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Registros recuperados: 36
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A Nematode of the Mid-Atlantic Ridge Hydrothermal Vents Harbors a Possible Symbiotic Relationship ArchiMer
Bellec, Laure; Cambon-bonavita, Marie-anne; Cueff-gauchard, Valerie; Durand, Lucile; Gayet, Nicolas; Zeppilli, Daniela.
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...
Tipo: Text Palavras-chave: Sulfur-oxidizing bacteria; Lucky Strike vent field; Meiofauna; Nematode; Endosymbiont.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00457/56846/58676.pdf
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Acquisition of epibiotic bacteria along the life cycle of the hydrothermal shrimp Rimicaris exoculata ArchiMer
Guri, Mathieu; Durand, Lucile; Cueff-gauchard, Valerie; Zbinden, Magali; Crassous, Philippe; Shillito, Bruce; Cambon-bonavita, Marie-anne.
The caridean shrimp Rimicaris exoculata dominates the fauna at several Mid-Atlantic Ridge hydrothermal vent sites. This shrimp has an enlarged gill chamber, harboring a dense ectosymbiotic community of chemoautotrophic bacteria associated with mineral oxide deposits. Until now, their acquisition is not fully understood. At three hydrothermal vent sites, we analyzed the epibionts diversity at different moult stages and also in the first stages of the shrimp life (eggs, hatched eggs (with larvae) and juveniles). Hatched eggs associated with young larvae were collected for the first time directly from gravid females at the Logachev vent site during the Serpentine cruise. An approach using 16S rRNA clone libraries, scanning and transmission electron...
Tipo: Text Palavras-chave: Symbiosis; Larvae; Methanotrophic symbiont; Rimicaris exoculata; Transmission pathways.
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00072/18318/15997.pdf
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Bacterial communities and syntrophic associations involved in anaerobic oxidation of methane process of the Sonora Margin cold seeps, Guaymas Basin ArchiMer
Vigneron, Adrien; Cruaud, Perrine; Pignet, Patricia; Caprais, Jean-claude; Gayet, Nicolas; Cambon-bonavita, Marie-anne; Godfroy, Anne; Toffin, Laurent.
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...
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Ano: 2014 URL: http://archimer.ifremer.fr/doc/00168/27921/27279.pdf
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Bacterial symbionts and mineral deposits in the branchial chamber of the hydrothermal vent shrimp Rimicaris exoculata: relationship to moult cycle ArchiMer
Corbari, Laure; Zbinden, Magali; Cambon-bonavita, Marie-anne; Gaill, Françoise; Compere, Philippe.
The shrimp Rimicaris exoculata is considered a primary consumer that dominates the fauna of most Mid-Atlantic Ridge hydrothermal ecosystems. The shrimps harbour in their gill chamber an important ectosymbiotic community of chemoautotrophic bacteria associated with iron oxide deposits. The settlement and development of this ectosymbiosis was investigated using microscopy techniques (light microscopy, LM; and scanning, transmission and environmental scanning electron microscopy: SEM and ESEM, respectively) for shrimps from 2 different vent fields (Rainbow, 36 degrees 14.0' N and TAG, 26 degrees 08.0' N). The results revealed a bacterial re-colonisation after each exuviation and a development of the bacterial community in 5 steps in relation to the moult...
Tipo: Text Palavras-chave: Iron oxides; Ectosymbiosis; Moult cycle; Shrimp; Hydrothermal vents.
Ano: 2008 URL: http://archimer.ifremer.fr/doc/2008/publication-4626.pdf
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Biogeographical distribution of Rimicaris exoculata resident gut epibiont communities along the Mid-Atlantic Ridge hydrothermal vent sites ArchiMer
Durand, Lucile; Roumagnac, Marie; Cueff-gauchard, Valerie; Jan, Cyrielle; Guri, Mathieu; Tessier, Claire; Haond, Marine; Crassous, Philippe; Zbinden, Magali; Arnaud-haond, Sophie; Cambon-bonavita, Marie-anne.
Rimicaris exoculata is a deep-sea hydrothermal vent shrimp which enlarged gill chamber houses a complex trophic epibiotic community. Its gut harbours an autochthonous and distinct microbial community. This species dominates hydrothermal ecosystems megafauna along the Mid-Atlantic Ridge, regardless of contrasted geochemical conditions prevailing in them. Here, the resident gut epibiont community at four contrasted hydrothermal vent sites (Rainbow/TAG/Logatchev/Ashadze) was analysed and compiled with previous data to evaluate the possible influence of site location, using 16S rRNA surveys and microscopic observations (TEM, SEM and FISH analyses). Filamentous epibionts inserted between the epithelial cells microvilli were observed on all examined samples....
Tipo: Text Palavras-chave: Epibiont; Extreme environments; Network analyses; Phylogeography.
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00288/39890/38443.pdf
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Caloranaerobacter azorensis gen. nov., sp nov., an anaerobic thermophilic bacterium isolated from a deep-sea hydrothermal vent ArchiMer
Wery, Nathalie; Moricet, Jean-marc; Cueff, Valerie; Jean, Joelle; Pignet, Patricia; Lesongeur, Francoise; Cambon-bonavita, Marie-anne; Barbier, Georges.
A thermophilic, anaerobic, chemo-organotrophic bacterium, designated MV1087(T), was isolated from a deep-sea hydrothermal chimney sample collected from the Mid-Atlantic Ridge. The cells were straight, motile and stained Gram-negative. Growth was observed from 45 to 65 degreesC, with an optimum around 65 degreesC. No growth was observed at 40 or 70 degreesC. Growth was observed from pH 5.5 to 9.0 and the optimum pH was around 7. The salinity range for growth was 10-100 g sea salt l(-1) (corresponding to 6.5-65 g NaCl l(-1)) with an optimum at 30 g sea salt l(-1) (20 g NaCl l(-1)). Strain MV1087(T) was heterotrophic, able to ferment proteinaceous substrates, such as brain/heart infusion and gluten, and carbohydrates, such as glucose, xylan and starch. The...
Tipo: Text Palavras-chave: Thermophile; Deep sea vent; Caloranaerobacter azorensis; Caloranaerobacter; Bacteria.
Ano: 2001 URL: http://archimer.ifremer.fr/doc/2001/publication-586.pdf
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Caminicella sporogenes gen. nov., sp nov., a novel thermophilic spore-forming bacterium isolated from an East-Pacific Rise hydrothermal vent ArchiMer
Alain, Karine; Pignet, Patricia; Zbinden, M; Quillevere, M; Duchiron, F; Donval, Jean-pierre; Lesongeur, Francoise; Raguenes, Gerard; Crassous, Philippe; Querellou, Joel; Cambon-bonavita, Marie-anne.
A novel thermophilic, anaerobic, strictly chemoorganoheterotrophic bacterium, designated as AM1114(T), was isolated from a deep-sea hydrothermal vent sample from the East-Pacific Rise (EPR 13degrees N). The cells were long (3-10 mum) rods, motile with peritrichous flagella, and exhibited a Gram-negative cell wall ultrastructure. In the late stationary phase of growth, cells formed an ovoid, refractile, terminal endospore. They grew at 45-65 degreesC inclusive (optimum 55-60 degreesC; doubling time approx. 45 min), at pH 4.5-8.0 inclusive (optimum pH 7.5-8.0) and at sea salt concentrations of 20-60 g l(-1) inclusive (optimum 25-30 g l(-1)). Strain AM1114(T) was an obligately heterotrophic bacterium able to ferment a mixture of 20 amino acids, complex...
Tipo: Text Palavras-chave: Caminicella sporogenes; Clostridiales; Thermophile; Deep sea hydrothermal vent.
Ano: 2002 URL: http://archimer.ifremer.fr/doc/2002/publication-528.pdf
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Comparative Study of Guaymas Basin Microbiomes: Cold Seeps vs. Hydrothermal Vents Sediments ArchiMer
Cruaud, Perrine; Vigneron, Adrien; Pignet, Patricia; Caprais, Jean-claude; Lesongeur, Francoise; Toffin, Laurent; Godfroy, Anne; Cambon-bonavita, Marie-anne.
In the Guaymas Basin, the presence at a few tens of kilometers of cold seeps and hydrothermal vents coupled with comparable sedimentary settings and depths offer a unique opportunity to assess and compare the microbial community composition of these deep-sea ecosystems. The microbial diversity in sediments from three cold seep and two hydrothermal vent assemblages were investigated using high-throughput 16S rRNA-sequencing. Numerous bacterial and archaeal lineages were detected in both cold seep and hydrothermal vent sediments. Various potential organic matter degraders (e.g., Chloroflexi, Atribacteria, MBG-D) and methane and sulfur cycling related microorganisms (e.g., ANME and methanogenic lineages, sulfate-reducing lineages) were detected in both...
Tipo: Text Palavras-chave: Microbial diversity; Hydrothermal vents; Cold seeps; Ribotypes; Methane; Extreme environments.
Ano: 2017 URL: https://archimer.ifremer.fr/doc/00415/52640/53496.pdf
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Comparison of microbial communities associated with three Atlantic ultramafic hydrothermal systems ArchiMer
Roussel, Erwan; Konn, Cecile; Charlou, Jean-luc; Donval, Jean-pierre; Fouquet, Yves; Querellou, Joel; Prieur, Daniel; Cambon-bonavita, Marie-anne.
The distribution of Archaea and methanogenic, methanotrophic and sulfate-reducing communities in three Atlantic ultramafic-hosted hydrothermal systems (Rainbow, Ashadze, Lost City) was compared using 16S rRNA gene and functional gene (mcrA, pmoA and dsrA) clone libraries. The overall archaeal community was diverse and heterogeneously distributed between the hydrothermal sites and the types of samples analyzed (seawater, hydrothermal fluid, chimney and sediment). The Lost City hydrothermal field, characterized by high alkaline warm fluids (pH>11; T<95 °C), harbored a singular archaeal diversity mostly composed of unaffiliated Methanosarcinales. The archaeal communities associated with the recently discovered Ashadze 1 site, one of the deepest active...
Tipo: Text Palavras-chave: Archaea; Hydrothermal vent; Mid-Atlantic Ridge; 16S rRNA gene; Sediment; Ultramafic.
Ano: 2011 URL: http://archimer.ifremer.fr/doc/00067/17836/15573.pdf
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Cruise MoMARDREAM-Naut and other MoMAR experiments at Rainbow and Lucky Strike in Summer 2007 ArchiMer
Gaill, Françoise; Ballu, V.; Cannat, M.; Crawford, W.; Dyment, J.; Escartin, J.; Fouquet, Yves; Goslin, J.; Reverdin, G.; Sarradin, Pierre-marie; Tarits, P.; Andreani, M.; Bonnivard, E.; Bucas, Karenn; Burgaud, G.; Cambon-bonavita, Marie-anne; Cueff, Valerie; Durand, C.; Gros, O.; Hamel, G.; Henriques, M.; Hois, E.; Ildefonse, B.; Konn, Cecile; Le Bris, Nadine; Le Guyader, H.; Ravaux, J.; Shilito, B.; Toullec, J.y.; Zbinden, M..
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Ano: 2007 URL: http://archimer.ifremer.fr/doc/00385/49650/50163.pdf
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Desulfurobacterium crinifex sp.nov., a novel thermophilic, pinkish-streamer forming, chemolithoautotrophic bacterium isolated from a Juan de Fuca Ridge hydrothermal vent and amendment of the genus Desulfurobacterium ArchiMer
Alain, Karine; Rolland, Sophie; Crassous, Philippe; Lesongeur, Francoise; Zbinden, Magali; Le Gall, Christian; Godfroy, Anne; Page, Antoine; Juniper, S Kim; Cambon-bonavita, Marie-anne; Duchiron, Francis; Querellou, Joel.
A novel thermophilic, chemolithoautotrophic T bacterium, designated as NE1206(T), was isolated from a Juan de Fuca Ridge hydrothermal vent sample (tubes of the annelid polychaete Paralvinella sulfincola attached to small pieces of hydrothermal chimney). The cells were rod-shaped (1.2-3.5x0.4-0.7 mum), occurring as single motile rods or forming macroscopic aggregates visible as pinkish to brownish streamers. The new isolate was anaerobic. It grew between 50 and 70 degreesC (optimum 60-65 degreesC doubling time approximately 1 h 15 min at 60 degreesC), between pH 5.0 and 7.5 (optimum pH around 6.0-6.5) and at sea salts concentrations between 20 and 40 g l(-1) (optimum 30 g l(-1)). Cells grew chemolithoautotrophically in an H-2/CO2 atmosphere (80/20, v/v; 200...
Tipo: Text Palavras-chave: Thermophile; Nitrate reducing; Lithotroph; Desulfurobacterium crinifex; Deep sea hydrothermal vent; Cell networks.
Ano: 2003 URL: https://archimer.ifremer.fr/doc/2003/publication-663.pdf
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Development of an ecotoxicological protocol for the deep-sea fauna using the hydrothermal vent shrimp Rimicaris exoculata ArchiMer
Auguste, M.; Mestre, N. C.; Rocha, T. L.; Cardoso, C.; Cueff-gauchard, Valerie; Le Bloa, Simon; Cambon-bonavita, Marie-anne; Shillito, B.; Zbinden, M.; Ravaux, J.; Bebianno, M. J..
In light of deep-sea mining industry development, particularly interested in massive-sulphide deposits enriched in metals with high commercial value, efforts are increasing to better understand potential environmental impacts to local fauna. The aim of this study was to assess the natural background levels of biomarkers in the hydrothermal vent shrimp Rimicaris exoculata and their responses to copper exposure at in situ pressure (30 MPa) as well as the effects of depressurization and pressurization of the high-pressure aquarium IPOCAMP. R. exoculata were collected from the chimney walls of the hydrothermal vent site TAG (Mid Atlantic Ridge) at 3630 m depth during the BICOSE cruise in 2014. Tissue metal accumulation was quantified in different tissues...
Tipo: Text Palavras-chave: Deep-sea mining; Hydrothermal vents; Biomarkers; Ipocamp; Copper; TAG.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00323/43465/42869.pdf
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Diversity and distribution of methane-oxidizing microbial communities associated with different faunal assemblages in a giant pockmark of the Gabon continental margin ArchiMer
Cambon-bonavita, Marie-anne; Nadalig, Thierry; Roussel, Erwan; Delage, Eloise; Duperron, Sebastien; Caprais, Jean-claude; Boetius, A.; Sibuet, Myriam.
A giant 800-m-diameter pockmark named REGAB was discovered on the Gabon continental margin actively emitting methane at a water depth of 3200 m. The microbial diversity in sediments from four different assemblages of chemosynthetic organisms, Mytilidae, Vesicomyidae, Sibogliniclae and a bacterial mat, was investigated using comparative 16S rRNA gene sequence analysis. Aggregates of anaerobic methanotrophic archaea (ANME-2) and bacteria of the Desulfosarcina/Desulfococcus cluster were found in all four chemosynthetic habitats. Fluorescence in situ hybridization targeting the ANME-2/Desulfosarcina/Desulfococcus aggregates showed their presence few centimeters (3-5cm) below the surface of sediment. 16S rRNA gene sequences from all known marine ANME groups...
Tipo: Text Palavras-chave: Microbial phylogeny; Faunal assemblage; Cold seep; Chemosynthetic ecosystems; AOM; REGAB.
Ano: 2009 URL: https://archimer.ifremer.fr/doc/2009/publication-7298.pdf
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Ecology and trophic role of Oncholaimus dyvae sp. nov. (Nematoda: Oncholaimidae) from the lucky strike hydrothermal vent field (Mid-Atlantic Ridge) ArchiMer
Zeppilli, Daniela; Bellec, Laure; Cambon-bonavita, Marie-anne; Decraemer, Wilfrida; Fontaneto, Diego; Fuchs, Sandra; Gayet, Nicolas; Mandon, Perrine; Michel, Loic; Portail, Marie; Smol, Nic; Sørensen, Martin V.; Vanreusel, Ann; Sarrazin, Jozee.
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...
Tipo: Text Palavras-chave: Oncholaimus dyvae sp. nov.; Hydrothermal vents; Deep sea; Carbon and nitrogen isotopic ratios.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00508/61985/66097.pdf
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Extending the sub-sea-floor biosphere ArchiMer
Roussel, Erwan; Cambon-bonavita, Marie-anne; Querellou, Joel; Cragg, B; Webster, G; Prieur, D; Parkes, R.
Sub-sea-floor sediments may contain two-thirds of Earth's total prokaryotic biomass. However, this has its basis in data extrapolation from ~500-meter to 4-kilometer depths, whereas the deepest documented prokaryotes are from only 842 meters. Here, we provide evidence for low concentrations of living prokaryotic cells in the deepest (1626 meters below the sea floor), oldest (111 million years old), and potentially hottest (~100°C) marine sediments investigated. These Newfoundland margin sediments also have DNA sequences related to thermophilic and/or hyperthermophilic Archaea. These form two unique clusters within Pyrococcus and Thermococcus genera, suggesting unknown, uncultured groups are present in deep, hot, marine sediments (~54° to 100°C). Sequences...
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Ano: 2008 URL: http://archimer.ifremer.fr/doc/2008/publication-4209.pdf
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EXtreme ecosystem studies in the deep OCEan: Technological Developments. EXOCET/D ArchiMer
Sarradin, Pierre-marie; Sarrazin, Jozee; Cadiou, Jean-francois; Olu, Karine; Desbruyeres, Damien; Rigaud, Vincent; Drogou, Jean-francois; Lecornu, Fabrice; Rolin, Jean-francois; Vuillemin, Renaud; Cambon-bonavita, Marie-anne; Sauter, E; Von Juterzenka, K; Boetius, A; Santos, Rs; Colaco, Ana; Pascoal, A; Oliveira, Paulo; Shillito, Bruce; Zal, F; Schultz, A; Taylor, P; Lane, D; Loke, Rob; Du Buf, H; Waldmann, C; Cormack, A; Sanfilippo, L; Masson, M.
The general objective of EXOCET/D is to develop, implement and test specific instruments aimed at exploring, describing, quantifying and monitoring biodiversity in deep-sea fragmented habitats as well as at identifying links between community structure and environmental dynamics. Onboard experimental devices will complement the approach, enabling experiments on species physiology. The EXOCET/D working fields include: video and acoustic imagery, in situ analysis of physico-chemical factors, quantitative sampling of macroand micro-organisms, in vivo experiments, integration of multidisciplinary data, implementation on European deep-submersibles and a final phase of technical and scientific validation
Tipo: Text Palavras-chave: Deep sea; Ecosystem; Imagery; In situ analysis; Faunal sampling; Submersibles; Observatory.
Ano: 2004 URL: https://archimer.ifremer.fr/doc/2007/publication-3600.pdf
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Gill chamber and gut microbial communities of the hydrothermal shrimp Rimicaris chacei Williams and Rona 1986: A possible symbiosis ArchiMer
Apremont, Vincent; Cambon-bonavita, Marie-anne; Cueff-gauchard, Valerie; Francois, David; Pradillon, Florence; Corbari, Laure; Zbinden, Magali.
Rimicaris chacei Williams and Rona 1986, formerly named as Chorocaris chacei, is a caridean shrimp living in deep-sea hydrothermal ecosystems. This shrimp is endemic to the Mid Atlantic Ridge (MAR) and lives at the periphery of aggregates of its well-known congeneric R. exoculata Williams and Rona 1986. Contrasting with the very dense and mobile clusters formed by R. exoculata, R. chacei lives in small groups of several individuals that are not very mobile. Although devoid of the characteristic hypertrophied cephalothorax of R. exoculata, which harbors the ectosymbionts, a microbial community has also been reported in the cephalothorax of R. chacei. Previous data on morphology, behavior and isotopic values indicate a diet based on a combination of feeding...
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Ano: 2018 URL: https://archimer.ifremer.fr/doc/00465/57680/59880.pdf
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Highlighting of quorum sensing lux genes and their expression in the hydrothermal vent shrimp Rimicaris exoculata ectosymbiontic community. Possible use as biogeographic markers ArchiMer
Le Bloa, Simon; Durand, Lucile; Cueff-gauchard, Valerie; Le Bars, Josiane; Taupin, Laure; Marteau, Charlotte; Bazire, Alexis; Cambon-bonavita, Marie-anne.
Rimicaris exoculata is a caridean shrimp that dominates the fauna at several hydrothermal vent sites of the Mid-Atlantic Ridge. It has two distinct and stable microbial communities. One of these epibiontic bacterial communities is located in the shrimp gut and has a distribution and role that are poorly understood. The second colonizes its enlarged gill chamber and is involved in host nutrition. It is eliminated after each molt, and has colonization processes reminiscent of those of a biofilm. The presence and expression of genes usually involved in quorum sensing (QS) were then studied. At four sites, Rainbow, TAG, Snake Pit and Logatchev, two lux genes were identified in the R. exoculata epibiontic community at different shrimp molt stages and life...
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Ano: 2017 URL: http://archimer.ifremer.fr/doc/00377/48841/49268.pdf
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Identification and Characterization of Carboxyl Esterases of Gill Chamber-Associated Microbiota in the Deep-Sea Shrimp Rimicaris exoculata by Using Functional Metagenomics ArchiMer
Alcaide, Maria; Tchigvintsev, Anatoli; Martinez-martinez, Monica; Popovic, Ana; Reva, Oleg N.; Lafraya, Alvaro; Bargiela, Rafael; Nechitaylo, Taras Y.; Matesanz, Ruth; Cambon-bonavita, Marie-anne; Jebbar, Mohamed; Yakimov, Michail M.; Savchenko, Alexei; Golyshina, Olga V.; Yakunin, Alexander F.; Golyshin, Peter N.; Ferrer, Manuel.
The shrimp Rimicaris exoculata dominates the fauna in deep-sea hydrothermal vent sites along the Mid-Atlantic Ridge (depth, 2,320 m). Here, we identified and biochemically characterized three carboxyl esterases from microbial communities inhabiting the R. exoculata gill that were isolated by naive screens of a gill chamber metagenomic library. These proteins exhibit low to moderate identity to known esterase sequences (<= 52%) and to each other (11.9 to 63.7%) and appear to have originated from unknown species or from genera of Proteobacteria related to Thiothrix/Leucothrix (MGS-RG1/RG2) and to the Rhodobacteraceae group (MGS-RG3). A library of 131 esters and 31 additional esterase/lipase preparations was used to evaluate the activity profiles of these...
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Ano: 2015 URL: http://archimer.ifremer.fr/doc/00256/36721/36438.pdf
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Influence of DNA Extraction Method, 16S rRNA Targeted Hypervariable Regions, and Sample Origin on Microbial Diversity Detected by 454 Pyrosequencing in Marine Chemosynthetic Ecosystems ArchiMer
Cruaud, Perrine; Vigneron, Adrien; Lucchetti-miganeh, Celine; Ciron, Pierre Emmanuel; Godfroy, Anne; Cambon-bonavita, Marie-anne.
Next-generation sequencing (NGS) opens up exciting possibilities for improving our knowledge of environmental microbial diversity, allowing rapid and cost-effective identification of both cultivated and uncultivated microorganisms. However, library preparation, sequencing, and analysis of the results can provide inaccurate representations of the studied community compositions. Therefore, all these steps need to be taken into account carefully. Here we evaluated the effects of DNA extraction methods, targeted 16S rRNA hypervariable regions, and sample origins on the diverse microbes detected by 454 pyrosequencing in marine cold seep and hydrothermal vent sediments. To assign the reads with enough taxonomic precision, we built a database with about 2,500...
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Ano: 2014 URL: http://archimer.ifremer.fr/doc/00204/31495/29907.pdf
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