Summary: A pluri‐disciplinary in situ colonization experiment was performed to study early stages of colonization in deep‐sea vent Alvinella spp. worm habitats. Four colonization devices were deployed onto Alvinella spp. colonies of different chimneys of the East‐Pacific Rise (EPR 13°N), for two different periods: a short (less than a week) and a longer one (3 weeks). Video imagery and monitoring of the thermal and physico‐chemical conditions were performed during the colonization experiments. Numerous microorganisms bearing specialized adhesion‐appendages and/or high amounts of polymeric extracellular matrix were observed on devices, which may efficiently contribute to the colonization of new surfaces. The microbial cohorts preceding and accompanying Alvinella spp. settlement were identified. In all cases, Archaea could not be detected and the microbial mats were essentially composed of e‐ Proteobacteria . Within this group, one phylotype ( Alvi H2) was found to dominate the libraries of three colonization devices. Dominance of e‐ Proteobacteria in the libraries may reflect the wide physiological variety encountered within this group or an adaptability of these microorganisms towards their changing environment. Bacteria affiliated to the Cytophaga‐Flavobacterium‐Bacteroides group or to the e‐ Proteobacteria , that grow either chemo‐organoheterotrophically by fermentation or chemolithoautotrophically with H ₂ as an electron donor and S°/S ₂ O ₃ ^2– or NO ₃ ^– as a terminal electron acceptor, were isolated from one of the microbial mat formed in 20 days.

The subsurface realm is colonized by microbial communities to depths of >1000 meters below the seafloor (m.b.sf.), but little is known about overall diversity and microbial distribution patterns at the most profound depths. Here we show that not only Bacteria and Archaea but also Eukarya occur at record depths in the subseafloor of the Canterbury Basin. Shifts in microbial community composition along a core of nearly 2 km reflect vertical taxa zonation influenced by sediment depth. Representatives of some microbial taxa were also cultivated using methods mimicking in situ conditions. These results suggest that diverse microorganisms persist down to 1922 m.b.sf. in the seafloor of the Canterbury Basin and extend the previously known depth limits of microbial evidence (i) from 159 to 1740 m.b.sf. for Eukarya and (ii) from 518 to 1922 m.b.sf. for Bacteria.

A novel sulfate-reducing bacterium, strain J2T, was isolated from a serpentinized peridotite sample from the Indian Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J2T clustered with the genus Desulfovibrio within the family Desulfovibrionaceae, but it showed low similarity (87.95%) to the type species Desulfovibrio desulfuricans DSM 642T. It was most closely related to D. portus MSL79T (96.96%), followed by D. aespoeensis Aspo-2T (96.11 %), D. piezophilus C1TLV30T (96.04 %) and D. profundus DSM11384T (95.17%). Other available sequences shared less than 93.33% 16S rRNA gene sequence similarity. Growth was observed at salinities ranging from 0.2 to 6% (optimum 2.5%), from pH 5 to 8 (optimum 6.5-7), and at temperatures between 9 and 40 °C (optimum 30-35 °C). Strain J2T used lactate, malate, pyruvate, formate and hydrogen as energy sources. Sulfate, thiosulfate, sulfite, fumarate, and nitrate were used as terminal electron acceptors. The main fatty acids were iso-C15:0, anteiso-C15:0, summed feature 9 (iso-C17:1ω9c and/or C16:0 10-methyl) and iso-C17:0. The DNA G+C content of strain J2T was 63.5 mol%. The combined genotypic and phenotypic data show that strain J2T 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 J2T (=MCCC 1A01867T = DSM 101483T). We also propose the reclassification of D. piezophilus as Pseudodesulfovibrio piezophilus comb. nov., D. profundus as P. profundus comb. nov., D. portus as P. portus comb. nov. and D. aespoeensis as P. aespoeensis comb. nov.