Marine culturable yeasts in deep-sea hydrothermal vents: species richness and association with fauna

The definitive version is available at ww3.interscience.wiley.com. Post-print en libre-accès sur Archimer : http://archimer.ifremer.fr/doc/00006/11704/8475.pdfInternational audienceInvestigations of the diversity of culturable yeasts at deep-sea hydrothermal sites have suggested possible interactions with endemic fauna. Samples were collected during various oceanographic cruises at the Mid-Atlantic Ridge, South Pacific Basins and East Pacific Rise. Cultures of 32 isolates, mostly associated with animals, were collected. Phylogenetic analyses of 26S rRNA gene sequences revealed that the yeasts belonged to Ascomycota and Basidiomycota phyla, with the identification of several genera: Rhodotorula, Rhodosporidium, Candida, Debaryomyces and Cryptococcus. Those genera are usually isolated from deep-sea environments. To our knowledge, this is the first report of yeasts associated with deep-sea hydrothermal animals

A Nematode of the Mid-Atlantic Ridge Hydrothermal Vents Harbors a Possible Symbiotic Relationship

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

Archaeal Methane Cycling Communities Associated with Gassy Subsurface Sediments of Marennes-Oléron Bay (France)

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2009/publication-6165.pdfInternational audienceIn Marennes-Oleacuteron Bay, a macro-tidal bay located on the French Atlantic coast, kilometer-scale acoustic turbidity reveals an accumulation of free gas in the sediment. Large concentrations of organic matter and rapid sedimentation rates provide ideal settings for biogenic methane cycling. We integrate seismic, sedimentologic, biogeochemical and molecular genetic approaches to determine whether microbial methane cycling is involved in this process. Here we show that the acoustic turbidity upper boundary matched with X-ray facies displaying fissures with the highest methane concentrations, demonstrating the existence of methane bubbles in the sediment. 16S rRNA and mcrA gene clone libraries were dominated by sequences affiliated to the three known ANME lineages and to putative methanogens. Sequences related to the marine benthic group B (MBG-B) and miscellaneous crenarchaeotal group (MCG) were also detected. However, the highest methane concentration facies was the only section where active Archaea were detected, using reverse-transcribed rRNA, indicating that these communities were involved either directly or indirectly in the methane cycling process. Moreover, three metabolically active novel uncultivated lineages, related to putative methane cycling Archaea, could be specifically associated to these methane bearing sediments. As methane cycling Archaea are commonly retrieved from deep subseafloor and methane seep sediment, the study of coastal gassy sediments, could therefore help to define the biogeochemical habitats of deep biosphere communities

Microbial diversity associated with the hydrothermal shrimp Rimicaris exoculata gut and occurrence of a resident microbial community

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/00000/11142/7919.pdfInternational audienceRimicaris exoculata dominates the megafauna of several Mid-Atlantic Ridge hydrothermal sites. Its gut is full of sulphides and iron-oxide particles and harbours microbial communities. Although a trophic symbiosis has been suggested, their role remains unclear. In vivo starvation experiments in pressurized vessels were performed on shrimps from Rainbow and Trans-Atlantic Geotraverse sites in order to expel the transient gut contents. Microbial communities associated with the gut of starved and reference shrimps were compared using 16S rRNA gene libraries and microscopic observations (light, transmission and scanning electron microscopy and FISH analyses). We show that the gut microbiota of shrimps from both sites included mainly Deferribacteres, Mollicutes, Epsilon- and Gammaproteobacteria. For the first time, we have observed filamentous bacteria, inserted between microvilli of gut epithelial cells. They remained after starvation periods in empty guts, suggesting the occurrence of a resident microbial community. The bacterial community composition was the same regardless of the site, except for Gammaproteobacteria retrieved only in Rainbow specimens. We observed a shift in the composition of the microbiota of long-starved specimens, from the dominance of Deferribacteres to the dominance of Gammaproteobacteria. These results reinforce the hypothesis of a symbiotic relationship between R. exoculata and its gut epibionts

Nautilia abyssi sp. nov., a thermophilic, chemolithoautotrophic, sulfur-reducing bacterium isolated from an East Pacific Rise hydrothermal vent

This is an author manuscript that has been accepted for publication in International Journal of Systematic and Evolutionary Microbiology, copyright Society for General Microbiology, but has not been copy-edited, formatted or proofed. Cite this article as appearing in International Journal of Systematic and Evolutionary Microbiology. This version of the manuscript may not be duplicated or reproduced, other than for personal use or within the rule of 'Fair Use of Copyrighted Materials' (section 17, Title 17, US Code), without permission from the copyright owner, Society for General Microbiology. The Society for General Microbiology disclaims any responsibility or liability for errors or omissions in this version of the manuscript or in any version derived from it by any other parties. The final copy-edited, published article, which is the version of record, can be found at http://mic.sgmjournals.org, and is freely available without a subscription.International audienceA novel strictly anaerobic, thermophilic, sulfur-reducing bacterium, designated PH1209(T), was isolated from an East Pacific Rise hydrothermal vent (1 degrees N) sample and studied using a polyphasic taxonomic approach. Cells were Gram-negative, motile rods (approx. 1.60 x 0.40 microm) with a single polar flagellum. Strain PH1209(T) grew at temperatures between 33 and 65 degrees C (optimum 60 degrees C), from pH 5.0 to 8.0 (optimum 6.0-6.5), and between 2 and 4 % (w/v) NaCl (optimum 3 %). Cells grew chemolithoautotrophically with H(2) as an energy source, S(0) as an electron acceptor and CO(2) as a carbon source. Strain PH1209(T) was also able to use peptone and yeast extract as carbon sources. The G+C content of the genomic DNA was 35 mol%. Phylogenetic analyses based on 16S rRNA gene sequencing showed that strain PH1209(T) fell within the order Nautiliales, in the class Epsilonproteobacteria. Comparative 16S rRNA gene sequence analysis indicated that strain PH1209(T) belonged to the genus Nautilia and shared 97.2 and 98.7 % 16S rRNA gene sequence identity, respectively, with the type strains of Nautilia lithotrophica and Nautilia profundicola. It is proposed, from the polyphasic evidence, that the strain represents a novel species, Nautilia abyssi sp. nov.; the type strain is PH1209(T) (=DSM 21157(T)=JCM 15390(T))

Extending the sub-sea-floor biosphere

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2008/publication-4209.pdfInternational audienceSub-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 degrees 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 degrees to 100 degrees C). Sequences of anaerobic methane-oxidizing Archaea were also present, suggesting a deep biosphere partly supported by methane. These findings demonstrate that the sub-sea-floor biosphere extends to at least 1600 meters below the sea floor and probably deeper, given an upper temperature limit for prokaryotic life of at least 113 degrees C and increasing thermogenic energy supply with depth

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

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

Étude de la diversité des peuplements épibiontes associés au tractus digestif de la crevette hydrothermale Rimicaris exoculata (une possible association mutualiste)

Dans les écosystèmes hydrothermaux profonds, la chimiosynthèse microbienne est à la base des réseaux trophiques. Les symbioses entre des invertébrés et des micro-organismes sont fréquentes et peuvent être de différente nature et jouer différents rôles. La crevette Rimicaris exoculata est une espèce endémique des sites hydrothermaux de la Ride medio-Atlantique (MAR) et représente l espèce majoritaire de la macrofaune de certains d entre eux. Elle présente deux zones de colonisation microbienne, au niveau du céphalothorax et du tube digestif, mais leur rôle n est pas encore établi. Ce travail a mis en évidence par approche moléculaire la présence de différentes communautés microbiennes dont une partie serait résidente, spécifique à R. exoculata et représentée par des Deferribacteres, des Mollicutes et des Epsilonproteobacteria. Les approches microscopiques montrent la dominance d épibiontes filamenteux étroitement associés à l épithélium intestinal dont la croissance et l installation semblent être contrôlées par l hôte. Les approches moléculaires ont montré que: (1) les épibiontes du site hydrothermal Rainbow présentent une originalité taxinomique supposant une histoire évolutive ancienne tandis que les sites hydrothermaux Logatche et Ashadzé semblent avoir été colonisés plus récemment, (2) les épibiontes, non retrouvés dans le milieux extérieur et monophylétiques le long de la MAR pourraient être transmis verticalement et (3) il s agirait d une association mutualiste à caractère obligatoire. Ce travail de recherche a donc permis de poser les bases dans la compréhension du modèle symbiotique digestif R. exoculata.In the deep-sea hydrothermal vents ecosystems, the driving energy comes from the microbial chemosynthesis. Symbioses between invertebrates and micro-organisms are common. They could be associations such as parasitism, commensalism or mutualism or even obligate symbioses and they could play distinct roles. The caridean shrimp Rimicaris exoculata is an endemic species of the Mid-Atlantic Ridge (MAR) hydrothermal sites. It is the main specie of the megafauna of some MAR sites. This crustacean harbors two microbial colonization regions, in the gill chamber and in the gut, but their roles are still unknown. Using various approaches, this work showed that there were distinct microbial communities among which a part would be resident and specific to R. exoculata. This community is composed of Deferribacteres, Mollicutes and Epsilonproteobacteria. The microscopic approaches revealed the dominance of a single filamentous morphotype closely associated with the gut epithelium. Its settlement and growth seemed to be managed by the host. The molecular approaches showed that: (1) the Rainbow site epibionts harbored a phylogenetic particularity suggesting an ancient evolutionnary history whereas the Logatchev and Ashadzé seemed to have been colonized more recently by the association host-epibionts, (2) the epibionts, not retrieved in the surrounding environment and clustering i a monophyletic group along the MAR, could be vertically-transmitted, and (3) the association between R. exoculata and the epibionts could be mutualistic and obligate. So, this research study gave the bases to understand the R. exoculata symbiotic model.BREST-BU Droit-Sciences-Sports (290192103) / SudocPLOUZANE-Bibl.La Pérouse (290195209) / SudocSudocFranceF