Patricia Pignet

Vibrio diabolicus sp. nov., a New Polysaccharide-Secreting Organism Isolated from a Deep-sea Hydrothermal Vent Polychaete Annelid, Alvinella pompejana

A deep-sea, facultatively anaerobic, heterotrophic, mesophilic new organism was isolated from the polychaete annelid Alvinella pompejana collected from a deep-sea hydrothermal field in the East Pacific Rise. On the basis of phenotypic characteristics, phylogenetic analyses, and DNA-DNA relatedness, this organism was identified as a new species of the genus Vibrio, for which the name Vibrio diabolicus is proposed. In batch cultures in the presence of glucose, this organism produced an innovative exopolysaccharide. This polymer had high contents of both uronic acids and hexosamines and was similar to other polysaccharides with interesting biological activities.

Caminibacter hydrogeniphilus gen. nov., sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium isolated from an East Pacific Rise hydrothermal vent

A novel thermophilic, anaerobic, hydrogen-oxidizing bacterium, designated strain AM1116T, was isolated from an East Pacific Rise hydrothermal vent sample. The cells were rod-shaped (1.01-5 x 0.5 microm), motile with polar flagella. They grew at temperatures between 50 and 70 degrees C (optimum 60 degrees C; doubling time approximately 1.5 h), at between pH 5.0 and 7.5 (optimum around pH 5.5-6.0) and in between 10 and 40 g NaCl l(-1) (optimum 20-25 g l(-1)). Cells grew chemolithoautotrophically in a H2/CO2 atmosphere (80:20; 200 kPa). Poor heterotrophic growth was observed on complex organic substrates. Elemental sulphur and nitrate served as electron acceptors, respectively yielding hydrogen sulphide and ammonia (doubling times were equal with the two electron acceptors). In contrast, when cystine was used as electron acceptor, growth was poor. The G+C content of the genomic DNA was 29 +/- 1 mol %. Phylogenetic analyses of the 16S rRNA gene located the strain within the epsilon-Proteobacteria, in the bacterial domain. On the basis of 16S rDNA sequence comparisons, physiological and biochemical characteristics, it is proposed that the isolate should be described as the type species of a new genus, Caminibacter gen. nov., as Caminibacter hydrogeniphilus sp. nov. The type strain is strain AM1116T (= DSM 14510T = CIP 107140T).

Alteromonas infernus sp. nov., a new polysaccharide- producing bacterium isolated from a deep-sea hydrothermal vent

A deep‐sea, aerobic, mesophilic and heterotrophic new bacterium was isolated from a sample of fluid collected among a dense population of Riftia pachyptila, in the vicinity of an active hydrothermal vent of the Southern depression of the Guaymas basin (Gulf of California). On the basis of phenotypic and phylogenetic analyses and DNA/DNA relatedness, the strain GY785 was recognized as a new species of the genus Alteromonas and the name of Alteromonas infernus is proposed. During the stationary phase in batch cultures in the presence of glucose, this bacterium secreted two unusual polysaccharides. The water‐soluble exopolysaccharide‐1 produced xrcontained glucose, galactose, galacturonic and glucuronic acids as monosaccharides. The gel‐forming exopolysaccharide‐2 was separated from the bacterial cells by dialysis against distilled water and partially characterized.

Caloranaerobacter azorensis gen. nov., sp. nov., an anaerobic thermophilic bacterium isolated from a deep-sea hydrothermal vent.

A thermophilic, anaerobic, chemo-organotrophic bacterium, designated MV1087T, 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 degrees C, with an optimum around 65 degrees C. No growth was observed at 40 or 70 degrees C. 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 MV1087T was heterotrophic, able to ferment proteinaceous substrates, such as brain/heart infusion and gluten, and carbohydrates, such as glucose, xylan and starch. The DNA G+C content was 27 mol%. Phylogenetic analyses using 16S rDNA sequences indicated that strain MV1087T belonged to cluster XII of the Clostridium subphylum. Due to its phenotypic and genotypic characteristics, isolate MV1087T is proposed as a novel species of a new genus, Caloranaerobacter azorensis gen. nov., sp. nov. The type strain is MV1087T (= CNCM I-2543T = DSM 13643T).

Marinitoga camini gen. nov., sp. nov., a rod-shaped bacterium belonging to the order Thermotogales, isolated from a deep-sea hydrothermal vent

A thermophilic, anaerobic, chemo-organotrophic sulfur-reducing bacterium, designated MV1075T, was isolated from a deep-sea hydrothermal chimney sample collected on the Mid-Atlantic Ridge. Cells were rod-shaped with a sheath-like outer structure, motile with polar flagella and stained Gram-negative. They appeared singly, in pairs or in short chains. The temperature range for growth was 25-65 degrees C, with an optimum at 55 degrees C. Growth was observed from pH 5 to pH 9, and the optimum pH was around 7. The salinity range for growth was 15-70 g sea salt l(-1) (corresponding to 10-45 g NaCl l(-1)), with an optimum at 30 g l(-1) (20 g NaCl l(-1)). The isolate was able to grow on a broad spectrum of carbohydrates or complex proteinaceous substrates. Sulfur was not necessary for growth. Growth was inhibited by H2, but, in presence of sulfur, this inhibition was removed and H2S was produced. The G+C content of the genomic DNA was 29 mol %. Phylogenetic analyses of the 16S rRNA gene located the strain within the order Thermotogales, in the domain Bacteria. On the basis of 16S rDNA sequence comparisons, in combination with morphological and physiological characteristics, it is proposed that the isolate should be described as a novel species of a new genus, Marinitoga gen. nov., of which Marinitoga camini sp. nov. is the type species. The type strain is MV1075T (= CNCM 1-2413T = DSM 13578T).

Caminicella sporogenes gen. nov., sp. nov., a novel thermophilic spore-forming bacterium isolated from an East-Pacific Rise hydrothermal vent

A novel thermophilic, anaerobic, strictly chemoorganoheterotrophic bacterium, designated as AM1114T, was isolated from a deep-sea hydrothermal vent sample from the East-Pacific Rise (EPR 13 degrees N). The cells were long (3-10 microm) 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 degrees C inclusive (optimum 55-60 degrees C; 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 AM1114T was an obligately heterotrophic bacterium able to ferment a mixture of 20 amino acids, complex proteinaceous substrates (such as yeast extract, brain-heart infusion or peptone), and carbohydrates such as glucose, galactose or maltose. The main fermentation products on glucose/yeast extract/peptone/sulfur medium were hydrogen, carbon dioxide, butyrate, ethanol, acetate, formate and L-alanine. The G+C content of the genomic DNA (determined by thermal denaturation) was 24.2+/-1 mol%. Phylogenetic analyses of the 16S rRNA gene located the strain within cluster XI of the lineage encompassing the genus Clostridium and related genera (sensu Collins et al., 1994), in the bacterial domain. On the basis of 16S rDNA sequence comparisons and physiological and biochemical characteristics, it is proposed that the isolate should be described as a novel genus, namely Caminicella gen. nov., of which Caminicella sporogenes sp. nov. is the type species. The type strain is AM1114T (= DSM 14501T = CIP 107141T).

Archaeal and anaerobic methane oxidizer communities in the Sonora Margin cold seeps, Guaymas Basin (Gulf of California)

Cold seeps, located along the Sonora Margin transform fault in the Guaymas Basin, were extensively explored during the ‘BIG’ cruise in June 2010. They present a seafloor mosaic pattern consisting of different faunal assemblages and microbial mats. To investigate this mostly unknown cold and hydrocarbon-rich environment, geochemical and microbiological surveys of the sediments underlying two microbial mats and a surrounding macrofaunal habitat were analyzed in detail. The geochemical measurements suggest biogenic methane production and local advective sulfate-rich fluxes in the sediments. The distributions of archaeal communities, particularly those involved in the methane cycle, were investigated at different depths (surface to 18 cm below the sea floor (cmbsf)) using complementary molecular approaches, such as Automated method of Ribosomal Intergenic Spacer Analysis (ARISA), 16S rRNA libraries, fluorescence in situ hybridization and quantitative polymerase chain reaction with new specific primer sets targeting methanogenic and anaerobic methanotrophic lineages. Molecular results indicate that metabolically active archaeal communities were dominated by known clades of anaerobic methane oxidizers (archaeal anaerobic methanotroph (ANME)-1, -2 and -3), including a novel ‘ANME-2c Sonora’ lineage. ANME-2c were found to be dominant, metabolically active and physically associated with syntrophic Bacteria in sulfate-rich shallow sediment layers. In contrast, ANME-1 were more prevalent in the deepest sediment samples and presented a versatile behavior in terms of syntrophic association, depending on the sulfate concentration. ANME-3 were concentrated in small aggregates without bacterial partners in a restricted sediment horizon below the first centimetres. These niche specificities and syntrophic behaviors, depending on biological surface assemblages and environmental availability of electron donors, acceptors and carbon substrates, suggest that ANME could support alternative metabolic pathways than syntrophic anaerobic oxidation of methane.

Microbial communities associated with benthic faunal assemblages at cold seep sediments of the Sonora Margin, Guaymas Basin

The Sonora Margin cold seeps present a seafloor mosaic pattern consisting of different faunal assemblages and microbial mats. To better understand if sedimentary microbial communities reflect this patchy distribution, all major habitats were investigated using four complementary approaches: 16S rRNA 454 pyrosequencing, quantitative polymerase chain reaction, fluorescence in situ hybridization and geochemistry analyses. This study reveals that sediments populated by different surface assemblages show distinct porewater geochemistry features and are associated with distinct microbial communities. In the sediments underlying the microbial mat and the surrounding macrofauna, microbial communities were dominated by anaerobic methane oxidizers (archaeal anaerobic methanotroph ANME) and sulfate-reducing Deltaproteobacteria. In contrast, sediment-associated microbial communities underlying the megafauna habitats (vesicomyids and siboglinids) were characterized by a lower biomass and important proportions of the Marine Benthic Group D (MBG-D), Chloroflexi as well as filamentous Gammaproteobacteria and Deltaproteobacteria. Together, geochemical and microbial surveys indicate that porewater methane concentrations play an important role in the microbial community structure and subsequently in the establishment of the surface colonizers. Furthermore, presence and activity of the surface colonizers influence the underlying microbial communities probably because of modification of energy source availabilities.

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

SUMMARY 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.

Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments.