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1. Microbial taxa related to natural hydrogen and methane emissions in serpentinite-hosted hyperalkaline springs of New Caledonia

Author: Marianne Quéméneur, Nan Mei, Christophe Monnin, Anne Postec, Sophie Guasco, Julie Jeanpert, Pierre Maurizot, Bernard Pelletier, and Gaël Erauso
Subjects: bacteria, archaea, high-pH water, microbial diversity, natural hydrogen, methane, Microbiology, QR1-502
Abstract: The southeastern part of New Caledonia main island (Grande Terre) is the location of a large ophiolitic formation that hosts several hyperalkaline springs discharging high pH (∼11) and warm (
Published: 2023
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2. 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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3. 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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4. Procaryotic Diversity and Hydrogenotrophic Methanogenesis in an Alkaline Spring (La Crouen, New Caledonia)

Author: Marianne Quéméneur, Nan Mei, Christophe Monnin, Anne Postec, Laura Wils, Manon Bartoli, Sophie Guasco, Bernard Pelletier, and Gael Erauso
Subjects: archaea, bacteria, Methanobacterium, alkaline spring, microbial diversity, alkaliphiles, Biology (General), QH301-705.5
Abstract: (1) Background: The geothermal spring of La Crouen (New Caledonia) discharges warm (42 °C) alkaline water (pH~9) enriched in dissolved nitrogen with traces of methane, but its microbial diversity has not yet been studied. (2) Methods: Cultivation-dependent and -independent methods (e.g., Illumina sequencing and quantitative PCR based on 16S rRNA gene) were used to describe the prokaryotic diversity of this spring. (3) Results: Prokaryotes were mainly represented by Proteobacteria (57% on average), followed by Cyanobacteria, Chlorofexi, and Candidatus Gracilibacteria (GN02/BD1-5) (each > 5%). Both potential aerobes and anaerobes, as well as mesophilic and thermophilic microorganisms, were identified. Some of them had previously been detected in continental hyperalkaline springs found in serpentinizing environments (The Cedars, Samail, Voltri, and Zambales ophiolites). Gammaproteobacteria, Ca. Gracilibacteria and Thermotogae were significantly more abundant in spring water than in sediments. Potential chemolithotrophs mainly included beta- and gammaproteobacterial genera of sulfate-reducers (Ca. Desulfobacillus), methylotrophs (Methyloversatilis), sulfur-oxidizers (Thiofaba, Thiovirga), or hydrogen-oxidizers (Hydrogenophaga). Methanogens (Methanobacteriales and Methanosarcinales) were the dominant Archaea, as found in serpentinization-driven and deep subsurface ecosystems. A novel alkaliphilic hydrogenotrophic methanogen (strain CAN) belonging to the genus Methanobacterium was isolated, suggesting that hydrogenotrophic methanogenesis occurs at La Crouen.
Published: 2021
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5. 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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6. From In Situ to satellite observations of pelagic Sargassum distribution and aggregation in the Tropical North Atlantic Ocean.

Author: Anouck Ody, Thierry Thibaut, Léo Berline, Thomas Changeux, Jean-Michel André, Cristèle Chevalier, Aurélie Blanfuné, Jean Blanchot, Sandrine Ruitton, Valérie Stiger-Pouvreau, Solène Connan, Jacques Grelet, Didier Aurelle, Mathilde Guéné, Hubert Bataille, Céline Bachelier, Dorian Guillemain, Natascha Schmidt, Vincent Fauvelle, Sophie Guasco, and Frédéric Ménard
Subjects: Medicine, Science
Abstract: The present study reports on observations carried out in the Tropical North Atlantic in summer and autumn 2017, documenting Sargassum aggregations using both ship-deck observations and satellite sensor observations at three resolutions (MSI-10 m, OLCI-300 m, VIIRS-750 m and MODIS-1 km). Both datasets reported that in summer, Sargassum aggregations were mainly observed off Brazil and near the Caribbean Islands, while they accumulated near the African coast in autumn. Based on in situ observations, we propose a five-class typology allowing standardisation of the description of in situ Sargassum raft shapes and sizes. The most commonly observed Sargassum raft type was windrows, but large rafts composed of a quasi-circular patch hundreds of meters wide were also observed. Satellite imagery showed that these rafts formed larger Sargassum aggregations over a wide range of scales, with smaller aggregations (of tens of m2 area) nested within larger ones (of hundreds of km2). Match-ups between different satellite sensors and in situ observations were limited for this dataset, mainly because of high cloud cover during the periods of observation. Nevertheless, comparisons between the two datasets showed that satellite sensors successfully detected Sargassum abundance and aggregation patterns consistent with in situ observations. MODIS and VIIRS sensors were better suited to describing the Sargassum aggregation distribution and dynamics at Atlantic scale, while the new sensors, OLCI and MSI, proved their ability to detect Sargassum aggregations and to describe their (sub-) mesoscale nested structure. The high variability in raft shape, size, thickness, depth and biomass density observed in situ means that caution is called for when using satellite maps of Sargassum distribution and biomass estimation. Improvements would require additional in situ and airborne observations or very high-resolution satellite imagery.
Published: 2019
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7. Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions

Author: Christian Tamburini, Fabrice Armougom, Hans-Peter Grossart, Sophie Guasco, Frédéric A. C. Le Moigne, Virginie Riou, Marc Garel, Chloé M. J. Baumas, Nagib Bhairy, 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: Geologic Sediments, Mesopelagic zone, Heterotroph, chemistry.chemical_element, Biology, Microbiology, Article, Microbial ecology, 03 medical and health sciences, 1234567890(), Seawater, Ecosystem, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Marine snow, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Total organic carbon, 0303 health sciences, Carbon dioxide in Earth's atmosphere, 030306 microbiology, Ecology, Heterotrophic Processes, Biogeochemistry, 15. Life on land, Prokaryotic Cells, chemistry, 13. Climate action, Species richness, Carbon
Abstract: The vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological processes such as community development of prokaryotes on different particle fractions (sinking vs. non-sinking) are yet virtually unknown. This prevents accurate predictions of mesopelagic organic carbon loss in response to changing ocean dynamics. Using combined measurements of prokaryotic heterotrophic production rates and species richness in the North Atlantic, we reveal that carbon loss rates and associated microbial richness are drastically different with particle fractions. Our results demonstrate a strong negative correlation between prokaryotic carbon losses and species richness. Such a trend may be related to prokaryotes detaching from fast-sinking particles constantly enriching non-sinking associated communities in the mesopelagic zone. Existing global scale data suggest this negative correlation is a widespread feature of mesopelagic microbes.
Published: 2021

8. 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

9. Procaryotic Diversity and Hydrogenotrophic Methanogenesis in an Alkaline Spring (La Crouen, New Caledonia)

Author: Bernard Pelletier, Marianne Quéméneur, Manon Bartoli, Nan Mei, Sophie Guasco, Gaël Erauso, Christophe Monnin, Laura Wils, Anne Postec, 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), Géosciences Environnement Toulouse (GET), Institut national des sciences de l'Univers (INSU - CNRS)-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-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), Géoazur (GEOAZUR 7329), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de la Côte d'Azur, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), 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)-Observatoire Midi-Pyrénées (OMP), 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), and ANR-19-CE02-0020,MICROPRONY,Fonctionnement de l'écosystème microbien du système hydrothermal alcalin de Prony, Nouvelle Calédonie(2019)
Subjects: 0301 basic medicine, Microbiology (medical), Methanobacterium, QH301-705.5, Methanogenesis, archaea, 030106 microbiology, Microbiology, Article, 03 medical and health sciences, Virology, Gammaproteobacteria, Botany, Hydrogenophaga, alkaline spring, Biology (General), bacteria, biology, Chemistry, alkaliphiles, methanogenesis, biology.organism_classification, Methanogen, 6. Clean water, 030104 developmental biology, 13. Climate action, microbial diversity, Methanosarcinales, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Proteobacteria, Archaea, hydrogenotrophy
Abstract: (1) Background: The geothermal spring of La Crouen (New Caledonia) discharges warm (42 °C) alkaline water (pH~9) enriched in dissolved nitrogen with traces of methane, but its microbial diversity has not yet been studied. (2) Methods: Cultivation-dependent and -independent methods (e.g., Illumina sequencing and quantitative PCR based on 16S rRNA gene) were used to describe the prokaryotic diversity of this spring. (3) Results: Prokaryotes were mainly represented by Proteobacteria (57% on average), followed by Cyanobacteria, Chlorofexi, and Candidatus Gracilibacteria (GN02/BD1-5) (each &gt, 5%). Both potential aerobes and anaerobes, as well as mesophilic and thermophilic microorganisms, were identified. Some of them had previously been detected in continental hyperalkaline springs found in serpentinizing environments (The Cedars, Samail, Voltri, and Zambales ophiolites). Gammaproteobacteria, Ca. Gracilibacteria and Thermotogae were significantly more abundant in spring water than in sediments. Potential chemolithotrophs mainly included beta- and gammaproteobacterial genera of sulfate-reducers (Ca. Desulfobacillus), methylotrophs (Methyloversatilis), sulfur-oxidizers (Thiofaba, Thiovirga), or hydrogen-oxidizers (Hydrogenophaga). Methanogens (Methanobacteriales and Methanosarcinales) were the dominant Archaea, as found in serpentinization-driven and deep subsurface ecosystems. A novel alkaliphilic hydrogenotrophic methanogen (strain CAN) belonging to the genus Methanobacterium was isolated, suggesting that hydrogenotrophic methanogenesis occurs at La Crouen.
Published: 2021
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10. A global metagenomic map of urban microbiomes and antimicrobial resistance

Author: Nadine Farhat, Tomoki Takeda, Astred Castro, Ken McGrath, Khaliun Sanchir, Iman Hajirasouliha, Eunice So, Laraib Zafar, Diana N. Nunes, Harun Mustafa, Amy Zhang, Priscilla Lisboa, Christian Schori, Marisano James, Jasna Chalangal, Sebastien Halary, Shahryar Rana, Yunmi Lee, Oli Schacher, Liliana Godoy, David A. Coil, Phanthira Pugdeethosal, Michelle D. Williams, German Marchandon, Angela Cantillo, Naoya Takahashi, Christopher Mozsary, Juana Gonzalez, Patrick K. H. Lee, Gerardo de Lamotte, Alessandro Robertiello, Steven Du, Fabienne Velter, Stefan G. Stark, Miguel Carbajo, Vincent Matthys, David A. Westfall, Julia Boeri, Irène Mauricette Mendy, Jonathan Cedillo, Francesco Oteri, Robert W. Crawford, Takayuki Ito, Tina Wunderlin, Maureen Muscat, David Paez-Espino, Carmen Urgiles, Aida Nesimi, Steffen Schaaf, Adan Ramirez-Rojas, Kunihiko Miyake, Christopher E. Mason, Anais Cardenas, Sharah Islam, Diego Benítez, Melissa Pool Pizzi, Kianna Ciaramella, Ciro Borrelli, Riham Islam, Dorottya Nagy-Szakal, Abd-Manaaf Bakere, Ait-hamlat Adel, Olha Lakhneko, Badamnyambuu Iderzorig, Ana Valeria Castro, Adam Phillips, Robert A. Petit, Flavia Corsi, Romain Conte, Krista Ryon, Soojin Jang, Joseph Benson, Fernanda de Souza Gomes Kehdy, Cindy Wang, Nicole Mathews, Jenn-Wei Chen, Rachel Paras, Paulina Pastuszek, Abigail Lyons, Paul Roldán, Muntaha Munia, Pierre Nicolas, Cassie L. Ettinger, Kyrylo Pyrshev, Katterinne N. Mendez, Eduardo Castro-Nallar, Valeriia Dotsenko, Michelle Tuz, Krizzy Mallari, Eileen Png, Yuya Sonohara, Tanja Miketic, Stéphane Delmas, Shu Zhang, Masaki Sato, Yuanting Zheng, Jifeng Zhu, Roland Häusler, Lucie Bittner, Savlatjon Rahmatulloev, Jonathan Foox, Bruno D'Alessandro, Alketa Plaku, Faisal Alquaddoomi, Yang Zhang, Kern Rei Chng, Juliana Lago, Allaeddine Chettouh, Tamera Henry, Houtan Noushmehr, Tranette Gregory, Sara Abdul Majid, Frank J. Kelly, Benjamin Pulatov, Laurie Casalot, Takema Kajita, Lennard Epping, Thais Fernanda Bartelli, Eftar Moniruzzaman, Renee Vivancos-Koopman, Thirumalaisamy P. Velavan, Tracy W. Liu, Yelyzaveta Tymoshenko, Alma Plaku, Nika Gurianova, Ambar Mendez, Anna Tomaselli, Sonia Dorado, Donato Giovannelli, Hira Choudhry, Synti Ng, Sheelta S. Kumar, Jennifer Q. Lu, Weijun Liang, Ellen Koag, Dennis Gankin, Maria João Amorim, Gwenola Simon, Kiyoshi Suganuma, Mikhail Karasikov, Christos A. Ouzounis, Madelyn May, Eran Elhaik, Stephan Ossowski, Kevin Bolzli, Matthew Arthur, Yuya Oto, Jananan Pathmanathan, Salah Mahmoud, Kou Takahashi, Brunna Marques, Kelly French, Felipe Sepúlveda, Shusei Yoshikawa, Paulo Thiago de Souza Santos, Andrew N. Gray, Juliana S Bernardes, Felipe Segato, Björn Brindefalk, George C. Yeh, Jhovana L. Velasco Flores, Jill Sullivan, Silva Baburyan, Denisse Flores, Russell Y. Neches, Sabrina Persaud, Rasheena Wright, Takumi Togashi, Verónica Antelo, Nao Kato, Skye Felice, Tatjana Mustac, Daisy Donnellan, Katerine Carrillo, Anna Litskevitch, Catalina García, Sota Ito, Naya Eady, Andrew Wan, Irene Meng, Sophie Guasco, Danilo Ercolini, Francesca De Filippis, Vincent Lemaire, Luice Fan, Lothar H. Wieler, Mariia Rybak, Jorge Sanchez, Jonathan S. Gootenberg, Itsuki Tomita, Maritza S Mosella, Laura Garcia, Natalka Makogon, Daisy Cheung, Hitler Francois Vasquez Arevalo, Freddy Asenjo, Gabriela P. Branco, Erika Cifuentes, Chloé Dequeker, Aspassia D. Chatziefthimiou, Alexis Terrero, Roy Meoded, Isabelle de Oliveira Moraes, Shaleni K. Singh, Orgil-Erdene Molomjamts, Karishma Miah, Laurent David, Wolfgang Haehr, Dao Phuong Giang, Romain Lannes, Prashanthi Ratnanandan, Ryota Yamanaka, Riccardo Vicedomini, Sadaf Ayaz, Oluwatosin M. Osuolale, Laura E. Vann, Gregory Chem, Andrea Gonzalez, Aszia Burrell, Ariel Chernomoretz, Sakura Ishizuka, Michelle Rivera, Avigdor Nosrati, Michelle B. Chen, Juliette Auvinet, Nils Ordioni, Tomoro Warashina, Guillaume Blanc, Tomislav Ivankovic, Christina Black, Lauren E. Hittle, David Hess-Homeier, Michael Kozhar, Hamood Suliman, Karobi Moitra, Saher Rahiel, Spyridon Gkotzis, Jenny Arevalo, Shaikh B. Iqbal, Beth Mutai, Mohammed Mohsin, Scott Tighe, Sylvie Collin, Yoshitaka Saito, Wayne Menary, Youping Deng, Lucy Lee, Esmeralda Jiminez, Ayuki Watanabe, Nikos C. Kyrpides, Natasha Mohan, Angelika Pupiec, Dedan Githae, Simone Cawthorne, Jonathan A. Eisen, Tomoki Iwashiro, Chiaki Homma, Thomas Saw Aung, Laura Molina, Marcus H. Y. Leung, Ophélie Da Silva, Yan Ling Wong, Hosna Noorzi, Mario Moreno, Alina Butova, Leming Shi, Brian W. Wong, Sarah S. Jackson, Moses Lin, Annabelle Meagher, Pujita Das, Catherine Burke, Mitsuki Ota, Maria Domenica Moccia, Nicolas Sprinsky, Catherine E. Pugh, David C. Green, Fazlina Fauzi, Erdenetsetseg Batdelger, Annie Geiger, Valeria Ventorino, Tolulope Oluwadare, Delisia Cuebas, Catalina Truong, Leonardo Posada, Michael Angelov, Tathiane M. Malta, Amanda Ng, Francesca Nadalin, Arya Hawkins-Zafarnia, Yuh Shiwa, Athena Mitsios, Milton Ozório Moraes, Manolo Laiola, Kalyn Ali, Jaden J.A. Hastings, Ikuto Saito, Maheen Shakil, Chisato Suzuki, Elena M. Vayndorf, Hubert Rehrauer, Ajay Menon, Kaitlan Russell, Aliyah Shari, Rebecca Smith, Gregorio Iraola, Max Priestman, Alan Briones, Silver A. Wolf, Camila Gonzalez-Poblete, Eleonora De Lazzari, Shirley Chiu, Michelle Ki, Irene Hoxie, Marianne Jaubert, Ayantu Jinfessa, Ryan J. King, Nghiem Xuan Hoan, Jalia Bynoe, Jacob Friedman, Aneisa Ramcharan, Pablo Fresia, Cristina Muñoz, Muhammad Afaq, Anyi Tang, Médine Benchouaia, Isabella Kuniko T. Takenaka, Anastasia Chasapi, Areeg Naeem, Hannah Benisty, Cecilia N. Cossio, Nathalie Hüsser, Mahfuza Sabina, Thais S. Sabedot, JoAnn Jacobs, Camila P. E. de Souza, Manuela Oliveira, Jean-Pierre Bouly, Mariko Usui, Wilson Miranda, Natalia Marciniak, Hiram Caballero, Samuel Weekes, Alexandra B. Graf, Emily Leong, Tatyana Nikolayeva, Dominique Thomas, Charlotte Greselle, Cecilia Salazar, Sreya Ray Chaudhuri, Kevin Becher, Sandra Roth, Ryusei Miura, Kari Oline Bøifot, Dimitri Manoir, Oliver Toth, Chandrima Bhattacharya, Manuel Perez, Isha Lamba, Takafumi Tsurumaki, Timothy D. Read, Anna-Lena M. Schinke, Ryan Sankar, Le Huu Song, Narasimha Rao Nedunuri, Emmanuel Dias-Neto, Ana Flávia Costa, Adiell Melamed, Christelle Desnues, Natalie R. Davidson, Aaron E. Darling, Hyung Jun Kim, Josephine Galipon, Jacqueline Orrego, Dimitar Vassilev, Michael Huber, Nur Hazlin Hazrin-Chong, Gaston H. Gonnet, Kaymisha Knights, Osman U. Sezerman, Dmitry Meleshko, Eunice Thambiraja, Jingcheng Yang, Aubin Fleiss, Gloria Nguyen, Katelyn Jackson, Nuria Aventin, Stephanie L. Hyland, Andrea Hässig, Catharine Aquino, Simona Lysakova, Israel O. Osuolale, Kasia Sluzek, Rania Siam, Alina Frolova, Samuel Hernandez, Yui Him Lo, Bazartseren Boldgiv, Ben Young, Maryna Korshevniuk, Majelia Ampadu, Yuk Man Tang, Amanda L. Muehlbauer, Sade Thomas, Gabriel Figueroa, Alexis Rivera, Lisbeth Pineda, Alexandra Dutan, Jennifer M. Tran, Chris K. Deng, Vedbar S. Khadka, Paola Florez de Sessions, Elizabeth Humphries, Hugues Richard, Hiba Naveed, Nora C. Toussaint, Mahshid Khavari, Maria del Mar Vivanco Ruiz, Antonin Thiébaut, Nicolás Rascovan, Marius Dybwad, Orhan Özcan, Lawrence Kwong, David Danko, Shaira Khan, Andrea Tassinari, Silvia Beurmann, Tsoi Ying Lai, Nanami Kubota, Tieliu Shi, Diana Chicas, Evan E. Afshin, Hirokazu Yano, Jonas Krebs, Mayuko Nakagawa, Hyun Jung Lee, Irene González Navarrete, Rachid Ounit, Lucia E. Alvarado-Arnez, Masaki Nasu, Allison Chan, Harilanto Andrianjakarivony, Jennifer Amachee, Mahdi Taye, Wan Chiew Ng, Kathryn O’Brien, Shino Ishikawa, Tristan Bitard-Feildel, Sora Takagi, Felix Hartkopf, Niamh B. O’Hara, Marcos A. S. Fonseca, Subhamitra Pakrashi, Amrit Kaur, Eva Hell, Patricia Vera-Wolf, Naimah Munim, Luiza Ferreira de Araújo, Mizuki Igarashi, Brianna Pompa-Hogan, Alessandra Carbone, Anne-Sophie Benoiston, Eric Helfrich, Michael A. Suarez-Villamil, Omar O. Abudayyeh, Natasha Abdullah, Jaime J. Fuentes, Juan Carlos Forero, Tetiana Yeskova, Denis Bertrand, Sambhawa Priya, Denisse Maldonado, Agier Nicolas, Ana Valeria B Castro, Starr Chatziefthimiou, André Kahles, Aaishah Francis, Fernanda Arredondo, Emilio Tarcitano, Irvind Buttar, Alex Alexiev, Jennifer Molinet, Sarah Shalaby, Itunu A. Oluwadare, Jason Sperry, Katrin Bakhl, Ana M. Cañas, Sofia Ahsanuddin, Miar Elaskandrany, Elodie Laine, Sven Bönigk, Johannes Werner, Stephen Eduard Boja Ruiz, Gargi Dayama, Paulina Buczansla, Brandon Valentine, Bharath Prithiviraj, Toni Bode, Stas Zubenko, Jake Cohen, Guilllaume Jospin, Zulena Saravi, Per O. Ljungdahl, Inderjit Kaur, Mauricio Moldes, Giuseppe KoLoMonaco, Denise Syndercombe Court, Sonia Bouchard, Sonia Losim, Sookwon Moon, Heba Shaaban, Suraj Patel, Sibo Zhu, Sarh Aly, Arif Asyraf Md Supie, LaShonda Dorsey, Juan Guerra, François Baudon, Rantimi A. Olawoyin, Alexia Bordigoni, Iqra Faiz, Mathilde Garcia, Gabriella Mason-Buck, María Gabriela Portilla, Niranjan Nagarajan, Fumie Takahara, Nancy Merino, Watson Andrew, Gina Kim, Yuma Sato, Hyenah Shim, Marie-Laure Jerier, Affifah Saadah Ahmad Kassim, Katerina Kuchin, Daniel Butler, Paweł P. Łabaj, Nadezhda Kobko-Litskevitch, Emmanuel F. Mongodin, Yuto Togashi, Paula Rodríguez, Pilar Lopez Hernandez, Xiaoqing Chen, Maria A. Sierra, Olga Nikolayeva, Manon Loubens, Colleen Conger, Hikaru Shirahata, Chenhao Li, Timothy Donahoe, Youngja Park, Lucia Elena Alvarado Arnez, Salama Chaker, Francisco Chavez, Alessandra Breschi, Jorge L. Sanchez, Kaung Myat San, Nayra Aguilar Rojas, Marcos Abraao, Kai Sasaki, Bryan Nazario, Olena Yemets, Klas I. Udekwu, Lynn M. Schriml, Anisia Peters, Aliaksei Holik, Mark Hernandez, Emile Faure, Malay Bhattacharyya, Josef W. Moser, Núria Andreu Somavilla, María Mercedes Zambrano, Kannan Rajendran, Gabriela E. Albuquerque, Tao Qing, Kazutoshi Tsuda, Ymke De Jong, Princess Osma, Mayra Arauco Livia, Javier Quilez Oliete, Carl Chrispin, Hyun Woo Joo, Ingrid Lafontaine, Nala An, Seisuke Sato, Felipe Segato Dezem, Andrew Maltez Thomas, Alexandre Desert, Xiao Wen Cai, O. Osuolale, Jun Wu, Coral Pardo-Esté, Courtney Robinson, Yuri Matsuzaki, Marina Nieto-Caballero, Cem Meydan, Ralph Schlapbach, Mark Menor, Sofia Castro, Rachel Kwong, Brittany Blyther, Olexandr Lykhenko, Jason R. Schriml, Christian Brion, Jenessa Orpilla, Juan A. Ugalde, Elsy Mankah Ngwa, Álvaro Aranguren, Lauren Mak, Matías Giménez, Ashanti Narce, Torsten Semmler, Stefan I. Tsonev, Abdollahi Nika, Katherine E. Dahlhausen, Monika Devi, Gunnar Rätsch, Oasima Muner, Carla Bello, Muhammad Al-Fath Amran, Anyelic Rosario, Melissa Ortega, Andrea Patrignani, Ante Peros, Elias McComb, Ryo Sato, Ireen Alam, Clara N. Dias, Soma Tanaka, Dayana Calderon, Ran Blekhman, Mathilde Mignotte, Alicia Boyd, Jochen Hecht, Thomas Neff, Xinzhao Tong, Josue Alicea, Kiara Olmeda, Sonia Marinovic, Carme Arnan, Kohei Ito, Samantha L. Goldman, Marianna S. Serpa, Renee Richer, Kaisei Sato, Jordana M. Silva, Akash Keluth Chavan, Sangwan Kim, Laís Pereira Ferreira, Sophie Vacant, Nowshin Sayara, Haruo Suzuki, Madeline Leahy, Juan C. Severyn, Sierra Vincent, Masaru Tomita, Maliha Mamun, Lucinda B. Davenport, Gabriella Oken, Dagmara Lewandowska, Gustavo Adolfo Malca Salas, Andrii Kuklin, Tyler Wong, Charlie Feigin, Eric Minwei Liu, Sonia L. Ghose, Daniela Bezdan, Antonietta La Storia, Juan P. Escalera-Antezana, Nuno Rufino de Sousa, Samuel M. Gerner, Weill Cornell Medicine [New York], Icahn School of Medicine at Mount Sinai [New York] (MSSM), Genome Institute of Singapore (GIS), Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), AUTRES, Massachusetts Institute of Technology (MIT), Indian Statistical Institute [Kolkata], University of Minnesota System, Universidad Andrés Bello [Santiago] (UNAB), California State University [Sacramento], University of Naples Federico II, University of Hawaii, 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), Medical Genomics Group, University College of London [London] (UCL)-UCL Cancer Institute, Norwegian Defence Research Establishment (FFI), Lund University [Lund], Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, University of Vienna [Vienna], King‘s College London, University of Colorado [Boulder], Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP), Institut Pasteur Korea - Institut Pasteur de Corée, Fudan University [Shanghai], City University of Hong Kong [Hong Kong] (CUHK), Stockholm University, University of Maryland School of Medicine, University of Maryland System, Fundação Oswaldo Cruz (FIOCRUZ), University of São Paulo (USP), Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Barcelona Institute of Science and Technology (BIST), Elizade University, Acibadem Mehmet Ali Aydınlar University, Paléogénomique microbienne - Microbial paleogenomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Robert Koch Institute [Berlin] (RKI), East China Normal University [Shangaï] (ECNU), Cairo University, Vietnamese-German Center for Medical Research, Keio University, Université du Vermont, Universidad del Desarrollo, University of Sofia, University of Alaska [Fairbanks] (UAF), Universitätsklinikum Tübingen - University Hospital of Tübingen, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Corporación Corpogen-Research Center, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Weill Cornell Medicine [Cornell University], Cornell University [New York], University of Naples Federico II = Università degli studi di Napoli Federico II, 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), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Universidade de São Paulo = University of São Paulo (USP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Софийски университет = Sofia University, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universidad Andrés Bello - UNAB (CHILE), Acibadem University Dspace, Danko, D., Bezdan, D., Afshin, E. E., Ahsanuddin, S., Bhattacharya, C., Butler, D. J., Chng, K. R., Donnellan, D., Hecht, J., Jackson, K., Kuchin, K., Karasikov, M., Lyons, A., Mak, L., Meleshko, D., Mustafa, H., Mutai, B., Neches, R. Y., Ng, A., Nikolayeva, O., Nikolayeva, T., Png, E., Ryon, K. A., Sanchez, J. L., Shaaban, H., Sierra, M. A., Thomas, D., Young, B., Abudayyeh, O. O., Alicea, J., Bhattacharyya, M., Blekhman, R., Castro-Nallar, E., Canas, A. M., Chatziefthimiou, A. D., Crawford, R. W., De Filippis, F., Deng, Y., Desnues, C., Dias-Neto, E., Dybwad, M., Elhaik, E., Ercolini, D., Frolova, A., Gankin, D., Gootenberg, J. S., Graf, A. B., Green, D. C., Hajirasouliha, I., Hastings, J. J. A., Hernandez, M., Iraola, G., Jang, S., Kahles, A., Kelly, F. J., Knights, K., Kyrpides, N. C., Labaj, P. P., Lee, P. K. H., Leung, M. H. Y., Ljungdahl, P. O., Mason-Buck, G., Mcgrath, K., Meydan, C., Mongodin, E. F., Moraes, M. O., Nagarajan, N., Nieto-Caballero, M., Noushmehr, H., Oliveira, M., Ossowski, S., Osuolale, O. O., Ozcan, O., Paez-Espino, D., Rascovan, N., Richard, H., Ratsch, G., Schriml, L. M., Semmler, T., Sezerman, O. U., Shi, L., Shi, T., Siam, R., Song, L. H., Suzuki, H., Court, D. S., Tighe, S. W., Tong, X., Udekwu, K. I., Ugalde, J. A., Valentine, B., Vassilev, D. I., Vayndorf, E. M., Velavan, T. P., Wu, J., Zambrano, M. M., Zhu, J., Zhu, S., Mason, C. E., Abdullah, N., Abraao, M., Adel, A. -H., Afaq, M., Al-Quaddoomi, F. S., Alam, I., Albuquerque, G. E., Alexiev, A., Ali, K., Alvarado-Arnez, L. E., Aly, S., Amachee, J., Amorim, M. G., Ampadu, M., Amran, M. A. -F., An, N., Andrew, W., Andrianjakarivony, H., Angelov, M., Antelo, V., Aquino, C., Aranguren, A., Araujo, L. F., Vasquez Arevalo, H. F., Arevalo, J., Arnan, C., Alvarado Arnez, L. E., Arredondo, F., Arthur, M., Asenjo, F., Aung, T. S., Auvinet, J., Aventin, N., Ayaz, S., Baburyan, S., Bakere, A. -M., Bakhl, K., Bartelli, T. F., Batdelger, E., Baudon, F., Becher, K., Bello, C., Benchouaia, M., Benisty, H., Benoiston, A. -S., Benson, J., Benitez, D., Bernardes, J., Bertrand, D., Beurmann, S., Bitard-Feildel, T., Bittner, L., Black, C., Blanc, G., Blyther, B., Bode, T., Boeri, J., Boldgiv, B., Bolzli, K., Bordigoni, A., Borrelli, C., Bouchard, S., Bouly, J. -P., Boyd, A., Branco, G. P., Breschi, A., Brindefalk, B., Brion, C., Briones, A., Buczansla, P., Burke, C. M., Burrell, A., Butova, A., Buttar, I., Bynoe, J., Bonigk, S., Boifot, K. O., Caballero, H., Cai, X. W., Calderon, D., Cantillo, A., Carbajo, M., Carbone, A., Cardenas, A., Carrillo, K., Casalot, L., Castro, S., Castro, A. V., Castro, A., Castro, A. V. B., Cawthorne, S., Cedillo, J., Chaker, S., Chalangal, J., Chan, A., Chasapi, A. I., Chatziefthimiou, S., Chaudhuri, S. R., Chavan, A. K., Chavez, F., Chem, G., Chen, X., Chen, M., Chen, J. -W., Chernomoretz, A., Chettouh, A., Cheung, D., Chicas, D., Chiu, S., Choudhry, H., Chrispin, C., Ciaramella, K., Cifuentes, E., Cohen, J., Coil, D. A., Collin, S., Conger, C., Conte, R., Corsi, F., Cossio, C. N., Costa, A. F., Cuebas, D., D'Alessandro, B., Dahlhausen, K. E., Darling, A. E., Das, P., Davenport, L. B., David, L., Davidson, N. R., Dayama, G., Delmas, S., Deng, C. K., Dequeker, C., Desert, A., Devi, M., Dezem, F. S., Dias, C. N., Donahoe, T. R., Dorado, S., Dorsey, L., Dotsenko, V., Du, S., Dutan, A., Eady, N., Eisen, J. A., Elaskandrany, M., Epping, L., Escalera-Antezana, J. P., Ettinger, C. L., Faiz, I., Fan, L., Farhat, N., Faure, E., Fauzi, F., Feigin, C., Felice, S., Ferreira, L. P., Figueroa, G., Fleiss, A., Flores, D., Velasco Flores, J. L., Fonseca, M. A. S., Foox, J., Forero, J. C., Francis, A., French, K., Fresia, P., Friedman, J., Fuentes, J. J., Galipon, J., Garcia, M., Garcia, L., Garcia, C., Geiger, A., Gerner, S. M., Ghose, S. L., Giang, D. P., Gimenez, M., Giovannelli, D., Githae, D., Gkotzis, S., Godoy, L., Goldman, S., Gonnet, G. H., Gonzalez, J., Gonzalez, A., Gonzalez-Poblete, C., Gray, A., Gregory, T., Greselle, C., Guasco, S., Guerra, J., Gurianova, N., Haehr, W., Halary, S., Hartkopf, F., Hawkins-Zafarnia, A., Hazrin-Chong, N. H., Helfrich, E., Hell, E., Henry, T., Hernandez, S., Hernandez, P. L., Hess-Homeier, D., Hittle, L. E., Hoan, N. X., Holik, A., Homma, C., Hoxie, I., Huber, M., Humphries, E., Hyland, S., Hassig, A., Hausler, R., Husser, N., Petit, R. A., Iderzorig, B., Igarashi, M., Iqbal, S. B., Ishikawa, S., Ishizuka, S., Islam, S., Islam, R., Ito, K., Ito, S., Ito, T., Ivankovic, T., Iwashiro, T., Jackson, S., Jacobs, J., James, M., Jaubert, M., Jerier, M. -L., Jiminez, E., Jinfessa, A., De Jong, Y., Joo, H. W., Jospin, G., Kajita, T., Ahmad Kassim, A. S., Kato, N., Kaur, A., Kaur, I., de Souza Gomes Kehdy, F., Khadka, V. S., Khan, S., Khavari, M., Ki, M., Kim, G., Kim, H. J., Kim, S., King, R. J., Kolomonaco, G., Koag, E., Kobko-Litskevitch, N., Korshevniuk, M., Kozhar, M., Krebs, J., Kubota, N., Kuklin, A., Kumar, S. S., Kwong, R., Kwong, L., Lafontaine, I., Lago, J., Lai, T. Y., Laine, E., Laiola, M., Lakhneko, O., Lamba, I., de Lamotte, G., Lannes, R., De Lazzari, E., Leahy, M., Lee, H., Lee, Y., Lee, L., Lemaire, V., Leong, E., Lewandowska, D., Li, C., Liang, W., Lin, M., Lisboa, P., Litskevitch, A., Liu, E. M., Liu, T., Livia, M. A., Lo, Y. H., Losim, S., Loubens, M., Lu, J., Lykhenko, O., Lysakova, S., Mahmoud, S., Majid, S. A., Makogon, N., Maldonado, D., Mallari, K., Malta, T. M., Mamun, M., Manoir, D., Marchandon, G., Marciniak, N., Marinovic, S., Marques, B., Mathews, N., Matsuzaki, Y., Matthys, V., May, M., Mccomb, E., Meagher, A., Melamed, A., Menary, W., Mendez, K. N., Mendez, A., Mendy, I. M., Meng, I., Menon, A., Menor, M., Meoded, R., Merino, N., Miah, K., Mignotte, M., Miketic, T., Miranda, W., Mitsios, A., Miura, R., Miyake, K., Moccia, M. D., Mohan, N., Mohsin, M., Moitra, K., Moldes, M., Molina, L., Molinet, J., Molomjamts, O. -E., Moniruzzaman, E., Moon, S., de Oliveira Moraes, I., Moreno, M., Mosella, M. S., Moser, J. W., Mozsary, C., Muehlbauer, A. L., Muner, O., Munia, M., Munim, N., Muscat, M., Mustac, T., Munoz, C., Nadalin, F., Naeem, A., Nagy-Szakal, D., Nakagawa, M., Narce, A., Nasu, M., Navarrete, I. G., Naveed, H., Nazario, B., Nedunuri, N. R., Neff, T., Nesimi, A., Ng, W. C., Ng, S., Nguyen, G., Ngwa, E., Nicolas, A., Nicolas, P., Nika, A., Noorzi, H., Nosrati, A., Nunes, D. N., O'Brien, K., O'Hara, N. B., Oken, G., Olawoyin, R. A., Oliete, J. Q., Olmeda, K., Oluwadare, T., Oluwadare, I. A., Ordioni, N., Orpilla, J., Orrego, J., Ortega, M., Osma, P., Osuolale, I. O., Osuolale, O. M., Ota, M., Oteri, F., Oto, Y., Ounit, R., Ouzounis, C. A., Pakrashi, S., Paras, R., Pardo-Este, C., Park, Y. -J., Pastuszek, P., Patel, S., Pathmanathan, J., Patrignani, A., Perez, M., Peros, A., Persaud, S., Peters, A., Phillips, A., Pineda, L., Pizzi, M. P., Plaku, A., Pompa-Hogan, B., Portilla, M. G., Posada, L., Priestman, M., Prithiviraj, B., Priya, S., Pugdeethosal, P., Pugh, C. E., Pulatov, B., Pupiec, A., Pyrshev, K., Qing, T., Rahiel, S., Rahmatulloev, S., Rajendran, K., Ramcharan, A., Ramirez-Rojas, A., Rana, S., Ratnanandan, P., Read, T. D., Rehrauer, H., Richer, R., Rivera, A., Rivera, M., Robertiello, A., Robinson, C., Rodriguez, P., Rojas, N. A., Roldan, P., Rosario, A., Roth, S., Ruiz, M., Boja Ruiz, S. E., Russell, K., Rybak, M., Sabedot, T. S., Sabina, M., Saito, I., Saito, Y., Malca Salas, G. A., Salazar, C., San, K. M., Sanchez, J., Sanchir, K., Sankar, R., de Souza Santos, P. T., Saravi, Z., Sasaki, K., Sato, Y., Sato, M., Sato, S., Sato, R., Sato, K., Sayara, N., Schaaf, S., Schacher, O., Schinke, A. -L. M., Schlapbach, R., Schori, C., Schriml, J. R., Segato, F., Sepulveda, F., Serpa, M. S., De Sessions, P. F., Severyn, J. C., Shakil, M., Shalaby, S., Shari, A., Shim, H., Shirahata, H., Shiwa, Y., Da Silva, O., Silva, J. M., Simon, G., Singh, S. K., Sluzek, K., Smith, R., So, E., Andreu Somavilla, N., Sonohara, Y., Rufino de Sousa, N., Souza, C., Sperry, J., Sprinsky, N., Stark, S. G., La Storia, A., Suganuma, K., Suliman, H., Sullivan, J., Supie, A. A. M., Suzuki, C., Takagi, S., Takahara, F., Takahashi, N., Takahashi, K., Takeda, T., Takenaka, I. K., Tanaka, S., Tang, A., Man Tang, Y., Tarcitano, E., Tassinari, A., Taye, M., Terrero, A., Thambiraja, E., Thiebaut, A., Thomas, S., Thomas, A. M., Togashi, Y., Togashi, T., Tomaselli, A., Tomita, M., Tomita, I., Toth, O., Toussaint, N. C., Tran, J. M., Truong, C., Tsonev, S. I., Tsuda, K., Tsurumaki, T., Tuz, M., Tymoshenko, Y., Urgiles, C., Usui, M., Vacant, S., Vann, L. E., Velter, F., Ventorino, V., Vera-Wolf, P., Vicedomini, R., Suarez-Villamil, M. A., Vincent, S., Vivancos-Koopman, R., Wan, A., Wang, C., Warashina, T., Watanabe, A., Weekes, S., Werner, J., Westfall, D., Wieler, L. H., Williams, M., Wolf, S. A., Wong, B., Wong, Y. L., Wong, T., Wright, R., Wunderlin, T., Yamanaka, R., Yang, J., Yano, H., Yeh, G. C., Yemets, O., Yeskova, T., Yoshikawa, S., Zafar, L., Zhang, Y., Zhang, S., Zhang, A., Zheng, Y., and Zubenko, S.
Subjects: Urban Population, Drug Resistance, Sequence assembly, Microbiologia, microbiome, global health, computer.software_genre, Medical and Health Sciences, shotgun sequencing, BGC, 0302 clinical medicine, Databases, Genetic, 11. Sustainability, Global health, AMR, 11 Medical and Health Sciences, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, built environment, metagenome, antimicrobial resistance, NGS, de novo assembly, biology, Shotgun sequencing, Microbiota, built Environment, Bacterial, Biodiversity, Biological Sciences, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infection, Biotechnology, Geospatial analysis, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Article, General Biochemistry, Genetics and Molecular Biology, Databases, 03 medical and health sciences, Antibiotic resistance, Genetic, Drug Resistance, Bacterial, International MetaSUB Consortium, Genetics, Humans, Microbiome, 030304 developmental biology, Human Genome, 06 Biological Sciences, 15. Life on land, biology.organism_classification, Resistènica als medicaments antiinfecciosos, SAÚDE PÚBLICA, Genòmica, 13. Climate action, Evolutionary biology, Metagenomics, Antimicrobial Resistance, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer, 030217 neurology & neurosurgery, Archaea, Developmental Biology
Abstract: Summary We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities., Graphical abstract, Highlights • Cities possess a consistent “core” set of non-human microbes • Urban microbiomes echo important features of cities and city-life • Antimicrobial resistance genes are widespread in cities • Cities contain many novel bacterial and viral species, This systematic, worldwide catalog of urban microbiomes represents a metagenomic atlas important for understanding the ecology, virulence, and antibiotic resistance of city-specific microbial communities.
Published: 2021

11. Evidence of high N2 fixation rates in the temperate northeast Atlantic

Author: Morgane Gallinari, Marc Elskens, Debany Fonseca-Batista, Julie LaRoche, Lei Chou, Manon Tonnard, Valérie Michotey, Nolwenn Lemaitre, Hélène Planquette, François Fripiat, Virginie Riou, Frédéric Planchon, Natacha Brion, Xuefeng Li, Frank Dehairs, Géraldine Sarthou, Sophie Guasco, and Florian Deman
Subjects: 0303 health sciences, 010504 meteorology & atmospheric sciences, Ecology, Spring bloom, 01 natural sciences, 03 medical and health sciences, 13. Climate action, Temperate climate, Nitrogen fixation, Environmental science, Photic zone, 14. Life underwater, Transect, Bloom, Bay, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0105 earth and related environmental sciences, Earth-Surface Processes, Redfield ratio
Abstract: Diazotrophic activity and primary production (PP) were investigated along two transects (Belgica BG2014/14 and GEOVIDE cruises) off the western Iberian Margin and the Bay of Biscay in May 2014. Substantial N2 fixation activity was observed at 8 of the 10 stations sampled, ranging overall from 81 to 384 µ mol N m −2 d −1 (0.7 to 8.2 nmol N L −1 d −1) , with two sites close to the Iberian Margin situated between 38.8 and 40.7 ∘ N yielding rates reaching up to 1355 and 1533 µ mol N m −2 d −1 . Primary production was relatively lower along the Iberian Margin, with rates ranging from 33 to 59 mmol C m −2 d −1 , while it increased towards the northwest away from the peninsula, reaching as high as 135 mmol C m −2 d −1 . In agreement with the area-averaged Chl a satellite data contemporaneous with our study period, our results revealed that post-bloom conditions prevailed at most sites, while at the northwesternmost station the bloom was still ongoing. When converted to carbon uptake using Redfield stoichiometry, N2 fixation could support 1 % to 3 % of daily PP in the euphotic layer at most sites, except at the two most active sites where this contribution to daily PP could reach up to 25 %. At the two sites where N2 fixation activity was the highest, the prymnesiophyte–symbiont Candidatus Atelocyanobacterium thalassa (UCYN-A) dominated the nifH sequence pool, while the remaining recovered sequences belonged to non-cyanobacterial phylotypes. At all the other sites, however, the recovered nifH sequences were exclusively assigned phylogenetically to non-cyanobacterial phylotypes. The intense N2 fixation activities recorded at the time of our study were likely promoted by the availability of phytoplankton-derived organic matter produced during the spring bloom, as evidenced by the significant surface particulate organic carbon concentrations. Also, the presence of excess phosphorus signature in surface waters seemed to contribute to sustaining N2 fixation, particularly at the sites with extreme activities. These results provide a mechanistic understanding of the unexpectedly high N2 fixation in productive waters of the temperate North Atlantic and highlight the importance of N2 fixation for future assessment of the global N inventory.
Published: 2019

12. Supplementary material to 'Phosphorus cycling in the upper waters of the Mediterranean Sea (Peacetime cruise): relative contribution of external and internal sources'

Author: Elvira Pulido-Villena, Karine Desboeufs, Kahina Djaoudi, France Van Wambeke, Stéphanie Barrillon, Andrea Doglioli, Anne Petrenko, Vincent Taillandier, Franck Fu, Tiphanie Gaillard, Sophie Guasco, Sandra Nunige, Sylvain Triquet, and Cécile Guieu
Published: 2021

13. Supplementary material to 'Subsurface iron accumulation and rapid aluminium removal in the Mediterranean following African dust deposition'

Author: Matthieu Bressac, Thibaut Wagener, Nathalie Leblond, Antonio Tovar-Sánchez, Céline Ridame, Samuel Albani, Sophie Guasco, Aurélie Dufour, Stéphanie Jacquet, François Dulac, Karine Desboeufs, and Cécile Guieu
Published: 2021

14. On the barium–oxygen consumption relationship in the Mediterranean Sea: implications for mesopelagic marine snow remineralization

Author: Christian Tamburini, Sophie Guasco, Dominique Lefèvre, Marc Garel, Frédéric A. C. Le Moigne, Stephanie Jacquet, Nagib Bhairy, 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, 010504 meteorology & atmospheric sciences, Mesopelagic zone, Heterotroph, lcsh:Life, chemistry.chemical_element, 01 natural sciences, Oxygen, Mediterranean sea, lcsh:QH540-549.5, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, 0105 earth and related environmental sciences, Earth-Surface Processes, Marine snow, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Remineralisation, 010604 marine biology & hydrobiology, lcsh:QE1-996.5, Barium, Particulates, lcsh:Geology, lcsh:QH501-531, Oceanography, chemistry, Environmental science, lcsh:Ecology
Abstract: In the ocean, remineralization rate associated with sinking particles is a crucial variable. Since the 1990s, particulate biogenic barium (Baxs) has been used as an indicator of carbon remineralization by applying a transfer function relating Baxs to O2 consumption (Dehairs's transfer function, Southern Ocean-based). Here, we tested its validity in the Mediterranean Sea (ANTARES/EMSO-LO) for the first time by investigating connections between Baxs, prokaryotic heterotrophic production (PHP) and oxygen consumption (JO2-Opt; optodes measurement). We show that (1) higher Baxs (409 pM; 100–500 m) occurs in situations where integrated PHP (PHP100/500=0.90) is located deeper, (2) higher Baxs occurs with increasing JO2-Opt, and (3) there is similar magnitude between JO2-Opt (3.14 mmol m−2 d−1; 175–450 m) and JO2-Ba (4.59 mmol m−2 d−1; transfer function). Overall, Baxs, PHP and JO2 relationships follow trends observed earlier in the Southern Ocean. We conclude that such a transfer function could apply in the Mediterranean Sea.
Published: 2021

15. In situ observations and modelling revealed environmental factors favouring occurrence of Vibrio in microbiome of the pelagic Sargassum responsible for strandings

Author: Louis Le Grand, Cristèle Chevalier, Jean Blanchot, Valérie Michotey, Léo Berline, Frédéric Diaz, Sandrine Ruitton, Marc Garel, Frédéric Ménard, Thierry Thibaut, Bruno Belloni, Fabrice Armougom, Sophie Guasco, Aurelie Blanfuné, Thomas Changeux, 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: Operational taxonomic unit, Environmental Engineering, 010504 meteorology & atmospheric sciences, West Indies, copepod, microbiome, Wind, 010501 environmental sciences, 01 natural sciences, Environmental Chemistry, Animals, wind, Seawater, 14. Life underwater, Alteromonas, Waste Management and Disposal, Mexico, 0105 earth and related environmental sciences, Vibrio, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Sargassum growth rate, biology, Ecology, Microbiota, nutrient, Sargassum, Pelagic zone, Copepod, biology.organism_classification, Pollution, [SDE.ES]Environmental Sciences/Environmental and Society, Caribbean Region, Benthic zone, Microbiome, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Nutrient
Abstract: International audience; Historically, pelagic Sargassum were only found in the Sargasso Sea. Since 2011, blooms were regularly observed in warmer water, further south. Their developments in Central Atlantic are associated with mass strandings on the coasts, causing important damages and potentially dispersion of new bacteria. Microbiomes associated with pelagic Sargassum were analysed at large scale in Central Atlantic and near Caribbean Islands with a focus on pathogenic bacteria. Vibrio appeared widely distributed among pelagic Sargassum microbiome of our samples with higher occurrence than previously found in Mexico Gulf. Six out the 16 Vibrio-OTUs (Operational Taxonomic Unit), representing 81.2 ± 13.1% of the sequences, felt in cluster containing pathogens. Among the four different microbial profiles of pelagic Sargassum microbiome, Vibrio attained about 2% in two profiles whereas it peaked, in the two others, at 6.5 and 26.8 % respectively, largely above the concentrations found in seawater surrounding raft (0.5%). In addition to sampling and measurements, we performed backward Lagrangian modelling of trajectories of rafts, and rebuilt the sampled rafts environmental history allowing us to estimate Sargassum growth rates along raft displacements. We found that Vibrio was favoured by high Sargassum growth rate and in situ ammonium and nitrite, modelled phosphate and nitrate concentrations, whereas zooplankters, benthic copepods, and calm wind (proxy of raft buoyancy near the sea surface) were less favourable for them. Relations between Vibrio and other main bacterial groups identified a competition with Alteromonas. According to forward Lagrangian tracking, part of rafts containing Vibrio could strand on the Caribbean coasts, however the strong decreases of modelled Sargassum growth rates along this displacement suggest unfavourable environment for Vibrio. For the conditions and areas observed, the sanitary risk seemed in consequence minor, but in other areas or conditions where high Sargassum growth rate occurred near coasts, it could be more important.
Published: 2020

16. Particulate biogenic barium tracer of mesopelagic carbon remineralization in the Mediterranean Sea (PEACETIME project)

Author: Stéphanie H. M. Jacquet, Christian Tamburini, Marc Garel, Aurélie Dufour, France Van-Vambeke, Frédéric A. C. Le Moigne, Nagib Bhairy, 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: 010504 meteorology & atmospheric sciences, Mesopelagic zone, Heterotroph, chemistry.chemical_element, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, Structural basin, 01 natural sciences, Mediterranean sea, Life, TRACER, QH501-531, 14. Life underwater, QH540-549.5, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Remineralisation, QE1-996.5, Ecology, Barium, Geology, Particulates, Oceanography, chemistry, 13. Climate action, [SDU]Sciences of the Universe [physics], Environmental science
Abstract: We report on the sub-basin variability in particulate organic carbon (POC) remineralization in the western and central Mediterranean Sea in late spring during the PEACETIME (ProcEss studies at the Air–sEa Interface after dust deposition in the MEditerranean sea) cruise. POC remineralization rates were estimated using the excess biogenic particulate barium (Baxs) inventories in the mesopelagic layers (100–1000 m depth) and compared with prokaryotic heterotrophic production (PHP). Baxs-based mesopelagic remineralization rates (MRs) ranged from 25±2 to 306±70 mgCm-2d-1. MRs were larger in the Algero-Provençal (ALG) Basin than in the Tyrrhenian (TYR) and Ionian (ION) basins. Our Baxs inventories and integrated PHP data also indicated that significant mesopelagic remineralization occurred down to 1000 m depth in the ALG Basin in contrast to the ION and TYR basins, where remineralization was mainly located above 500 m depth. We propose that the higher and deeper MRs in the ALG Basin were sustained by an additional particle export event driven by deep convection. The TYR Basin (in contrast to the ALG and ION basins) presented the impact of a previous dust event, as reflected by our particulate Al water column concentrations. The ION and TYR basins showed small-scale heterogeneity in remineralization processes, reflected by our Baxs inventories and integrated PHP data at the Tyrr long-duration station. This heterogeneity was linked to the mosaic of blooming and non-blooming patches reported in this area during the cruise. In contrast to the western Mediterranean Sea (ALG Basin), the central Mediterranean Sea (ION and TYR basins) showed lower remineralization rates restricted to the upper mesopelagic layer during the late spring PEACETIME cruise.
Published: 2020

17. On the barium-oxygen consumption relationship in the Mediterranean Sea: implications for mesopelagic marine snow remineralisation

Author: Stéphanie H. M. Jacquet, Dominique Lefèvre, Christian Tamburini, Marc Garel, Frédéric A. C. Le Moigne, Nagib Bhairy, Marie Roumagnac, 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)-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: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 13. Climate action, 14. Life underwater
Abstract: In the ocean, remineralisation rate associated with sinking particles is a crucial variable. Since the 90's, particulate biogenic barium (Baxs) has been used as an indicator of carbon remineralization by applying a transfer function relating Baxs to O2 consumption (Dehairs's transfer function, Southern Ocean-based). Here, we tested its validity in the Mediterranean Sea (ANTARES / EMSO-LO) for the first time by investigating connections between Baxs, prokaryotic heterotrophic production (PHP) and oxygen consumption (JO2-Opt; optodes measurement). We show that: (1) higher Baxs (409 pM; 100–500 m) in situations where integrated PHP (PHP100/500 = 0.90) is located deeper, (2) higher Baxs with increasing JO2-Opt, and (3) similar magnitude between JO2-Opt (3.14 mmol m−2 d−1; 175–450 m) and JO2-Ba (4.59 mmol m−2 d−1; transfer function). Overall, Baxs, PHP and JO2 relationships follow trends observed in the Southern Ocean. We believe that such transfer function could apply in the Mediterranean Sea with no restriction.
Published: 2020

18. Supplementary material to 'Spatial patterns of biphasic ectoenzymatic kinetics related to biogeochemical properties in the Mediterranean Sea'

Author: France Van Wambeke, Elvira Pulido, Julie Dinasquet, Kahina Djaoudi, Anja Engel, Marc Garel, Sophie Guasco, Sandra Nunige, Vincent Taillandier, Birthe Zäncker, and Christian Tamburini
Published: 2020

19. 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

20. 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

21. From In Situ to satellite observations of pelagic Sargassum distribution and aggregation in the Tropical North Atlantic Ocean

Author: Jean-Michel André, Hubert Bataille, Didier Aurelle, Sophie Guasco, Jacques Grelet, Dorian Guillemain, Jean Blanchot, Céline Bachelier, Mathilde Guéné, Valérie Stiger-Pouvreau, Léo Berline, A. Ody, Cristèle Chevalier, Sandrine Ruitton, Thierry Thibaut, Natascha Schmidt, Aurelie Blanfuné, Frédéric Ménard, Vincent Fauvelle, Solène Connan, Thomas Changeux, 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), Instrumentation, Moyens analytiques, Observatoires en Géophysique et Océanographie (IMAGO), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institut de Recherche pour le Développement (IRD), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), SAREDAs4 project, European Project: 1166-39417,FEDER, Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-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) Marseille (IRD Marseille), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)
Subjects: Satellite Imagery, 0106 biological sciences, Atmospheric Science, Topography, 010504 meteorology & atmospheric sciences, Range (biology), Atmospheric clouds, Cloud cover, Transportation, Wind, 01 natural sciences, Satellite imagery, Biomass, Atmospheric Dynamics, Atlantic Ocean, Islands, Biomass (ecology), Multidisciplinary, Sea, Ecology, biology, Physics, Eukaryota, Plants, Geophysics, Oceanography, Physical Sciences, Medicine, Engineering and Technology, Seasons, Sargasso Sea, Brazil, Research Article, Ecological Metrics, Algae, Science, West Indies, Mesoscale meteorology, Meteorology, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Bodies of water, Clouds, 14. Life underwater, Ships, 0105 earth and related environmental sciences, Landforms, 010604 marine biology & hydrobiology, ACL, Ecology and Environmental Sciences, Sargassum, Organisms, Biology and Life Sciences, Geomorphology, Pelagic zone, Sargasso, biology.organism_classification, Atmospheric Physics, Marine and aquatic sciences, Earth Sciences, Environmental science, Satellite, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; The present study reports on observations carried out in the Tropical North Atlantic in summer and autumn 2017, documenting Sargassum aggregations using both ship-deck observations and satellite sensor observations at three resolutions (MSI-10 m, OLCI-300 m, VIIRS-750 m and MODIS-1 km). Both datasets reported that in summer, Sargassum aggre-gations were mainly observed off Brazil and near the Caribbean Islands, while they accumulated near the African coast in autumn. Based on in situ observations, we propose a five-class typology allowing standardisation of the description of in situ Sargassum raft shapes and sizes. The most commonly observed Sargassum raft type was windrows, but large rafts composed of a quasi-circular patch hundreds of meters wide were also observed. Satellite imagery showed that these rafts formed larger Sargassum aggregations over a wide range of scales, with smaller aggregations (of tens of m 2 area) nested within larger ones (of hundreds of km 2). Match-ups between different satellite sensors and in situ observations were limited for this dataset, mainly because of high cloud cover during the periods of observation. Nevertheless, comparisons between the two datasets showed that satellite sensors successfully detected Sargassum abundance and aggregation patterns consistent with in situ observations. MODIS and VIIRS sensors were better suited to describing the Sargas-sum aggregation distribution and dynamics at Atlantic scale, while the new sensors, OLCI and MSI, proved their ability to detect Sargassum aggregations and to describe their (sub-) mesoscale nested structure. The high variability in raft shape, size, thickness, depth and biomass density observed in situ means that caution is called for when using satellite maps of Sargassum distribution and biomass estimation. Improvements would require additional in situ and airborne observations or very high-resolution satellite imagery.
Published: 2019

22. 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

23. 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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24. 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

25. Evidence of high N2 fixation rates in productive waters of the temperate Northeast Atlantic

Author: Morgane Gallinari, Lei Chou, Nolwenn Lemaitre, Forian Deman, Xuefeng Li, Frank Dehairs, Natacha Brion, Sophie Guasco, Debany Fonseca-Batista, Hélène Planquette, Valérie Michotey, Marc Elskens, Manon Tonnard, Géraldine Sarthou, François Fripiat, Virginie Riou, and Frédéric Planchon
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, biology, 010604 marine biology & hydrobiology, Spring bloom, biology.organism_classification, 01 natural sciences, Zooplankton, Oceanography, Algae, Phytoplankton, Nitrogen fixation, Temperate climate, Environmental science, Diazotroph, Bay, 0105 earth and related environmental sciences
Abstract: Diazotrophic activity and primary production (PP) were investigated along two transects (Belgica BG2014/14 and GEOVIDE cruises) off the western Iberian Margin and the Bay of Biscay (38.8–46.5° N; 8.0–19.7° W) in May 2014 close to the end of the spring bloom. We report substantial N2 fixation activities, reaching up to 65 nmol N L−1 d−1 and 1533 µmol N m−2 d−1 close to the Iberian Margin between 38.8° N and 40.7° N. Similar figures in the basin have only been reported in the temperate and tropical western North Atlantic waters with coastal, shelf or mesohaline characteristics, as opposed to the mostly open ocean conditions studied here. In agreement with previous studies, the qualitative assessment of nifH gene diversity (encoding the nitrogenase enzyme that fixes N2) suggested a predominance of heterotrophic diazotrophs, and the absence of filamentous cyanobacteria. At the sites where N2 fixation activity was highest sequences affiliated to UCYN-A1, obligate symbiont of eukaryotic prymnesiophyte algae, were recovered. The remaining phylotypes were non-cyanobacterial diazotrophs, known to live in association with suspended particles and zooplankton (i.e., Bacteroidetes, Firmicutes and Proteobacteria). Outside the area of exceptional activity, N2 fixation in the open ocean and at shelf-influenced sites was also relatively high, ranging from 81 to 384 µmol N m−2 d−1, but was undetectable in the central Bay of Biscay. We propose that the unexpectedly high heterotrophic N2 fixation activity recorded at the time of our study was sustained by the availability of phytoplankton derived organic matter (dissolved and/or particulate) resulting from the ongoing to post spring bloom. We pose that this organic material not only sustained bacterial production, but also provided sufficient nutrients essential for the nitrogenase activity (e.g., phosphorus). Dissolved Fe was supplied through atmospheric dust deposition during the month preceding our study and through advection of surface waters from the subtropical region and the shelf area. Our findings stress the need for a more detailed monitoring of the spatial and temporal distribution of oceanic N2 fixation in productive waters of the temperate North Atlantic to better constrain the basin-scale nitrogen input to the ocean inventory.
Published: 2018

26. Supplementary material to 'Evidence of high N2 fixation rates in productive waters of the temperate Northeast Atlantic'

Author: Debany Fonseca-Batista, Xuefeng Li, Virginie Riou, Valérie Michotey, Forian Deman, François Fripiat, Sophie Guasco, Natacha Brion, Nolwenn Lemaitre, Manon Tonnard, Morgane Gallinari, Hélène Planquette, Frédéric Planchon, Géraldine Sarthou, Marc Elskens, Lei Chou, and Frank Dehairs
Published: 2018

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. 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

29. 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

30. 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

31. 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

32. 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

33. 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

34. 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

35. Trends in salinity and inorganic nitrogen compounds in the Berre lagoon (1994-2011) bacterial activities and nitrogen budgets

Author: Sophie Guasco, Guillaume Bernard, Patrick Raimbault, Patricia Bonin, Imen Zaghmouri, Valérie Michotey, Nicole Garcia, MEB, 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 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), and ANR-05-PADD-0012,PRODDIG,Promotion du Développement Durable par les Indications Géographiques(2005)
Subjects: 0106 biological sciences, Geologic Sediments, Salinity, Denitrification, 010504 meteorology & atmospheric sciences, [SDE.MCG]Environmental Sciences/Global Changes, Aquatic Science, Oceanography, 01 natural sciences, chemistry.chemical_compound, Nitrate, Seawater, 14. Life underwater, Nitrogen Compounds, Nitrogen cycle, Ecosystem, 0105 earth and related environmental sciences, Bacteria, 010604 marine biology & hydrobiology, Sediment, Keywords: Sediment Nitrification Denitrification Anammox Coupled nitrification/denitrification Berre lagoon, Nitrogen Cycle, Pollution, Anoxic waters, 6. Clean water, chemistry, Anammox, Environmental chemistry, Environmental science, Nitrification, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Water Microbiology, Water Pollutants, Chemical, Environmental Monitoring
Abstract: International audience; The Berre lagoon receives freshwater from two natural rivers but the implementation of the hydroelectric power plant led to strong changes in the ecosystem structure and functioning. Sediments are important sites for nitrogen cycling because the O2 sharp gradient allows oxic nitrification as well as anoxic denitrification and anammox to operate in close proximity. Seasonal and short-term variations in the coastal nitrogen processes were quantified at two stations: SA1 located in the northern part of the lagoon directly under the inflows of freshwater and SA3 in the southern part of the lagoon influenced mainly by the marine water inflows. Results revealed that most of the nitrate formed by nitrification was denitrified. Total denitrification was the main N2 removal process. The high primary production based on N-NH4 might be explained by mineralization rates, while the primary production based on N-NH3 was not fully explained by nitrification.
Published: 2013

36. Anaerobic bacterial degradation of pristenes and phytenes in marine sediments does not lead to pristane and phytane during early diagenesis

Author: Jean-François Rontani, John K. Volkman, Sophie Guasco, Patricia Bonin, Frédéric Vaultier, 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)-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), MEB, Marine and Atmospheric Research, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), 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 ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Toulon ( UTLN ) -Aix Marseille Université ( AMU ) -Institut de Recherche pour le Développement ( IRD ), and Commonwealth Scientific and Industrial Research Organisation [Canberra] ( CSIRO )
Subjects: Double bond, [SDE.MCG]Environmental Sciences/Global Changes, Phytane, 010502 geochemistry & geophysics, 01 natural sciences, Catalysis, 03 medical and health sciences, chemistry.chemical_compound, pristenes, Geochemistry and Petrology, Organic chemistry, Incubation, 0105 earth and related environmental sciences, phytane, chemistry.chemical_classification, 0303 health sciences, 030306 microbiology, Pristane, sediments, Substrate (chemistry), Metabolism, Diagenesis, [ SDE.MCG ] Environmental Sciences/Global Changes, chemistry, early diagenesis, biohydrogenation, phytenes, Geology
Abstract: International audience; Anaerobic degradation of mixtures of isomeric pristenes and phytenes by sedimentary bacterial communities was investigated. These isoprenoid alkenes were quickly metabolized without formation of the corresponding alkanes. Identification of several bacterial metabolites allowed us to confirm the key role played by hydration in the metabolism of alkenes. Despite the increasing production of 5alpha-stanols during incubation, attesting to the involvement or biohydrogenation, this process did not act significantly on the double bond of pristenes and phytenes. Their resistance is attributed to the lack of binding polar group(s) to anchor the substrate to the enzyme and thus allow the double bond to reach the reductive catalytic site. It therefore seems that microbial hydrogenation of pristenes and phytenes does not account for the presence of pristane and phytane in recent sediments during early diagenesis.
Published: 2013

37. Spatio-temporal diversity of free-living and particle-attached prokaryotes in the tropical lagoon of Ahe atoll (Tuamotu Archipelago) and its surrounding oceanic waters

Author: Dominique Boeuf, Sophie Guasco, Patricia Bonin, Loïc Charpy, Valérie Michotey, B. Durieux, N. Morezzi, MEB, 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 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), 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), 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: 0106 biological sciences, Wet season, Archaea Bacteria Biodiversity Lagoon Pacific Ocean, Coral, Biodiversity, Atoll, Aquatic Science, Biology, Oceanography, 01 natural sciences, Polynesia, 03 medical and health sciences, Water column, Abundance (ecology), Dry season, Seawater, 14. Life underwater, Phylogeny, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, geography, geography.geographical_feature_category, Bacteria, 030306 microbiology, Ecology, Coral Reefs, 010604 marine biology & hydrobiology, fungi, Genetic Variation, Plankton, Pollution, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Environmental Monitoring
Abstract: International audience; Spatio-temporal variability of prokaryotic water column communities inside and outside a Polynesian tropical lagoon subjected to pearl oysters farming was assessed in terms of abundance by quantitative PCR and diversity by DGGE. Communities and operational taxonomic units (OTUs) were analysed according to dry/rainy seasons and free-living/particle-attached state. Bacterial density was higher in the lagoon compared to ocean and a seasonal trend was observed. No influence of the localisation within lagoon or of the planktonic/attached states was noticed on bacterial abundance and diversity. The OTUs belonged to Cyanobacteria, to heterotrophic groups in Proteobacteria and Flavobacteria. Archaeal abundance showed seasonal tendency and particle-prevalence, but no effect of lagoon or oceanic location was observed. Lagoon and oceanic archaeal diversity were different and Euryarchaeota (MG-II, MBG, and Halobacteria) were detected. During the dry season, planktonic and particle-associated community differed, whereas at rainy season, both communities were similar and included members usually associated with coral
Published: 2012

38. Desulfosoma profundi sp nov., a thermophilic sulfate-reducing bacterium isolated from a deep terrestrial geothermal spring in France

Author: Patricia Bonin, Sophie Guasco, Bernard Ollivier, Valérie Michotey, Joël Lagiere, Jean Cambar, Patrick Gregoire, Marie Laure Fardeau, 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: Deltaproteobacteria, Syntrophobacteraceae, Hot Springs, chemistry.chemical_compound, Thermophilic, RNA, Ribosomal, 16S, Anaerobiosis, Sulfate-reducing bacteria, Phylogeny, Thiosulfate, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Isovalerate, biology, Sulfates, Fatty Acids, General Medicine, Sulfate-reducing bacterium, 6. Clean water, RNA, Bacterial, Biochemistry, ACID, TREES, France, Water Microbiology, Oxidation-Reduction, DNA, Bacterial, Anaerobic, Molecular Sequence Data, DNA, Ribosomal, Microbiology, 03 medical and health sciences, Species Specificity, Sequence Homology, Nucleic Acid, Molecular Biology, 030304 developmental biology, 030306 microbiology, GEN-NOV, RENATURATION RATES, Thermophile, DNA HYBRIDIZATION, Ribosomal RNA, 16S ribosomal RNA, biology.organism_classification, FIELD WATER, chemistry, OIL-PRODUCING WELL, Fermentation, Deep hot aquifer, Sequence Alignment, Bacteria
Abstract: A novel strictly anaerobic bacterium designated SPDX02-08(T) was isolated from a deep terrestrial geothermal spring located in southwest France. Cells (1-2 x 2-6 mu m) were non-motile, non sporulating and stained Gram negative. Strain SPDX02-08(T) grew at a temperature between 40 and 60A degrees C (optimum 55A degrees C), pH between 6.3 and 7.3 (optimum 7.2) and a NaCl concentration between 0 and 5 g/l (optimum 2 g/l). Sulfate, thiosulfate and sulfite were used as terminal electron acceptors, but not elemental sulfur, nitrate, nitrite, Fe (III) or fumarate. In the presence of sulfate, strain SPDX02-08(T) completely oxidized pyruvate, propionate, butyrate, isobutyrate, valerate, isovalerate and hexadecanoate. Stoichiometric measurements revealed a complete oxidation of part of lactate (0.125 mol of acetate produced per mole lactate oxidized). Strain SPDX02-08(T) required yeast extract to oxidize formate and H-2 but did not grow autotrophically on H-2. Among the substrates tested, only pyruvate was fermented. The G+C content of the genomic DNA was 57.6 mol%. Major cellular fatty acids of strain SPDX02-08(T) were iso-C-15:0, C-15:0, and C-16:0. Phylogenetic analysis of the 16S small-subunit (SSU) ribosomal RNA gene sequence indicated that strain SPDX02-08(T) belongs to the genus Desulfosoma, family Syntrophobacteraceae, having Desulfosoma caldarium as its closest phylogenetic relative (97.6% similarity). The mean DNA/DNA reassociation value between strain SPDX02-08(T) and Desulfosoma caldarium was 16.9 +/- A 2.7%. Based on the polyphasic differences, strain SPDX02-08(T) is proposed to be assigned as a new species of the genus Desulfosoma, Desulfosoma profundi sp. nov. (DSM 22937(T) = JCM 16410(T)). GenBank accession number for the 16S rRNA gene sequence of strain SPDX02-08(T) is HM056226.
Published: 2012

39. Denitrification prevails over anammox in tropical mangrove sediments (Goa, India)

Author: Sophie Guasco, Patricia Bonin, P. A. Loka Bharathi, Sheryl Oliveira Fernandes, Valérie Michotey, MEB, 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 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), CSIR National Institute of Oceanography [India] (NIO), 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), 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: 0106 biological sciences, Geologic Sediments, Denitrification, Nitrogen, MARINE-SEDIMENTS, India, Aquatic Science, Oceanography, 01 natural sciences, Sediments, 03 medical and health sciences, Denitrifying bacteria, NITROGEN-CYCLE, CONTINENTAL-SHELF, Water column, Anammox, INORGANIC NITROGEN, Nitrogen Fixation, Botany, Proteobacteria, Mangroves, Humans, Nitrogen cycle, Ecosystem, MICROBIAL MAT, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Tropical Climate, biology, Bacteria, 030306 microbiology, 010604 marine biology & hydrobiology, NITRITE REDUCTASE, Rhizophoraceae, General Medicine, 15. Life on land, biology.organism_classification, Pollution, ANAEROBIC AMMONIUM OXIDATION, WATER COLUMN, DENITRIFYING BACTERIA, NITRATE REDUCTION, Denitrifiers, Mangrove, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Denitrification, anammox (Anx) and di-nitrogen fixation were examined in two mangrove ecosystemsthe anthropogenically influenced Divar and the relatively pristine Tuvem. Stratified sampling at 2 cm increments from 0 to 10 cm depth revealed denitrification as the main process of N-2 production in mangrove sediments. At Divar, denitrification was similar to 3 times higher than at Tuvem with maximum activity of 224.51 +/- 6.63 nmol N-2 g(-1) h(-1) at 0-2 cm. Denitrifying genes (nosZ) numbered up to 2 x 10(7) copies g(-1) sediment and belonged to uncultured microorganisms clustering within Proteobacteria. Anammox was more prominent at deeper depths (8-10 cm) mainly in Divar with highest activity of 101.15 +/- 87.73 nmol N-2 g(-1) h(-1) which was 5 times higher than at Tuvem. Di-nitrogen fixation was detected only at Tuvem with a maximum of 12.47 +/- 8.36 nmol N-2 g(-1) h(-1). Thus, in these estuarine habitats prone to high nutrient input, N-2-fixation is minimal and denitrification rather than Anx serves as an important mechanism for counteracting N loading. (C) 2011 Elsevier Ltd. All rights reserved.
Published: 2012

40. Anaerobic ammonium oxidation mediated by Mn-oxides: from sediment to strain level

Author: Mathieu Canton, Patricia Bonin, Valérie Michotey, Pierre Anschutz, Cedric Javanaud, Sophie Guasco, Nicole Garcia, MEB, 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 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 de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2-Institut méditerranéen d'océanologie (MIO), CE, 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 de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, ANR-05-PADD-0012,PRODDIG,Promotion du Développement Durable par les Indications Géographiques(2005), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)-Institut méditerranéen d'océanologie (MIO), 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), and Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)
Subjects: Chemoautotrophic Growth, Geologic Sediments, Denitrification, MARINE-SEDIMENTS, SAMPLES, Colony Count, Microbial, DIAGENESIS, ANOXIC NITRIFICATION, 010501 environmental sciences, Nitrogen cycle, 01 natural sciences, chemistry.chemical_compound, BACTERIAL PROCESSES, Nitrate, RNA, Ribosomal, 16S, Anaerobiosis, Nitrite, Phylogeny, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Ecology, Oxides, General Medicine, DENITRIFICATION, Nitrification, Anaerobic ammonium oxidation, Bays, Environmental chemistry, France, Oxidation-Reduction, Anaerobic respiration, SHEWANELLA, Biology, Microbiology, 03 medical and health sciences, Denitrifying bacteria, Aerobic denitrification, Marinobacter, Seawater, 14. Life underwater, Molecular Biology, Nitrites, 030304 developmental biology, 0105 earth and related environmental sciences, Manganese, Nitrates, MANGANESE REDUCTION, QUANTIFICATION, Quaternary Ammonium Compounds, NITROGEN, chemistry, Manganese Compounds, Anaerobic oxidation of methane, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Nitrite and N-29(2) productions in slurry incubations of anaerobically sediment after (NO3)-N-15 or (NH4)-N-15 labelling in the presence of Mn-oxides suggested that anaerobic Mn-oxides mediated nitrification coupled with denitrification in muddy intertidal sediments of Arcachon Bay (SW Atlantic French coast). From this sediment, bacterial strains were isolated and physiologically characterized in terms of Mn-oxides and nitrate reduction as well as potential anaerobic nitrification. One of the isolated strain, identified as Marinobacter daepoensis strain M4AY 14, was a denitrifier. Nitrous oxide production by this strain was demonstrated in the absence of nitrate and with Mn-oxides and NH4 amendment, giving indirect proof of anaerobic nitrate or nitrite production. Anaerobic Mn-oxide-mediated nitrification was confirmed by N-29(2) production in the presence of (NO3)-N-15 and (NH4)-N-14 under denitrifying conditions. Anaerobic nitrification by M4AY14 seemed to occur only in the absence of nitrate, or at nitrate levels lower than that of Mn-oxides. Most of the other isolates were affiliated with the Shewanella genus and were able to use both nitrate and Mn-oxides as electron acceptors. When both electron acceptors were present, whatever their concentrations, nitrate and Mn-oxide reduction co-occurred. These data indicate that bacterial Mn-oxide reduction could be an important process in marine sediments with low oxygen concentrations, and demonstrate for the first time the role of bacteria in anaerobic Mn-mediated nitrification. (C) 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.
Published: 2011

41. Caldilinea tarbellica sp nov., a filamentous, thermophilic, anaerobic bacterium isolated from a deep hot aquifer in the Aquitaine Basin

Author: Manon Joseph, Patrick Gregoire, Marie-Laure Fardeau, Jean Cambar, Sophie Guasco, Patricia Bonin, Bernard Ollivier, Jean Luc Cayol, Valérie Michotey, Malek Bohli, Karine Dubourg, MEB, 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 ), Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1-Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1-Institut méditerranéen d'océanologie ( MIO ), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2-Centre d'océanologie de Marseille ( COM ), Centre National de la Recherche Scientifique ( CNRS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique ( CNRS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Centre d'océanologie de Marseille ( COM ), Centre National de la Recherche Scientifique ( CNRS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1-Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, 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 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 la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1-Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1-Institut méditerranéen d'océanologie (MIO), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2-Centre d'océanologie de Marseille (COM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de la Méditerranée - Aix-Marseille 2, Centre d'océanologie de Marseille (COM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de la Méditerranée - Aix-Marseille 2, Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS)-Centre d'océanologie de Marseille (COM), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), and Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Arabinose, Hot Temperature, SPHAEROBACTER-THERMOPHILUS, EMENDED DESCRIPTION, Sodium Chloride, chemistry.chemical_compound, RNA, Ribosomal, 16S, Cluster Analysis, Anaerobiosis, Raffinose, Phylogeny, 0303 health sciences, Base Composition, biology, Sulfates, Fatty Acids, Nucleic Acid Hybridization, RENATURATION, General Medicine, THERMOMICROBIA, LINEAGE, Hydrogen-Ion Concentration, 6. Clean water, Bacterial Typing Techniques, Biochemistry, Carbohydrate Metabolism, PHYLUM CHLOROFLEXI, GEN. NOV, France, Water Microbiology, DNA, Bacterial, Stereochemistry, Molecular Sequence Data, Microbiology, DNA, Ribosomal, 03 medical and health sciences, Caldilinea aerophila, PHOTOTROPHIC BACTERIA, Thermomicrobia, Yeast extract, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Nitrates, 030306 microbiology, Thermophile, Fructose, Maltose, Chloroflexi, Sequence Analysis, DNA, DNA, biology.organism_classification, chemistry, OIL-PRODUCING WELL, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: An anaerobic, thermophilic, filamentous (0.45 × >100 µm) bacterium, designated D1-25-10-4T, was isolated from a deep hot aquifer in France. Cells were non-motile and Gram-negative. Growth was observed at 43–65 °C (optimum 55 °C), at pH 6.8–7.8 (optimum pH 7.0) and with 0–5 g NaCl l−1 (optimum 0 g NaCl l−1). Strain D1-25-10-4T was a chemo-organotroph and fermented ribose, maltose, glucose, galactose, arabinose, fructose, mannose, sucrose, raffinose, xylose, glycerol, fumarate, peptone, starch and xylan. Yeast extract was required for growth. Sulfate, thiosulfate, sulfite, elemental sulfur, nitrate, nitrite and fumarate were not used as terminal electron acceptors. The G+C content of the DNA was 61.9 mol%. The major cellular fatty acids of strain D1-25-10-4T were C17 : 0, C18 : 0, C16 : 0 and iso-C17 : 0. The closest phylogenetic relative of strain D1-25-10-4T was Caldilinea aerophila STL-6-O1T (97.9 % 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain D1-25-10-4T and Caldilinea aerophila DSM 14535T was 8.7±1 %. On the basis of phylogenetic, genotypic and phenotypic characteristics, strain D1-25-10-4T represents a novel species within the genus Caldilinea, class Caldilineae, phylum Chloroflexi, for which the name Caldilinea tarbellica sp. nov. is proposed. The type strain is D1-25-10-4T ( = DSM 22659T = JCM 16120T).
Published: 2011

42. Isolation and characterization of Thermanaerothrix daxensis gen. nov., sp. nov., a thermophilic anaerobic bacterium pertaining to the phylum 'Chloroflexi', isolated from a deep hot aquifer in the Aquitaine Basin

Author: Marie-Laure Fardeau, Sophie Guasco, Valérie Michotey, Patricia Bonin, Sandra Biasutti, Francette Hamaide, Manon Joseph, Patrick Gregoire, Bernard Ollivier, Laboratoire de Microbiologie et Biotechnologie des Environnements Chauds, Université de la Méditerranée - Aix-Marseille 2-Université de Provence - Aix-Marseille 1, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines ( LMGEM ), Centre National de la Recherche Scientifique ( CNRS ) -Université de la Méditerranée - Aix-Marseille 2, Centre d'océanologie de Marseille ( COM ), Centre National de la Recherche Scientifique ( CNRS ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Université de la Méditerranée - Aix-Marseille 2, 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 de Géochimie et d'Ecologie Marines (LMGEM), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Centre d'océanologie de Marseille (COM), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-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 ), and Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2
Subjects: [ SDU.OCEAN ] Sciences of the Universe [physics]/Ocean, Atmosphere, ESPECE NOUVELLE, Hot Temperature, LEVEL, ADN, DIVERSITY, Hot aquifer, Xylose, Acetates, Applied Microbiology and Biotechnology, Hot Springs, chemistry.chemical_compound, Thermophilic, Cell Wall, RNA, Ribosomal, 16S, PHYLOGENIE, Microscopy, Phase-Contrast, Raffinose, Thermanaerothrix daxensis, Phylogeny, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Base Composition, biology, Hydrogen-Ion Concentration, Aquitaine Basin, Bacterial Typing Techniques, Phenotype, BACTERIE THERMOPHILE, TREES, Carbohydrate Metabolism, France, Water Microbiology, Anaerobic, Molecular Sequence Data, Phylum "Chloroflexi, Microbiology, 03 medical and health sciences, Botany, Lactic Acid, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, Gram-Negative Anaerobic Bacteria, Base Sequence, 030306 microbiology, Thermophile, Fructose, Genes, rRNA, Chloroflexi, biology.organism_classification, Chloroflexi (class), Glucose, chemistry, Genes, Bacterial, Galactose, Phylum "Chloroflexi", OIL-PRODUCING WELL, Fermentation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, MILIEU AQUATIQUE, GENRE NOUVEAU, Bacteria, Hydrogen
Abstract: A new strictly anaerobic thermophilic multicellular filamentous bacterium (0.2-0.3 mu m x > 100 mu m), designated GNS-1(T), was isolated from a deep hot aquifer in France. It was non-motile, and stained Gram-negative. Optimal growth was observed at 65 degrees C, pH 7.0, and 2 g L-1 of NaCl. Strain GNS-1(T) was chemoorganotrophic fermenting ribose, glucose, galactose, arabinose, fructose, mannose, maltose, sucrose, xylose, raffinose, pyruvate, and xylan. Yeast extract was required for growth. The end products of glucose fermentation were lactate, acetate, CO2, and H-2. The G + C content of the DNA was 57.6 mol%. Its closest phylogenetic relative was Bellilinea caldifistulae with 92.5% similarity. Based on phylogenetic, genotypic and phenotypic characteristics, strain GNS-1(T) (DSM 23592(T), JCM 169801) is proposed to be assigned to a novel species of a novel genus within the class Anaerolineae (subphylum I), phylum "Chloroflexi". Thermanaerothrix daxensis gen. nov., sp. nov. The GenBank accession number is HM596746. (C) 2011 Elsevier GmbH. All rights reserved.
Published: 2010

43. Potential alteration of U37K' paleothermometer due to selective degradation of alkenones by marine bacteria isolated from the haptophyte Emiliania huxleyi

Author: Nathalie, Zabeti, Patricia, Bonin, John K, Volkman, Ian D, Jameson, Sophie, Guasco, and Jean-François, Rontani
Subjects: DNA, Bacterial, Bacteria, Chlorophyta, RNA, Ribosomal, 16S, Temperature, Ketones, Oxidation-Reduction
Abstract: The unsaturation ratio of C(37) alkenones (U(37)(K')) produced by haptophyte microalgae such as Emiliania huxleyi is often used as proxy for past sea surface temperature. In this study, 29 bacterial strains were isolated from cultures of the strain E. huxleyi TWP1. Among alkenone-degrading isolates, the strain Dietzia maris sp. S1 appeared to be able to selectively degrade alkenones leading to increases in the palaeoenvironmental proxy U(37)(K') by +0.05 to +0.10 units, which is equivalent to the change seen when the growth temperature is increased by 1.5-3.0 degrees C. This degradation was shown to involve initial epoxidation of the alkenone double bonds presumably by a monooxygenase, which showed a preference for oxidation of the omega29 double bond. Inconsistencies observed in previous studies of the aerobic microbial degradation of alkenones may simply reflect which species of bacteria were present. Our results confirm that intense aerobic bacterial degradative processes can introduce a bias in palaeotemperature reconstructions especially when there is evidence of substantial aerobic bacterial degradation of the deposited organic matter. The widespread occurrence of epoxyalkenones in the marine environment strongly suggests that selective aerobic bacterial degradation could be major source of uncertainty for palaeotemperature estimation.
Published: 2010

44. Potential alteration of U 37K′ paleothermometer due to selective degradation of alkenones by marine bacteria isolated from the haptophyte Emiliania huxleyi

Author: Patricia Bonin, Nathalie Zabeti, Sophie Guasco, Ian Jameson, Jean-François Rontani, and John K. Volkman
Subjects: 0303 health sciences, Alkenone, Degree of unsaturation, Ecology, 030306 microbiology, Aerobic bacteria, Microbial metabolism, Biology, biology.organism_classification, Applied Microbiology and Biotechnology, Microbiology, Haptophyte, 03 medical and health sciences, Paleothermometer, Marine bacteriophage, 13. Climate action, Environmental chemistry, Botany, 14. Life underwater, 030304 developmental biology, Emiliania huxleyi
Abstract: The unsaturation ratio of C(37) alkenones (U(37)(K')) produced by haptophyte microalgae such as Emiliania huxleyi is often used as proxy for past sea surface temperature. In this study, 29 bacterial strains were isolated from cultures of the strain E. huxleyi TWP1. Among alkenone-degrading isolates, the strain Dietzia maris sp. S1 appeared to be able to selectively degrade alkenones leading to increases in the palaeoenvironmental proxy U(37)(K') by +0.05 to +0.10 units, which is equivalent to the change seen when the growth temperature is increased by 1.5-3.0 degrees C. This degradation was shown to involve initial epoxidation of the alkenone double bonds presumably by a monooxygenase, which showed a preference for oxidation of the omega29 double bond. Inconsistencies observed in previous studies of the aerobic microbial degradation of alkenones may simply reflect which species of bacteria were present. Our results confirm that intense aerobic bacterial degradative processes can introduce a bias in palaeotemperature reconstructions especially when there is evidence of substantial aerobic bacterial degradation of the deposited organic matter. The widespread occurrence of epoxyalkenones in the marine environment strongly suggests that selective aerobic bacterial degradation could be major source of uncertainty for palaeotemperature estimation.
Published: 2010

45. Aerobic Metabolism of Vitamin E by Marine Bacteria: Interaction with Free Radical Oxidation (Autoxidation) Processes

Author: Mina Nassiry, Sophie Guasco, Abdelkrim Mouzdahir, Patricia Bonin, and Jean-François Rontani
Subjects: 010504 meteorology & atmospheric sciences, 010502 geochemistry & geophysics, 01 natural sciences, 0105 earth and related environmental sciences
Published: 2010

46. Formation of pristane from a-tocopherol under simulated anoxic sedimentary conditions : A combination of biotic and abiotic degradative processes

Author: Valérie Michotey, Mina Nassiry, Patricia Bonin, Sophie Guasco, Jean-François Rontani, 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: Abiotic component, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Ecology, Pristane, Phytane, 010501 environmental sciences, Biodegradation, 010502 geochemistry & geophysics, 01 natural sciences, Anoxic waters, 6. Clean water, Diagenesis, chemistry.chemical_compound, Denitrifying bacteria, chemistry, 13. Climate action, Geochemistry and Petrology, Environmental chemistry, Sedimentary organic matter, 14. Life underwater, Geology, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract: Incubation of intact and oxidized α-tocopherol (vitamin E) in anaerobic sediment slurries allowed us to demonstrate that, as previously suggested by Goossens et al. (1984), the degradation of α-tocopherol in anoxic sediments results in the formation of pristane. The conversion of α-tocopherol to this isoprenoid alkane involves a combination of biotic and abiotic degradative processes, i.e. the anaerobic biodegradation (which seems to be mainly induced by denitrifying bacteria) of trimeric structures resulting from the abiotic oxidation of α-tocopherol. On the basis of the results obtained, it is proposed that in the marine environment most of the α-tocopherol present in phytoplanktonic cells should be quickly degraded within the water column and the oxic zone of sediments by way of aerobic biodegradation, photo- and autoxidation processes. Abiotic transformation of this compound mainly results in the production of trimeric oxidation products, sufficiently stable to be incorporated into anoxic sediments and whose subsequent anaerobic bacterial degradation affords pristane. These results confirm that the ratio pristane to phytane cannot be used as an indicator of the oxicity of the environment of deposition; in contrast, they support the use of PFI (Pristane Formation Index) as a proxy for the state of diagenesis of sedimentary organic matter.
Published: 2009

47. Aerobic metabolism of vitamin E by marine bacteria : interaction with free radical oxidation (autoxidation) processes

Author: Abdelkrim Mouzdahir, Mina Nassiry, Patricia Bonin, Jean-François Rontani, Sophie Guasco, 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 Chimie Bioorganique, Université Chouaib Doukkali (UCD), 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, 0303 health sciences, Autoxidation, Ecology, Vitamin E, medicine.medical_treatment, Microorganism, Free-radical reaction, Metabolism, Biology, Biodegradation, 010502 geochemistry & geophysics, biology.organism_classification, 01 natural sciences, 03 medical and health sciences, Marine bacteriophage, Biochemistry, 13. Climate action, Geochemistry and Petrology, medicine, Bacteria, 030304 developmental biology, 0105 earth and related environmental sciences
Abstract: The degradation of vitamin E by aerobic bacterial communities, isolated from marine sediment and microbial mat samples, was investigated. PCR-DGGE profiles and cloning/sequencing experiments revealed that biodegradation of vitamin E in sediments is mainly carried out by strains belonging to the genera Idiomarina and Bacillus for which the DGGE pattern matched with the pattern obtained from the second sediment subculture. Biodegradation processes appeared to involve an initial ω-oxidation of the isoprenoid side chain and subsequent β-oxidation sequences affording 2,5,7,8-tetramethyl–2(2’-carboxyethyl)-6-hydroxychroman (α-CEHC). This compound was not accumulated at the end of the growth, showing that the bacterial degradation of vitamin E is not limited to its isoprenoid side chain. In cultures still containing residual sediment, the presence of metabolites with a shortened side chain and an opened chroman ring (e.g., α-tocopheronolactone and α-tocopherylhydroquinonolactone) attested to the simultaneous involvement of biodegradation and autoxidation processes. The induction of autoxidation during these incubations was attributed to some of the sediment components, which could act as catalysts of free radical reactions. In oxic environments, the combination of free radical oxidation and aerobic biodegradation processes should result in a very fast degradation of vitamin E. Different pathways are proposed to explain the formation of the different compounds resulting from these interactions.
Published: 2008

48. Degradation of alkenones by aerobic heterotrophic bacteria : Selective or not ?

Author: Narayan B. Bhosle, Jean-François Rontani, John K. Volkman, Patricia Bonin, Fredrick G. Prahl, Ranjita Harji, Sophie Guasco, Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, National Institute of Oceanography (CSIR), CSIR National Institute of Oceanography [India] (NIO), College of Oceanic and Atmospheric Sciences [Corvallis], Oregon State University (OSU), 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, 0303 health sciences, Degree of unsaturation, Alkenone, Strain (chemistry), 030306 microbiology, Aerobic bacteria, fungi, Biodegradation, Biology, 010502 geochemistry & geophysics, biology.organism_classification, 01 natural sciences, 03 medical and health sciences, Biochemistry, 13. Climate action, Geochemistry and Petrology, Microbial mat, Bacteria, 0105 earth and related environmental sciences, Emiliania huxleyi
Abstract: Four bacterial communities were isolated from Emiliania huxleyi strain TWP1 cultures before and after the algal cells had been treated with different antibiotics. Incubation of E. huxleyi with these bacterial communities resulted in dramatically different extents of alkenone degradation, ranging from effectively none to extensive. Selective degradation of the more unsaturated alkenones was observed in experiments using the total bacterial community and one of the communities isolated from antibiotic-treated algal cells. The observed increases in U 37 K ′ are equivalent to a +2 °C and +3.3 °C change in the inferred temperature. Our results clearly show that intense aerobic microbial degradative processes have the potential to introduce a significant ‘warm’ bias in palaeotemperature reconstruction and could explain apparent anomalies in palaeotemperatures inferred from alkenone distributions in strongly oxidizing sedimentary environments. The results show that aerobic bacteria capable of selectively degrading alkenones are not limited to particular environments such as microbial mats and can be actually associated with living E. huxleyi cells. The detection of epoxyketones in some cultures indicates that metabolic pathways involving attack at the terminal groups of the molecule are essentially non-selective, while those acting on alkenone double bonds are selective. The epoxyketones resulting from bacterial epoxidation of alkenone double bonds could be useful indicators of aerobic bacterial alteration of the alkenone unsaturation ratio in situ. The production of alkenols during incubation with one of the bacterial communities demonstrated for the first time that bacterial reduction of alkenones can be a potential source of these compounds in the environment. The intriguing production of small amounts of monounsaturated alkenones by one of the bacterial communities also raises the possibility of a bacterial reduction of alkenone double bonds.
Published: 2008

49. Crystallization and preliminary crystallographic study of an extremophile cytochrome c4 from Thiobacillus ferrooxidans

Author: Giselle Leroy, Mireille Bruschi, Sophie Guasco, Chantal Abergel, Sabine Chenivesse, and Marie-Thérèse Guidici-Orticoni
Subjects: Cytochrome, Molecular mass, Cytochrome c Group, General Medicine, Periplasmic space, Biology, biology.organism_classification, Crystallography, X-Ray, Thiobacillus, law.invention, Crystal, Crystallography, Protein structure, Structural Biology, law, biology.protein, Extremophile, Crystallization, Bacteria
Abstract: Soluble periplasmic dihaemic cytochrome c(4), of 21 293 Da molecular mass, has been characterized from Thiobacillus ferrooxidans, an acidophilic bacteria. The native cytochrome has been purified from the bacteria using ion-exchange chromatography and crystallized using solution 27 of the Hampton Research Crystal Screen II. The crystals belong to the hexagonal space group P6(2)22 or P6(4)22, with unit-cell parameters a = 101.59, b = 101.59, c = 151.59 A. Frozen crystals diffract to 2.17 A resolution. The MAD method is currently being used (four Fe atoms per asymmetric unit) to solve the protein structure.
Published: 2000

50. Crystallization and preliminary crystallographic study of HIP/PAP, a human C-lectin overexpressed in primary liver cancers

Author: Chantal Abergel, Laurence Christa, Eve Devinoy, Marie-Georges Stinnakre, Jean-Michel Claverie, Christian Bréchot, Sabine Chenivesse, Sophie Guasco, Unité de biologie cellulaire et moléculaire, and Institut National de la Recherche Agronomique (INRA)
Subjects: Carcinoma, Hepatocellular, [SDV]Life Sciences [q-bio], Mice, Transgenic, Pancreatitis-Associated Proteins, Crystallography, X-Ray, law.invention, 03 medical and health sciences, Mice, 0302 clinical medicine, Antigen, Structural Biology, law, C-type lectin, Antigens, Neoplasm, Lectins, medicine, Biomarkers, Tumor, Animals, Humans, Lectins, C-Type, Crystallization, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, Chemistry, Lithostathine, Liver Neoplasms, Lectin, Proteins, General Medicine, Anatomy, medicine.disease, CANCER, Molecular biology, Milk, 030220 oncology & carcinogenesis, Hepatocellular carcinoma, biology.protein, Orthorhombic crystal system, Female, Acute-Phase Proteins
Abstract: Human HIP/PAP is an adhesion protein expressed in normal pancreatic and Paneth cells and overexpressed in hepatocellular carcinoma. HIP/PAP was crystallized using the Hampton Research Crystal Screen and SAmBA software to define the optimal crystallization protocol. The crystals belong to the orthorhombic space group P212121, with unit-cell parameters a = 30.73, b = 49.35, c = 92.15 Å and one molecule in the asymmetric unit. Flash-frozen crystals diffract to 1.78 Å resolution using synchrotron radiation. A molecular-replacement solution was obtained using the human Reg/lithostathine structure and the AMoRe software.
Published: 1999

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