosis, medicine, Environmental Chemistry, Petroleum Pollution, 14. Life underwater, Marine sediment, Phylogeny, 030304 developmental biology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, Marinobacter santoriniensis, Marinobacter vinifirmus, 030306 microbiology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, Lipid Metabolism, Pollution, Hydrocarbons, 6. Clean water, Marinobacter nanhaiticus, Electron donor pattern, Biochemistry, 13. Climate action, Denitrification, Marinobacter maritimus, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Genome, Bacterial, Marinobater, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; The impact of petroleum contamination and of burrowing macrofauna on abundances of Marinobacter and denitrifiers was tested in marine sediment mesocoms after 3 months incubation. Quantification of this genus by qPCR with a new primer set showed that the main factor favoring Marinobacter abundance was hydrocarbon amendment followed by macrofauna presence. In parallel, proportion of nosZ-harboring bacteria increased in the presence of marcrofauna. Quantitative finding were explained by physiological data from a set of 34 strains and by genomic analysis of 16 genomes spanning 15 different Marinobacter-validated species (Marinobacter hydrocarbonoclasticus, Marinobacter daeopensis, Marinobacter santoriniensis, Marinobacter pelagius, Marinobacter flavimaris, Marinobacter adhaerens, Marinobacter xestospongiae, Marinobacter algicola, Marinobacter vinifirmus, Marinobacter maritimus, Marinobacter psychrophilus, Marinobacter lipoliticus, Marinobacter manganoxydans, Marinobacter excellens, Marinobacter nanhaiticus) and 4 potential novel ones. Among the 105 organic electron donors tested in physiological analysis, Marinobacter pattern appeared narrow for almost all kinds of organic compounds except lipid ones. Strains of this set could oxidize a very large spectrum of lipids belonging to glycerolipids, branched, fatty acyls, and aromatic hydrocarbon classes. Physiological data were comforted by genomic analysis, and genes of alkane 1-monooxygenase, haloalkane dehalogenase, and flavin-binding monooxygenase were detected in most genomes. Denitrification was assessed for several strains belonging to M. hydrocarbonoclasticus, M. vinifirmus, Marinobacter maritinus, and M. pelagius species indicating the possibility to use nitrate as alternative electron acceptor. Higher occurrence of Marinobacter in the presence of petroleum appeared to be the result of a broader physiological trait allowing this genus to use lipids including hydrocarbon as principal electron donors.
Published: 2015

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