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1. Symbiont Acquisition Strategies in Post‐Settlement Stages of Two Co‐Occurring Deep‐Sea Rimicaris Shrimp

Author

Marion Guéganton, Pierre Methou, Johanne Aubé, Cyril Noël, Ouafae Rouxel, Valérie Cueff‐Gauchard, Nicolas Gayet, Lucile Durand, Florence Pradillon, and Marie‐Anne Cambon‐Bonavita

Subjects
acquisition, FISH, hydrothermal vent, metabarcoding, microscopy, symbiosis, Ecology, QH540-549.5
Abstract

ABSTRACT At deep‐sea hydrothermal vents, deprived of light, most living communities are fueled by chemosynthetic microorganisms. These can form symbiotic associations with metazoan hosts, which are then called holobionts. Among these, two endemic co‐occurring shrimp of the Mid‐Atlantic Ridge (MAR), Rimicaris exoculata and Rimicaris chacei are colonized by dense and diversified chemosynthetic symbiotic communities in their cephalothoracic cavity and their digestive system. Although both shrimp harbor similar communities, they exhibit widely different population densities, distribution patterns at small scale and diet, as well as differences in post‐settlement morphological modifications leading to the adult stage. These contrasting biological traits may be linked to their symbiotic development success. Consequently, key questions related to the acquisition of the symbiotic communities and the development of the three symbiotic organs are still open. Here we examined symbiotic development in juveniles of R. exoculata and R. chacei from TAG and Snake Pit using 16S metabarcoding to identify which symbiotic lineages are present at each juvenile stage. In addition, we highlighted the abundance and distribution of microorganisms at each stage using Fluorescence in situ Hybridization (FISH) and Scanning Electron Microscopy (SEM). For the first time, Candidatus Microvillispirillaceae family with Candidatus Rimicarispirillum spp. (midgut tube), Candidatus Foregutplasma rimicarensis and Candidatus BG2‐rimicarensis (foregut) were identified in late juvenile stages. However, these lineages were absent in early juvenile stages, which coincides for the midgut tube with our observations of an immature tissue, devoid of microvilli. Conversely, symbiotic lineages from the cephalothoracic cavity were present from the earliest juvenile stages of both species and their overall diversities were similar to those of adults. These results suggest different symbiont acquisition dynamics between the cephalothoracic cavity and the digestive system, which may also involve distinct transmission mechanisms.

Published
2024
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2. Anatomy and Symbiosis of the Digestive System of the Vent Shrimp Rimicaris Exoculata and Rimicaris Chacei Revealed Through Imaging Approaches

Author

Marion Guéganton, Ouafae Rouxel, Lucile Durand, Valérie Cueff-Gauchard, Nicolas Gayet, Florence Pradillon, and Marie-Anne Cambon-Bonavita

Subjects
Rimicaris, digestive-symbiosis, Deferribacteres, Mycoplasmatales, microscopy, FISH-probes, Science, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

The shrimp Rimicaris exoculata and Rimicaris chacei are visually dominant fauna co-occurring at deep-sea hydrothermal sites of the Mid-Atlantic Ridge (MAR). Their co-existence was related to contrasted life-history traits, including differences in their diet and reliance on chemoautotrophic symbionts at the adult stage. Both species of shrimp are colonized by diversified chemosynthetic symbiotic microbial communities in their cephalothoracic cavity. Symbiotic association with bacteria was also evidenced in their digestive system, and the major lineages were identified through sequencing (with Mycoplasmatales in the foregut and Deferribacteres in the midgut) but their precise distribution within each host species was not assessed. For the first time, we used Fluorescence in situ Hybridization (FISH) to visualize these lineages and describe their association with digestive structures of their host. The aim of the study was to identify possible differences between host species that could be related to their different life-history traits. For this purpose, we developed new specific FISH probes targeting Deferribacteres and Mycoplasmatales lineages identified in the digestive system of these shrimp. Our FISH results showed a partitioning of the bacterial lineages according to the digestive organ corroborating sequencing data, and highlighted their association with specific anatomical structures. Despite morphological differences between the foreguts of R. exoculata and R. chacei that could be related to the adult diet, our FISH results showed overall similar distribution of digestive symbionts for the two host species. However, a more comprehensive study is needed with specimens at different life or molt stages to reveal potential host specific patterns. Such comparisons are now possible thanks to our newly designed FISH probes. The tools used in our study are valuable for tracking symbiont lineages in the environment, allowing a better understanding of their relationship with their host along its life cycle, including their acquisition mechanisms.

Published
2022
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3. Ecology and trophic role of Oncholaimus dyvae sp. nov. (Nematoda: Oncholaimidae) from the lucky strike hydrothermal vent field (Mid-Atlantic Ridge)

Author

Daniela Zeppilli, Laure Bellec, Marie-Anne Cambon-Bonavita, Wilfrida Decraemer, Diego Fontaneto, Sandra Fuchs, Nicolas Gayet, Perrine Mandon, Loïc N. Michel, Marie Portail, Nic Smol, Martin V. Sørensen, Ann Vanreusel, and Jozée Sarrazin

Subjects
Oncholaimus dyvae sp. nov., Hydrothermal vents, Deep sea, Carbon and nitrogen isotopic ratios, Zoology, QL1-991
Abstract

Abstract Background Nematodes are an important component of deep-sea hydrothermal vent communities, but only few nematode species are able to cope to the harsh conditions of the most active vent sites. The genus Oncholaimus is known to tolerate extreme geothermal conditions and high sulphide concentrations in shallow water hydrothermal vents, but it was only occasionally reported in deep-sea vents. In this study, we performed morphological, genetic and ecological investigations (including feeding strategies) on an abundant species of Oncholaimus recently discovered at Lucky strike vent field on the Mid-Atlantic Ridge at 1700 m water depth. Results We described this species as Oncholaimus dyvae sp. nov.. This new species differs from all other members of the genus by the combination of the following characters: body length (up to 9 mm), the presence of a long spicule (79 μm) with a distally pointed end, a complex pericloacal setal ornamentation with one precloacal papilla surrounded by short spines, and a body cuticule with very fine striation shortly posterior to the amphid opening. Overall, O. dyvae sp. nov. abundance increased with increasing temperature and vent emissions. Carbon isotopic ratios suggest that this species could consume both thiotroph and methanotrophic producers. Furthermore sulfur-oxidizing bacteria related to Epsilonproteobacteria and Gammaproteobacteria were detected in the cuticle, in the digestive cavity and in the intestine of O. dyvae sp. nov. suggesting a potential symbiotic association. Conclusions This study improves our understanding of vent biology and ecology, revealing a new nematode species able to adapt and be very abundant in active vent areas due to their association with chemosynthetic micro-organisms. Faced by the rapid increase of anthropogenic pressure to access mineral resources in the deep sea, hydrothermal vents are particularly susceptible to be impacted by exploitation of seafloor massive sulfide deposits. It is necessary to document and understand vent species able to flourish in these peculiar ecosystems.

Published
2019
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4. Microbial Communities of the Shallow-Water Hydrothermal Vent Near Naples, Italy, and Chemosynthetic Symbionts Associated With a Free-Living Marine Nematode

Author

Laure Bellec, Marie-Anne Cambon-Bonavita, Lucile Durand, Johanne Aube, Nicolas Gayet, Roberto Sandulli, Christophe Brandily, and Daniela Zeppilli

Subjects
nematode, shallow-water hydrothermal vent, sulfur-oxidizing bacteria, iron cycle, Zetaproteobacteria, Microbiology, QR1-502
Abstract

Shallow-water hydrothermal vents are widespread, especially in the Mediterranean Sea, owing to the active volcanism of the area. Apart free microbial communities’ investigations, few biological studies have been leaded yet. Investigations of microbial communities associated with Nematoda, an ecologically important group in sediments, can help to improve our overall understanding of these ecosystems. We used a multidisciplinary-approach, based on microscopic observations (scanning electron microscopy: SEM and Fluorescence In Situ Hybridization: FISH) coupled with a molecular diversity analysis using metabarcoding, based on the 16S rRNA gene (V3-V4 region), to characterize the bacterial community of a free-living marine nematode and its environment, the shallow hydrothermal vent near Naples (Italy). Observations of living bacteria in the intestine (FISH), molecular and phylogenetic analyses showed that this species of nematode harbors its own bacterial community, distinct from the surrounding sediment and water. Metabarcoding results revealed the specific microbiomes of the sediment from three sites of this hydrothermal area to be composed mainly of sulfur oxidizing and reducing related bacteria.

Published
2020
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5. Is It First the Egg or the Shrimp? – Diversity and Variation in Microbial Communities Colonizing Broods of the Vent Shrimp Rimicaris exoculata During Embryonic Development

Author

Pierre Methou, Ivan Hernández-Ávila, Johanne Aube, Valérie Cueff-Gauchard, Nicolas Gayet, Louis Amand, Bruce Shillito, Florence Pradillon, and Marie-Anne Cambon-Bonavita

Subjects
hydrothermal, shrimp, microbial colonization, Alvinocarididae, egg development, Microbiology, QR1-502
Abstract

Rimicaris exoculata is one of the most well-known and emblematic species of endemic vent fauna. Like many other species from these ecosystems, Rimicaris shrimps host important communities of chemosynthetic bacteria living in symbiosis with their host inside the cephalothorax and gut. For many of these symbiotic partners, the mode of transmission remains to be elucidated and the starting point of the symbiotic relationship is not yet defined, but could begin with the egg. In this study, we explored the proliferation of microbial communities on R. exoculata broods through embryonic development using a combination of NGS sequencing and microscopy approaches. Variations in abundance and diversity of egg microbial communities were analyzed in broods at different developmental stages and collected from mothers at two distinct vent fields on the Mid-Atlantic Ridge (TAG and Snake Pit). We also assessed the specificity of the egg microbiome by comparing communities developing on egg surfaces with those developing on the cuticle of pleopods, which are thought to be exposed to similar environmental conditions because the brood is held under the female’s abdomen. In terms of abundance, bacterial colonization clearly increases with both egg developmental stage and the position of the egg within the brood: those closest to the exterior having a higher bacterial coverage. Bacterial biomass increase also accompanies an increase of mineral precipitations and thus clearly relates to the degree of exposure to vent fluids. In terms of diversity, most bacterial lineages were found in all samples and were also those found in the cephalothorax of adults. However, significant variation occurs in the relative abundance of these lineages, most of this variation being explained by body surface (egg vs. pleopod), vent field, and developmental stage. The occurrence of symbiont-related lineages of Epsilonbacteraeota, Gammaproteobacteria, Zetaproteobacteria, and Mollicutes provide a basis for discussion on both the acquisition of symbionts and the potential roles of these bacterial communities during egg development.

Published
2019
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6. A Nematode of the Mid-Atlantic Ridge Hydrothermal Vents Harbors a Possible Symbiotic Relationship

Author

Laure Bellec, Marie-Anne Cambon-Bonavita, Valérie Cueff-Gauchard, Lucile Durand, Nicolas Gayet, and Daniela Zeppilli

Subjects
sulfur-oxidizing bacteria, Lucky Strike vent field, meiofauna, nematode, endosymbiont, Microbiology, QR1-502
Abstract

Deep-sea hydrothermal vent meiofauna have been the focus of recent research and the discovery of an abundant well-adapted free-living marine nematode on the Mid-Atlantic Ridge offers new perspectives on adaptations to the vent environment. Indeed, knowledge concerning biological interactions of microbes and meiofauna in marine extreme environments is scarce, especially for nematodes. In this study, we used microscopic observations [fluorescence in situ hybridization (FISH) and scanning electron microscopy (SEM)] and metabarcoding of 16S rRNA to characterize the bacterial community of the nematode species Oncholaimus dyvae, an overlooked but ecologically important vent organism. Detection of bacteria in the buccal cavity and on the cuticle (SEM) and epibionts in its intestine (FISH) suggests that O. dyvae harbors its own bacterial community. Molecular results and phylogenetic analysis show that bacteria associated with this species are related to symbiotic lineages typical of hydrothermal vent fauna, such as sulfur-oxidizing bacteria related to Epsilonproteobacteria and Gammaproteobacteria. This multi-approach study suggests a potential symbiotic role of bacteria with its nematode host and opens new research perspectives on vent meiofauna.

Published
2018
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7. Use of Natural Antimicrobial Peptides and Bacterial Biopolymers for Cultured Pearl Production

Author

Christelle Simon-Colin, Yannick Gueguen, Evelyne Bachere, Achraf Kouzayha, Denis Saulnier, Nicolas Gayet, and Jean Guezennec

Subjects
pearl oyster, exopolysaccharide, tachyplesin, antimicrobial, Biology (General), QH301-705.5
Abstract

Cultured pearls are the product of grafting and rearing of Pinctada margaritifera pearl oysters in their natural environment. Nucleus rejections and oyster mortality appear to result from bacterial infections or from an inappropriate grafting practice. To reduce the impact of bacterial infections, synthetic antibiotics have been applied during the grafting practice. However, the use of such antibiotics presents a number of problems associated with their incomplete biodegradability, limited efficacy in some cases, and an increased risk of selecting for antimicrobial resistant bacteria. We investigated the application of a marine antimicrobial peptide, tachyplesin, which is present in the Japanese horseshoe crab Tachypleus tridentatus, in combination with two marine bacterial exopolymers as alternative treatment agents. In field studies, the combination treatment resulted in a significant reduction in graft failures vs. untreated controls. The combination of tachyplesin (73 mg/L) with two bacterial exopolysaccharides (0.5% w/w) acting as filming agents, reduces graft-associated bacterial contamination. The survival data were similar to that reported for antibiotic treatments. These data suggest that non-antibiotic treatments of pearl oysters may provide an effective means of improving oyster survival following grafting procedures.

Published
2015
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9. Symbioses of alvinocaridid shrimps from the South West Pacific: No chemosymbiotic diets but partially conserved gut microbiomes

Author

Pierre Methou, Valérie Cueff-Gauchard, Loïc N. Michel, Nicolas Gayet, Florence Pradillon, and Marie-Anne Cambon-Bonavita

Subjects
trophic ecology, stable isotopes, Crustacean, symbioses, hydrothermal vent, chemosynthesis
Abstract

Rimicaris exoculatashrimps from hydrothermal vent ecosystems are known to host dense epibiotic communities inside their enlarged heads and digestive systems. Conversely, other shrimps from the family, described as opportunistic feeders have received less attention. We examined the nutrition and bacterial communities colonizing “head” chambers and digestive systems of three other alvinocaridids –Rimicaris variabilis,Nautilocaris saintlaurentaeandManuscarissp. – using a combination of electron microscopy, stable isotopes and sequencing approaches. Our observations inside “head” cavities and on mouthparts showed only a really low coverage of bacterial epibionts. In addition, no clear correlation between isotopic ratios and relative abundance of epibionts on mouthparts could be established among shrimp individuals. Altogether, these results suggest that none of these alvinocaridids rely on chemosynthetic epibionts as their main source of nutrition. Our analyses also revealed a substantial presence of several Firmicutes within the foreguts and midguts of these shrimps, which closest known lineages were systematically digestive epibionts associated with alvinocaridids, and more broadly from digestive systems of other crustaceans from marine and terrestrial ecosystems. Overall, our study opens new perspectives not only about chemosynthetic symbioses of vent shrimps, but more largely about digestive microbiomes with potential ancient and evolutionarily conserved bacterial partnerships among crustaceans.

Published
2023

11. Thermococcus camini sp. nov., a hyperthermophilic and piezophilic archaeon isolated from a deep-sea hydrothermal vent at the Mid-Atlantic Ridge

Author

Nicolas Gayet, Xavier Philippon, Erwann Vince, Lois Maignien, Damien Courtine, Karine Alain, Zongze Shao, Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), This work was supported by the program MERLIN Abyss to K.A, the ‘Laboratoire d'Excellence’ LabexMER Axis 3 programs ENDIV and CULTIVENT (ANR-10-LABX-1) to K.A., the Sino-French IRP 1211 MicrobSea to K.A. The study was supported by a grant from the French Ministry of Higher Education and Research, to D.C.The LABGeM (CEA/Genoscope and CNRS UMR8030), the France Génomique and French Bioinformatics Institute national infrastructures (funded as part of Investissement d'Avenir program managed by Agence Nationale pour la Recherche, contracts ANR-10-INBS-09 and ANR-11-INBS-0013) are acknowledged for support within the MicroScope annotation platform., ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
TAPS, hydrothermal, [(2-Hydroxy-1, piezophilic. Abbreviations: ANI, PIPES, Microbiology, 2-(N-morpholino)ethanesulfonic acid, 03 medical and health sciences, N'-bis(2-ethanesulfonic acid), Ribosomal protein, Botany, Yeast extract, CAPSO, 4-bis(2-ethanesulfonic acid), 1-bis(hydroxymethyl)ethyl)amino]-1-propanesulfonic acid, mid-atlantic ridge, DMSO, piezophilic, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, UBOCC, University of Brest (UBO) Culture Collection, Strain (chemistry), biology, 030306 microbiology, N-cyclohexyl-3-aminopropanesulfonic acid, hyperthermophilic, average nucleotide identity, International Committee on Systematics of Prokaryotes, General Medicine, Homopiperazine-1, piperazine-N, biology.organism_classification, 16S ribosomal RNA, dimethylsulfoxide, Thermococcales, Thermococcus, Type species, MAR, HOMOPIPES, ICSP, N-[Tris(hydroxymethyl)methyl]-3-aminopropanesulfonic acid, MES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, HEPES, Hydrothermal vent
Abstract

A coccoid-shaped, strictly anaerobic, hyperthermophilic and piezophilic organoheterotrophic archaeon, strain Iri35cT, was isolated from a hydrothermal chimney rock sample collected at a depth of 2300 m at the Mid-Atlantic Ridge (Rainbow vent field). Cells of strain Iri35cT grew at NaCl concentrations ranging from 1–5 % (w/v) (optimum 2.0 %), from pH 5.0 to 9.0 (optimum 7.0–7.5), at temperatures between 50 and 90 °C (optimum 75–80 °C) and at pressures from 0.1 to at least 50 MPa (optimum: 10–30 MPa). The novel isolate grew on complex organic substrates, such as yeast extract, tryptone, peptone or beef extract, preferentially in the presence of elemental sulphur or l-cystine; however, these molecules were not necessary for growth. Its genomic DNA G+C content was 54.63 mol%. The genome has been annotated and the metabolic predictions are in accordance with the metabolic characteristics of the strain and of Thermococcales in general. Phylogenetic analyses based on 16S rRNA gene sequences and concatenated ribosomal protein sequences showed that strain Iri35cT belongs to the genus Thermococcus, and is closer to the species T. celericrescens and T. siculi . Average nucleotide identity scores and in silico DNA–DNA hybridization values between the genome of strain Iri35cT and the genomes of the type species of the genus Thermococcus were below the species delineation threshold. Therefore, and considering the phenotypic data presented, strain Iri35cT is suggested to represent a novel species, for which the name Thermococcus camini sp. nov. is proposed, with the type strain Iri35cT (=UBOCC M-2026T=DSM 111003T).

Published
2021
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12. Authigenic pyrite formation in iron-dominated marine sediments of the Mozambique Margin

Author

Mark Zindorf, Jurjen Rooze, Christof Meile, Gwenael Jouet, Christian März, Robert Newton, Olivier Rouxel, Ewan Pelleter, Christophe Brandily, Nicolas Gayet, and Lucie Pastor

Abstract

Sediment deposition along continental margins and especially close to the outlets of major river systems is highly dynamic and influenced by changing environmental conditions, such as sea-level variations and the shifting of ocean currents. The upper slope of the Mozambique margin (SE Africa) receives its sediments from the Zambezi River and is the largest river-fed deposition center along the Eastern African Margin. Global sea level rise during the last glacial-Holocene transition led to a re-routing of the Zambezi River sediment plume. This caused order-of-magnitude changes in sedimentation rates along the shelf break of the Mozambique margin. The variable sediment input as well as changing organic matter load and quality resulted in non-steady state early diagenesis leading to changes in formation and upward flow of methane. This is reflected in temporally and spatially variable formation conditions of authigenic minerals (such as pyrite), especially at the sulfate-methane transition zone (SMTZ) where upward-diffusing methane is anaerobically oxidized by sulfate. Pyrite accumulations in sediment cores can be used to define the past positioning of SMTZs. The isotopic composition of sulfur in pyrite can provide information about the geochemical and environmental factors (e.g., availability of methane, sulfate, reactive iron) controlling the formation of these authigenic minerals during different times of sediment deposition.We present geochemical data from sediment cores acquired in 2015 during the PAMELA-MOZ4 campaign onboard R/V Pourquoi Pas? offshore Mozambique. A reactive transport model is used to simulate the evolution of early diagenetic conditions over the time of sediment deposition (i.e., the last 27,000 years). By reproducing the currently observed mineral accumulations, the temporal development of methane generation and upward flux, and the past positioning of the SMTZ, can be reconstructed. With this, we are able to put a time constraint on past events of authigenic mineral accumulation and reveal their response to sedimentation rate changes caused by sea-level rise. We further discuss isotope signatures of small-scale diagenetic processes at the Mozambique margin.This research was co-funded by TOTAL and IFREMER as part of the PAMELA scientific project.

Published
2020
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13. Ecophysiological differences between vesicomyid species and metabolic capabilities of their symbionts influence distribution patterns of the deep‐sea clams

Author

Alexis Khripounoff, Patricia Pignet, Cecile Cathalot, Anne Godfroy, Sophie Arnaud-Haond, Marie-Anne Cambon-Bonavita, Nicolas Gayet, Jean-Claude Caprais, Carole Decker, Adrien Vigneron, Karine Olu, Perrine Cruaud, Claire Papot, Jocelyn Le Baut, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD)

Subjects
0106 biological sciences, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, Deep sea, pliocardinae bivalve, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, evolutionary relationships, Ecosystem, Guaymas Basin, 14. Life underwater, sulfur storage, vesicomyid movements, deep-sea ecosystems, Ecology, Evolution, Behavior and Systematics, Chemosynthesis, Ecology, biology, hydrothermal vent clam, 010604 marine biology & hydrobiology, marine ecology, Community structure, biology.organism_classification, Cold seep, Calyptogena magnifica, calyptogena-magnifica, sulfide-rich sediments, chemoautotrophic bacteria, cold seeps, community structure, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, gulf-of-california, macrofaunal communities, Hydrothermal vent
Abstract

WOS:000472949800006; This study provides an analysis of vesicomyid bivalve-symbiont community distribution across cold seep and hydrothermal vent areas in the Guaymas Basin (Gulf of California, Mexico). Using a combination of morphological and molecular approaches including fluorescent in situ hybridization (FISH), and electronic microscopy observations, vesicomyid clam species and their associated symbionts were characterized and results were analyzed in light of geochemical conditions and other on-site observations. A greater diversity of vesicomyids was found at cold seep areas, where three different species were present (Phreagena soyoae [syn. kilmeri], Archivesica gigas, and Calyptogena pacifica). In contrast, A. gigas was the only species sampled across the hydrothermal vent area. The same haplotype of A. gigas was found in both hydrothermal vent and cold seep areas, highlighting possible contemporary exchanges among neighboring vents and seeps. In either ecosystem, molecular characterization of the symbionts confirmed the specificity between symbionts and hosts and supported the hypothesis of a predominantly vertical transmission. In addition, patterns of clams could reflect potential niche preferences for each species. The occurrence of numerous traces of vesicomyid movements on sediments in the sites colonized by A. gigas seemed to indicate that this species might have a better ability to move. Furthermore, variation in gill sulfur content could reveal a higher plasticity and sulfur storage capacity in A. gigas. Thus, the distribution of vesicomyid species across the chemosynthetic areas of the Guaymas Basin could be explained by differences in biological traits of the vesicomyid species that would allow A. gigas to more easily exploit transient and punctual sources of available sulfide than P. soyoae.

Published
2019
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14. Benthic foraminiferal response to sedimentary disturbance in the Capbreton canyon (Bay of Biscay, NE Atlantic)

Author

Nicolas Gayet, Angélique Roubi, Bernard Dennielou, R. Martinez Lamas, Sabine Schmidt, Pauline Duros, Emeric Gautier, and R. Silva Jacinto

Subjects
Capbreton canyon, 010504 meteorology & atmospheric sciences, Habitat disturbance, Submarine canyon, Aquatic Science, Turbidite, 010502 geochemistry & geophysics, Oceanography, 01 natural sciences, Foraminifera, 14. Life underwater, 0105 earth and related environmental sciences, Canyon, geography, geography.geographical_feature_category, biology, Benthic foraminifera, Sediment, 15. Life on land, biology.organism_classification, Terrace (geology), Benthic zone, Sedimentary rock, Bay, Geology
Abstract

Living (Rose Bengal stained) and dead benthic foraminifera were investigated at 6 deep-sea sites sampled in the Capbreton canyon area (Bay of Biscay, France). Three sites were located along the canyon axis at 301 m, 983 m and 1478 m and 3 stations were positioned on adjacent terraces at 251 m, 894 m and 1454 m. Sedimentary features indicate that frequent sedimentary disturbances of different magnitudes occur along the Capbreton canyon axis and adjacent terraces. Such environmental conditions cause the presence of very particular benthic environments. Along the 6 studied sites, different foraminiferal responses to various sedimentary patterns are observed revealing the complexity of this canyon environment. Some sites (Gitan 3 (canyon axis), Gitan 5 (canyon axis) and Gitan 6 (terrace)) are characterized by moderate to low standing stocks and low diversity and are mainly dominated by pioneer taxa such as Fursenkoina brady , Reophax dentaliniformis and Technitella melo suggesting a recent response to turbidite deposits recorded at these sites. Others sites (Gitan 1 and Gitan 2) show extremely high standing stocks and are mainly dominated by the opportunistic Bolivina subaenariensis and Bulimina marginata . Such faunal characteristics belonging to a more advanced stage of ecosystem colonization indicates strongly food-enriched sediment but extremely unstable conditions. Moderate standing stocks and diverse assemblage composed of species such as Uvigerina mediterranea and U. peregrina has only been observed at the terrace site Gitan 4. More stable sedimentary conditions recorded at this terrace seem to be suitable to the development of a dense and diverse foraminiferal community. Numerous neritic allochtonous species were observed in the dead foraminiferal fauna. These allochthonous species mainly originate from shelf areas (

Published
2017
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15. Contribution of resuspended sedimentary particles to dissolved iron and manganese in the ocean : an experimental study

Author

Nicolas Gayet, Eric Viollier, Ewan Pelleter, Hélène Planquette, Marie Cheize, Eva Bucciarelli, Robert M. Sherrell, Sandrine Cheron, Jessica N. Fitzsimmons, M. Le Goff, C. Liorzou, Christophe Lambert, Géraldine Sarthou, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Géosciences Marines (Ifremer) (GM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Rutgers University [Newark], Rutgers University System (Rutgers), Department of Oceanography [College Station], Texas A&M University [College Station], Laboratoire Géosciences Océan (LGO), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Laboratoire Environnement Profond (LEP), ANR-12-PDOC-0025,BITMAP,Biodisponibilité du fer et des métaux traces dans les particules marines(2012), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Centre de Brest, Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), 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), Laboratoire Cycles Géochimiques et ressources (LCG), Géosciences Marines (GM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Université de Bretagne Sud (UBS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut de Physique du Globe de Paris (IPGP (UMR_7154)), Institut national des sciences de l'Univers (INSU - CNRS)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and Etudes des Ecosystèmes Profonds (EEP)

Subjects
Biogeochemical cycle, 010504 meteorology & atmospheric sciences, Geotraces, Iron, Biogenic silica, 010502 geochemistry & geophysics, 01 natural sciences, Kerguelen, Water column, Geochemistry and Petrology, Phytoplankton, [SDU.STU.VO]Sciences of the Universe [physics]/Earth Sciences/Volcanology, 14. Life underwater, Southern Ocean, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, [SDU.STU.TE]Sciences of the Universe [physics]/Earth Sciences/Tectonics, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Manganese, Suspended particle dissolution, ACL, Sediment, Geology, Particulates, 13. Climate action, Environmental chemistry, Seawater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology
Abstract

A number of trace metals play essential roles in marine ecosystem structure and biological productivity. Until recently, it has been argued that phytoplankton access primarily dissolved iron, while particulate iron was considered a refractory material with little use biologically and limited interaction with the dissolved pool. In order to assess the transfer mechanisms between sediment-sourced particulate trace metals and the dissolved pool, we conducted a 14-month incubation that reacted resuspended sediments with natural seawater, both originating from the Kerguelen area (KEOPS cruises; Southern Ocean), in the dark, and at concentrations replicating natural conditions. Three types of sediments were investigated (named BioSi, BioSi + Ca, and Basalt), mostly composed of (i) biogenic silica (bSiO2), (ii) bSiO2 and calcite, and (iii) basaltic fragments, respectively. The release of dissolved silicon (dSi), iron (dFe) and manganese (dMn) was monitored regularly throughout the incubation, as well as living bacteria density and Fe organic ligands. Depending on the origin and composition of the sediment, unique dFe and dMn fluxes were observed, including a strong decoupling between dFe and dMn. The basaltic sediment released up to 1.09 ± 0.04 nmol L−1 of dFe and 0.28 ± 0.09 nmol L−1 of dMn, while the biogenic sediments released a higher 3.91 ± 0.04 nmol L−1 and 8.03 ± 0.42 nmol L−1 of dFe and dMn, respectively. Several factors influencing the release and removal of dFe and dMn were discernable at the temporal sampling resolution of the incubation, including the structural composition of the sediment, bacterial abundance, and the formation of manganese oxides. The regular sampling over short timescales and the extended sampling over one year proved to be critical to constrain the processes and exchanges that govern the contribution of the particulate to the dissolved pools. Overall, this incubation provides a strong basis for reassessing the role of resuspended sedimentary particles in the marine biogeochemical cycles of Fe and Mn. Indeed, we show that biogenic silica, calcite-rich and basaltic particles can contribute substantial dissolved Fe and Mn to the overlying water column. In the future, the global extent of this previously overlooked external metal source should be quantified through further process studies and biogeochemical models. This article is part of a special issue entitled: “Cycles of trace elements and isotopes in the ocean – GEOTRACES and beyond” - edited by Tim M. Conway, Tristan Horner, Yves Plancherel, and Aridane G. Gonzalez.

Published
2019
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17. Living (stained) deep-sea foraminifera from the Sea of Marmara : a preliminary study

Author

François Baudin, Florence Savignac, Nicolas Gayet, Ewan Pelleter, Angélique Roubi, Delphine Dissard, Mathilde Pitel, Emmanuel Ponzevera, Audrey Boissier, Vivien Guyader, Briony Mamo, Françoise Lesongeur, S. Bermell-Fleury, Sandrine Cheron, Livio Ruffine, Christophe Fontanier, UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Variabilité à long terme du climat de l'océan (VALCO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), 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 de Paris (UP)-École normale supérieure - Paris (ENS Paris), 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 de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), 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 de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Unité de recherche Géosciences Marines (Ifremer) (GM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Department of Biological Sciences [North Ryde], Macquarie University, Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Laboratoire de Géochimie et de Métallogénie, Institut des Sciences de la Terre de Paris (iSTeP), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS), Laboratoire Géodynamique et enregistrement Sédimentaire - Geosciences Marines (GM-LGS), Laboratoire Environnement Profond (LEP), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), European program 'MARsite', under grant ENV.2012.6.4-2, Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), 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)-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 Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-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), Environnements et Paléoenvironnements OCéaniques (EPOC), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), 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)), 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), Géosciences Marines (GM), Laboratoire Géochimie et Métallogénie (LGM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire Géodynamique et enregistrement Sédimentaire (LGS), and Etudes des Ecosystèmes Profonds (EEP)

Subjects
Sea of Marmara, Trace elements, 010504 meteorology & atmospheric sciences, biology, Stable isotope ratio, Living (stained) benthic foraminifera, Extreme ecosystems, 010502 geochemistry & geophysics, Oceanography, biology.organism_classification, 01 natural sciences, Deep sea, Cold seep, Foraminifera, Bottom water, chemistry.chemical_compound, chemistry, 13. Climate action, Carbonate, 14. Life underwater, Geology, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Stable isotopes
Abstract

International audience; In this preliminary study, we investigate living (stained) foraminifera from the Sea of Marmara. We focus on the faunal composition and geochemical signatures (trace elements, carbon and oxygen stable isotopes) in foraminiferal tests at two deep-sea sites (329 and ~ 1240 m depth respectively). Documented by ROV observations and sampling, both study areas are heterogeneous (including bacterial mats and carbonate concretions), proximal to cold seeps and consist of dysoxic bottom water (O2 < 20 µmol/L). The prevailing dysoxia at both study areas restricts foraminiferal diversity to very low values (S < 9, H’ < 0.97). Stress-tolerant species Bolivina vadescens and Globobulimina affinis dominate living faunas at both sites. The highest foraminiferal standing stock is recorded at the shallowest site underneath a spreading bacterial mat. No benthic foraminifera from either site possess geochemical signatures of methane seepage. Our biogeochemical results show that use of foraminiferal Mn/Ca ratios as a proxy for bottom water oxygenation depends strongly on regional physiography, sedimentary processes and water column structure.

Published
2018
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18. The Congolobe project, a multidisciplinary study of Congo deep-sea fan lobe complex: Overview of methods, strategies, observations and sampling

Author

Nicolas Gayet, Karine Charlier, Mélanie Raimonet, Olivier Ragueneau, Philippe Noel, J. Le Saout, Christophe Rabouille, Florence Savignac, Laurent Toffin, Gilles Vétion, Ming-Yi Sun, Lucie Pastor, Perrine Cruaud, S. Bourgeois, Anne Godfroy, Françoise Lesongeur, F. Toussaint, Julie Tourolle, François Baudin, Olivier Mouchel, Elsa Stetten, Philippe Rodier, Audrey M. Pruski, Martine Bez, Cecile Cathalot, Martial Taillefert, Sophie Arnaud-Haond, Lara Pozzato, Rudolph Corvaisier, Laurence Méjanelle, N. Tisnerat-Laborde, Claire Croguennec, Christophe Brandily, Philippe Martinez, Jean-Claude Caprais, Arunima Sen, Bernard Dennielou, Bruno Bombled, Sandrine Bessette, C. Senyarich, Alexis Khripounoff, Karine Olu, Laurence Droz, M. Lesaout, Marie Picot, Stéphane Hourdez, Jordon S. Beckler, J. Le Bruchec, Johann Schnyder, Patricia Pignet, Nathalie Babonneau, Livio Ruffine, M. Rabiller, J.L. Reyss, P. Michalopoulos, J.-M. Jouanneau, C. Bayle, Carole Decker, Sara Teixeira, B. Ruesch, Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Océan et Interfaces (OCEANIS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Laboratoire Environnement Profond (LEP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Evolution et Modélisation des Bassins Sédimentaires (EMBS), Institut des Sciences de la Terre de Paris (iSTeP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS), Unité de recherche Géosciences Marines (Ifremer) (GM), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Domaines Océaniques (LDO), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Observatoire des Sciences de l'Univers-Institut d'écologie et environnement-Centre National de la Recherche Scientifique (CNRS), School of Earth and Atmospheric Sciences [Atlanta], Georgia Institute of Technology [Atlanta], Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Adaptation et Biologie des Invertébrés en Conditions Extrêmes (ABICE), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Hellenic Centre for Marine Research (HCMR), Department of Marine Sciences [Athens], University of Georgia [USA], Centre of Marine Sciences [Faro] (CCMAR), University of Algarve [Portugal], Géochrononologie Traceurs Archéométrie (GEOTRAC), TOTAL-Scientific and Technical Center Jean Féger (CSTJF), TOTAL FINA ELF, ANR-11-BS56-0030,CONGOLOBE,Transfert de carbone organique et fonctionnement des écosystèmes dans les lobes terminaux de l'éventail sous-marin du Congo(2011), 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), 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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-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)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Etudes des Ecosystèmes Profonds (EEP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Géosciences Marines (GM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Environnements et Paléoenvironnements OCéaniques (EPOC), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), 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), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre scientifique et Technique Jean Feger (CSTJF), and Centre National de la Recherche Scientifique (CNRS)-Institut d'écologie et environnement-Observatoire des Sciences de l'Univers-Université de Brest (UBO)-Institut national des sciences de l'Univers (INSU - CNRS)

Subjects
Turbidity current, Continental-Margin, 010504 meteorology & atmospheric sciences, Fine sediment, Sedimentation rate, Transport, Submarine canyon, Vesicomyidae, 010502 geochemistry & geophysics, Oceanography, Turbidite, 01 natural sciences, Deep sea, Particulate Materials, Guaymas Basin, 14. Life underwater, Congo deep-sea fan, Chemosynthetic habitats, Turbidity-Current, 0105 earth and related environmental sciences, Canyon, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, geography, geography.geographical_feature_category, ACL, Organic-Carbon Accumulation, Particle Fluxes, Estuary, Seafloor morphology, 15. Life on land, M Water Depth, 13. Climate action, Mud Volcano, [SDE]Environmental Sciences, Chemosynthetic Ecosystems, Submarine pipeline, Sedimentary rock, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Geology
Abstract

The presently active region of the Congo deep-sea fan (around 330,000 km(2)), called the terminal lobes or lobe complex, covers an area of 2500 km(2) at 4700-5100 m water depth and 750-800 km offshore. It is a unique sedimentary area in the world ocean fed by a submarine canyon and a channel-levee system which presently deliver large amounts of organic carbon originating from the Congo River by turbidity currents. This particularity is due to the deep incision of the shelf by the Congo canyon, up to 30 km into the estuary, which funnels the Congo River sediments into the deep-sea. The connection between the river and the canyon is unique for major world rivers. In 2011, two cruises (WACS leg 2 and Congolobe) were conducted to simultaneously investigate the geology, organic and inorganic geochemistry, and micro- and macro-biology of the terminal lobes of the Congo deep-sea fan. Using this multidisciplinary approach, the morpho-sedimentary features of the lobes were characterized along with the origin and reactivity of organic matter, the recycling and burial of biogenic compounds, the diversity and function of bacterial and archaeal communities within the sediment, and the biodiversity and functioning of the faunal assemblages on the seafloor. Six different sites were selected for this study: Four distributed along the active channel from the lobe complex entrance to the outer rim of the sediment deposition zone, and two positioned cross-axis and at increasing distance from the active channel, thus providing a gradient in turbidite particle delivery and sediment age. This paper aims to provide the general context of this multidisciplinary study. It describes the general features of the site and the overall sampling strategy and provides the initial habitat observations to guide the other in-depth investigations presented in this special issue. Detailed bathymetry of each sampling site using 0.1-1 m resolution multibeam obtained with a remotely operated vehicle (ROV) shows progressive widening and smoothing of the channel-levees with increasing depth and reveals a complex morphology with channel bifurcations, erosional features and massive deposits. Dense ecosystems surveyed in the study area gather high density clusters of two large-sized species of symbiotic Vesicomyidae bivalves and microbial mats. These assemblages, which are rarely observed in sedimentary zones, resemble those based on chemosynthesis at cold-seep sites, such as the active pockmarks encountered along the Congo margin, and share with these sites the dominant vesicomyid species Christineconcha regab. Sedimentation rates estimated in the lobe complex range between 0.5 and 10 cm yr(-1), which is 2-3 orders of magnitude higher than values generally encountered at abyssal depths. The bathymetry, faunal assemblages and sedimentation rates make the Congo lobe complex a highly peculiar deep-sea habitat driven by high inputs of terrigenous material delivered by the Congo channel-levee system. (c) 2016 Elsevier Ltd. All rights reserved. ZAIANGO ANR Congolobe (ANR Blanc SIMI5-6) [11 BS56 030] IFREMER CEA through LSCE U.S. National Science Foundation [OCE-0831156] info:eu-repo/semantics/acceptedVersion

Published
2017
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19. Bacterial communities and syntrophic associations involved in anaerobic oxidation of methane process of the Sonora Margin cold seeps, Guaymas Basin

Author

Laurent Toffin, Anne Godfroy, Perrine Cruaud, Jean-Claude Caprais, Marie-Anne Cambon-Bonavita, Patricia Pignet, Adrien Vigneron, and Nicolas Gayet

Subjects
Ecological niche, 0303 health sciences, biology, 030306 microbiology, Ecology, biology.organism_classification, Microbiology, 6. Clean water, Cold seep, 03 medical and health sciences, Petroleum seep, Water column, 13. Climate action, Guaymas Basin, Anaerobic oxidation of methane, 14. Life underwater, Microbial mat, Ecology, Evolution, Behavior and Systematics, Bacteria, 030304 developmental biology
Abstract

The Sonora Margin cold seeps present on the seafloor a patchiness pattern of white microbial mats surrounded by polychaete and gastropod beds. These surface assemblages are fuelled by abundant organic inputs sedimenting from the water column and upward-flowing seep fluids. Elevated microbial density was observed in the underlying sediments. A previous study on the same samples identified anaerobic oxidation of methane (AOM) as the potential dominant archaeal process in these Sonora Margin sediments, probably catalysed by three clades of archaeal anaerobic methanotrophs (ANME-1, ANME-2 and ANME-3) associated with bacterial syntrophs. In this study, molecular surveys and microscopic observations investigating the diversity of Bacteria involved in AOM process, as well as the environmental parameters affecting the composition and the morphologies of AOM consortia in the Sonora Margin sediments were carried out. Two groups of Bacteria were identified within the AOM consortia, the Desulfosarcina/Desulfococcus SEEP SRB-1a group and a Desulfobulbus-related group. These bacteria showed different niche distributions, association specificities and consortia architectures, depending on sediment surface communities, geochemical parameters and ANME-associated phylogeny. Therefore, the syntrophic AOM process appears to depend on sulphate-reducing bacteria with different ecological niches and/or metabolisms, in a biofilm-like organic matrix.

Published
2013
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20. Desulfurobacterium indicum sp. nov., a thermophilic sulfur-reducing bacterium from the Indian Ocean

Author

Zongze Shao, Karine Alain, Mohamed Jebbar, Junwei Cao, Nicolas Gayet, Tiphaine Birien, and Zhaobin Huang

Subjects
0301 basic medicine, DNA, Bacterial, Thiosulfates, chemistry.chemical_element, Biology, hydrothermal vent, medicine.disease_cause, Microbiology, chemolithoautotroph, 03 medical and health sciences, chemistry.chemical_compound, Hydrothermal Vents, RNA, Ribosomal, 16S, Botany, medicine, sulfur-reducer, Indian Ocean, Ecology, Evolution, Behavior and Systematics, Phylogeny, Thiosulfate, Base Composition, Strain (chemistry), Sulfur-Reducing Bacteria, Thermophile, Fatty Acids, General Medicine, Sequence Analysis, DNA, thermophilic, 16S ribosomal RNA, biology.organism_classification, Sulfur, 6. Clean water, Desulfurobacterium, Bacterial Typing Techniques, Desulfurobacterium atlanticum, 030104 developmental biology, chemistry, Aquificae, Bacteria
Abstract

A novel sulfur-reducing bacterium, strain K6013(T), was isolated from a sulfide sample collected at a depth of 2771 m from a high-temperature hydrothermal vent in the Indian Ocean. Cells were Gram-stain-negative, anaerobic, motile rods (0.92.2 x 0.4-0.6 mu m). The strain grew at NaCl concentrations ranging from 1 to 4.5% (w/v) (optimum 2.5 %), at pH 5 to 8 (optimum pH 6), and at temperatures between 40 and 75 degrees C (optimum 65 degrees C). K6013(T) was an obligate chemolithoautotroph, using thiosulfate, sulfur and nitrate as terminal electron acceptors in the presence of H-2 but not sulfate, sulfite nor nitrite. The major cellular fatty acids were C-16 : 0 (17.4 %), C-18 : 1 omega 7c/C-18 : 1 omega 6c (ummed feature 8, 37.91 %), C-18 : 0 (18.29 %) and C-14 : 0 3-OH/iso-C-16: I-1 (summed feature 2, 8.56 %). The DNA G+C content was 38.2 mol%. The results of phylogenetic 16S rRNA gene sequence analyses indicated that K6013(T) represents a member of the genus Desulfurobacterium within the class Aquificae, with highest sequence similarity of 96.93% to Desulfurobacterium atlanticum SL22(T). On the basis of genotypic and phenotypic data, K6013(T) is considered to represent a novel species of the genus Desulfurobacterium, for which the name Desulfurobacterium indicum sp. nov. is proposed, with the type strain K6013(T) (=DSM 101677(T)=MCCC 1A01868(T)).

Published
2017

21. Pseudodesulfovibrio indicus gen. nov., sp nov., a piezophilic sulfate-reducing bacterium from the Indian Ocean and reclassification of four species of the genus Desulfovibrio

Author

Karine Alain, Nicolas Gayet, Mohamed Jebbar, Zongze Shao, Xiang Zeng, and Junwei Cao

Subjects
0301 basic medicine, DNA, Bacterial, Biology, medicine.disease_cause, 7. Clean energy, Microbiology, 03 medical and health sciences, RNA, Ribosomal, 16S, Botany, medicine, Sulfate-reducing bacteria, Indian Ocean, Ecology, Evolution, Behavior and Systematics, Desulfovibrio aespoeensis, Phylogeny, Base Composition, Strain (chemistry), Sulfur-Reducing Bacteria, Fatty Acids, General Medicine, Sequence Analysis, DNA, Ribosomal RNA, 16S ribosomal RNA, biology.organism_classification, Desulfovibrio, Bacterial Typing Techniques, Type species, 030104 developmental biology, Energy source, Oxidation-Reduction
Abstract

A novel sulfate-reducing bacterium, strain J2(T), was isolated from a serpentinized peridotite sample from the Indian Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J2(T) clustered with the genus Desulfovibrio within the family Desulfovibrionaceae, but it showed low similarity (87.95 %) to the type species Desulfovibrio desulfuricans DSM 642(T). It was most closely related to Desulfovibrio portus MSL79(T) (96.96 %), followed by Desulfovibrio aespoeensis Aspo-2(T) (96.11 %), Desulfovibrio piezophilus C1TLV30(T) (96.04 %) and Desulfovibrio profundus DSM 11384(T) (95.17 %). Other available sequences shared less than 93.33 % 16S rRNA gene sequence similarity. Cells were Gram-staining-negative, anaerobic, motile vibrios (2-6 x 0.4-0.6 mu m). Growth was observed at salinities ranging from 0.2 to 6 % (optimum 2.5 %), from pH 5 to 8 (optimum pH 6.5-7) and at temperatures between 9 and 40 degrees C (optimum 30-35 degrees C). J2(T) was piezophilic, growing optimally at 10 MPa (range 0-30 MPa). J2(T) used lactate, malate, pyruvate, formate and hydrogen as energy sources. Sulfate, thiosulfate, sulfite, fumarate and nitrate were used as terminal electron acceptors. Lactate and pyruvate were fermented. The main fatty acids were iso-C-15:0, anteiso-C-15:0, summed feature 9 (iso-C-17:1 omega 9c and/or C-16:0 10-methyl) and iso-C-17:0. The DNA G+C content of strain J2(T) was 63.5 mol%. The combined genotypic and phenotypic data show that strain J2(T) represents a novel species of a novel genus in the family Desulfovibrionaceae, for which the name Pseudodesulfovibrio indicus gen. nov., sp. nov. is proposed, with the type strain J2(T) (= MCCC 1A01867(T) = DSM 101483(T)). We also propose the reclassification of D. piezophilus as Pseudodesulfovibrio piezophilus comb. nov., D. profundus as Pseudodesulfovibrio profundus comb. nov., D. portus as Pseudodesulfovibrio portus comb. nov. and D. aespoeensis as Pseudodesulfovibrio aespoeensis comb. nov.

Published
2016

22. Living (stained) benthic foraminifera from the Mozambique Channel (eastern Africa): Exploring ecology of deep-sea unicellular meiofauna

Author

Eline Garnier, Bruno Deflandre, Nicolas Gayet, Thibaut Eugene, Antoine Grémare, Christophe Fontanier, Christophe Brandily, Bernard Dennielou, Sabrina Bichon, and Mickael Rovere

Subjects
0301 basic medicine, 010504 meteorology & atmospheric sciences, Meiobenthos, Mozambique Channel, Foraminifera, Aquatic Science, Oceanography, 01 natural sciences, Deep sea, 03 medical and health sciences, Sedimentary organic matter, Organic matter, 14. Life underwater, 0105 earth and related environmental sciences, chemistry.chemical_classification, Diversity, biology, Ecology, Sediment, 15. Life on land, biology.organism_classification, 030104 developmental biology, chemistry, Benthic zone, Allogromiida, Microhabitat
Abstract

Live (Rose-Bengal stained) deep-sea foraminiferal faunas have been studied at four stations between 530 and 3200-m depth in the Mozambique Channel (eastern Africa) to understand how complex environmental conditions (e.g., organic matter, oxygenation) control their ecological structure (i.e., diversity, density, and microhabitats). Two upper-slope stations, located at 530- and 780-m depth off Madagascar, are bathed by well-oxygenated bottom waters. They are characterized by fine sediments enriched in highly degraded organic matter (low amino-acid bio-availability and reduced chlorophyllic freshness). Mineralization of organic compounds results in relatively moderate oxygen penetration depth (i.e., 15 and 30 mm) in sediment. Interestingly, foraminiferal species richness (S) is exceptionally high at both sites. The highest densities are observed in the 780-m deep station, where peculiar sedimentary facies of organic matter are recorded (OC >2.0% DW). Redox conditions and sedimentary organic matter control the composition and the vertical distribution (i.e. microhabitat) of benthic faunas at both upper-slope sites. Bolivina alata , Bulimina marginata, Haplophragmoides bradyi and Nouria compressa are relevant bio-indicators of enhanced burial of organic matter prevailing at the 780-m deep station (i.e., eutrophic conditions), whereas Uvigerina hispida and Uvigerina semiornata are dominant at the 530-m deep station (i.e., relatively mesotrophic conditions). Two other stations are located on well-ventilated terraces from the deep-sea canyons of Tsiribihina and Zambezi (>3000-m depth). They are characterized by carbonate ooze, which is depleted in degraded organic matter and, where oxygen penetration depth is relatively deep (i.e.,>80 mm). Because of food scarcity, S and densities are relatively low, and agglutinated and organic-walled taxa dominate foraminiferal faunas. Hospitella fulva, a foraminiferal species belonging to Allogromiida, occupies very deep infaunal microhabitat, what disrupts the classical scheme of microhabitat patterns in oligotrophic settings.

Published
2016

23. Pyrococcus kukulkanii sp. nov., a hyperthermophilic, piezophilic archaeon isolated from a deep-sea hydrothermal vent

Author

Nicolas Gayet, Grégoire Michoud, Anne Godfroy, Nolwenn Callac, Philippe Oger, Olivier Rouxel, Pauline Vannier, Mickael Beauverger, Mohamed Jebbar, Françoise Lesongeur, Jayne E. Rattray, Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Adaptation aux milieux extrêmes (AME), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Stockholm University, Laboratoire Environnement Profond (LEP), Etudes des Ecosystèmes Profonds (EEP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)

Subjects
0301 basic medicine, Hot Temperature, Pyrococcus, Stereochemistry, [SDV]Life Sciences [q-bio], Microbiology, 03 medical and health sciences, Hydrothermal Vents, RNA, Ribosomal, 16S, Piezophile, Hydrostatic Pressure, Seawater, Phylogeny, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Base Composition, biology, Strain (chemistry), Sequence Analysis, DNA, General Medicine, biology.organism_classification, Archaea, Hyperthermophile, Thermococcales, DNA, Archaeal, 030104 developmental biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, Fermentation, Hydrothermal vent, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; A novel hyperthermophilic, piezophilic, anaerobic archaeon, designated NCB100(T), was isolated from a hydrothermal vent flange fragment collected in the Guaymas basin at the hydrothermal vent site named 'Rebecca's Roost' at a depth of 1997 m. Enrichment and isolation were performed at 100 degrees C under atmospheric pressure. Cells of strain NCB100(T) were highly motile, irregular cocci with a diameter of -1 mu m. Growth was recorded at temperatures between 70 and 112 degrees C (optimum 105 degrees C) and hydrostatic pressures of 0.1-80 MPa (optimum 40-50 MPa). Growth was observed at pH 3.5-8.5 (optimum pH 7) and with 1.5-7% NaCl (optimum at 2.5-3 %). Strain NCB100(T) was a strictly anaerobic chemo-organoheterotroph and grew on complex proteinaceous substrates such as yeast extract, peptone and tryptone, as well as on glycogen and starch. Elemental sulfur was required for growth and was reduced to hydrogen sulfide. The fermentation products from complex proteinaceous substrates were CO2 and H-2. The G+C content of the genomic DNA was 41.3 %. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain NCB100(T) belongs to the genus Pyrococcus, showing 99% similarity with the other described species of the genus Pyrococcus. On the basis of physiological characteristics, DNA G+C content, similarity level between ribosomal proteins and an average nucleotide identity value of 79 %, strain NCB100(T) represents a novel species for which the name Pyrococcus kukulkanii sp. nov. is proposed. The type strain is NCB100(T) (=DSM 101590(T) =Souchotheque de Bretagne BG1337(T)).

Published
2016
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24. Bacterial communities and syntrophic associations involved in anaerobic oxidation of methane process of the Sonora Margin cold seeps, Guaymas Basin

Author

Adrien, Vigneron, Perrine, Cruaud, Patricia, Pignet, Jean-Claude, Caprais, Nicolas, Gayet, Marie-Anne, Cambon-Bonavita, Anne, Godfroy, and Laurent, Toffin

Subjects
DNA, Bacterial, Geologic Sediments, Sulfur-Reducing Bacteria, RNA, Ribosomal, 16S, Microbial Consortia, Seawater, Sequence Analysis, DNA, Methane, Oxidation-Reduction, Ecosystem, Phylogeny
Abstract

The Sonora Margin cold seeps present on the seafloor a patchiness pattern of white microbial mats surrounded by polychaete and gastropod beds. These surface assemblages are fuelled by abundant organic inputs sedimenting from the water column and upward-flowing seep fluids. Elevated microbial density was observed in the underlying sediments. A previous study on the same samples identified anaerobic oxidation of methane (AOM) as the potential dominant archaeal process in these Sonora Margin sediments, probably catalysed by three clades of archaeal anaerobic methanotrophs (ANME-1, ANME-2 and ANME-3) associated with bacterial syntrophs. In this study, molecular surveys and microscopic observations investigating the diversity of Bacteria involved in AOM process, as well as the environmental parameters affecting the composition and the morphologies of AOM consortia in the Sonora Margin sediments were carried out. Two groups of Bacteria were identified within the AOM consortia, the Desulfosarcina/Desulfococcus SEEP SRB-1a group and a Desulfobulbus-related group. These bacteria showed different niche distributions, association specificities and consortia architectures, depending on sediment surface communities, geochemical parameters and ANME-associated phylogeny. Therefore, the syntrophic AOM process appears to depend on sulphate-reducing bacteria with different ecological niches and/or metabolisms, in a biofilm-like organic matrix.

Published
2013

25. Structure optimization of electro-optic polymer waveguides for low half-wave voltage modulators

Author

Duc Minh Nguyen, Nicolas Gayet, Dominique Bosc, Pierre-Antoinne Bonnardel, Mathieu Halbwax, Hind Mahé, Fabrice Odobel, Fonctions Optiques pour les Technologies de l'informatiON (FOTON), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-École Nationale Supérieure des Sciences Appliquées et de Technologie (ENSSAT)-Télécom Bretagne, Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Produits Chimiques Auxiliaires et de Synthéses (PCAS), PCAS, Institut d'électronique fondamentale (IEF), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), ANR-07-TCOM-0010,MODPOL,MODulateurs à base de POLymères électro-optiques(2007), Institut d’Électronique, de Microélectronique et de Nanotechnologie - UMR 8520 (IEMN), Centrale Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École Nationale Supérieure des Sciences Appliquées et de Technologie (ENSSAT)-Télécom Bretagne-Centre National de la Recherche Scientifique (CNRS), and Université de Nantes (UN)-Université de Nantes (UN)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
010302 applied physics, Permittivity, Materials science, business.industry, Wave propagation, Single-mode optical fiber, Nonlinear optics, Cladding (fiber optics), 01 natural sciences, Waveguide (optics), 010309 optics, Tunnel effect, Optics, 0103 physical sciences, [SPI.OPTI]Engineering Sciences [physics]/Optics / Photonic, business, Quantum tunnelling
Abstract

conference 7728 " Nonlinear Optics and its Applications ", session " Posters--Tuesday " [7728-52]; International audience; In this article, we discuss the waveguide dimensions optimization aiming to reduce the Vπ. For that purpose, various cover materials are investigated leading to a minimum effective core area " Aeff". The index contrast (core-cladding) at λ= 1550 nm, is varying from 0.07 to 0.21. As a result, the Aeff decreases from 12 μm2 down to 2.3 μm2, the total thickness of the waveguide is thus reduced and consequently the Vπ. Optimal parameters were calculated at λ= 1550 nm for single mode inverted-rib waveguides structure. The PAS1 a new polymer is used as electro-optic material for the core. An analytical model taking account the losses by tunnelling, allowed us to estimate the optimum distance between electrodes to reduce the Vπ which could be about 1.6V ( 0.8 V in a push-pull configuration). Related with the bandwidth of the modulator, permittivity measurements were carried out on core and cladding polymers as well. The process of waveguides fabrication is described in details and several waveguides are performed. Finally, a new experimental technique for precision measurements of the propagation losses in waveguides is presented. The principle is simple, and the propagation losses measured is found to be independent of coupling conditions.

Published
2010
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26. Metal partitioning after in situ filtration at deep-sea vents of the Lucky Strike hydrothermal field (EMSO-Azores, Mid-Atlantic Ridge, 37 degrees N)

Author

Valérie Chavagnac, Cecile Cathalot, Pierre-Marie Sarradin, Agathe Laes-Huon, Laura Cotte, Matthieu Waeles, Ricardo Riso, Gabriel Dulaquais, Ewan Pelleter, 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), Laboratoire Environnement Profond (LEP), Etudes des Ecosystèmes Profonds (EEP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Géosciences Environnement Toulouse (GET), 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), Laboratoire Cycles Géochimiques et ressources (LCG), Géosciences Marines (GM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), We are grateful to captains and crew of the R/V Pourquoi Pas?, R/V l'Atalante and the Victor 6000 ROV for their assistance at sea, Nicolas Gayet for help in collecting samples, Julie Tourolle for the bathymetric map, C.eline Liorzou, Marie-Laure Rouget and Bleuenn Gueguen (PSO) for ICP-AES and ICP-MS measurements. We are also grateful to Mathilde Cannat, Pierre-Marie Sarradin and J.erome Blandin coordinators of the projects and PI cruises (MomarSat 2014, doi.org: 10.17600/14000300, MomarSat 2015, doi.org: 10.17600/15000200, MomarSat 2016, doi. org: 10.17600/16001200). We acknowledge financial support from the French ANR Luckyscales project (ANR-14-CE02-0008-02), the EU project EMSO (http://www.emso-eu.org/) and the 'Laboratoire d'Excellence' LabexMER (ANR-10-LABX-19)., ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), ANR-14-CE02-0008,LuckyScales,De la chambre magmatique aux micro-habitats: dynamique des écosystèmes hydrothermaux marins profonds(2014), European Project: 211816,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2007-1,EMSO(2008), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut 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), Unité de recherche Géosciences Marines (Ifremer) (GM), and Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne)

Subjects
Deep-sea vents, 010504 meteorology & atmospheric sciences, distributions, Geochemistry, Mid-Atlantic Ridge, east pacific rise, Precipitation, Aquatic Science, 010502 geochemistry & geophysics, Oceanography, 01 natural sciences, Deep sea, fe, Hydrothermal circulation, law.invention, dissolved iron, particulate metals, law, trace-metals, In-situ filtration, Filtration, 0105 earth and related environmental sciences, plume, Metal, Mixing gradient, ACL, North Atlantic Deep Water, Hydrothermal, Plume, oxidation-kinetics, 13. Climate action, rare-earth-elements, south atlantic, Seawater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Geology, Hydrothermal vent
Abstract

WOS:000521509000009; International audience; Metal partitioning between the dissolved and particulate phases is still poorly constrained within the early mixing of hydrothermal fluids and deep seawater. In this study, in situ filtration has been used to collect early buoyant plume fluids. This has provided the unique opportunity to reassess precisely metal partitioning along the mixing gradient by limiting chemical exchange processes between the dissolved (\textless0.45 mu m) and particulate (\textgreater0.45 mu m) phases during sampling. We report on the partitioning of three major metals (Fe, Cu, Zn) in the early buoyant plume of six black and clear smokers from the Lucky Strike hydrothermal field (37 degrees N, MAR; EMSO-Azores deep sea observatory). We show that chemical changes are limited in the warmest part of the plume [50-150 degrees C, dMn \textgreater 40 mu M; dilution factor (DF) of similar to 1-10 by NADW] as metal partitioning displays a chemical signature similar to the end-member one. However, as the dilution ratio between the hydrothermal fluid and North-Atlantic Deep-water (NADW) increases (4-50 degrees C, dMn \textless 40 mu M; DF of 10-100 by NADW), metal partitioning is affected by different precipitation and oxidation processes. Molar ratios normalized to Fe in the particles highlight the onset of Fe oxides formation, the precipitation of barite and the decreasing contribution of sulfide minerals (mainly Cu-Fe sulfides and sphalerite/wurtzite) along with fluid dilution.

Published
2020
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