Molecular phylogenetic analyses of reverse‐transcribed bacterial rRNA obtained from deep‐sea cold seep sediments

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Abstract
A depth profile of naturally occurring bacterial community structures associated with the deep‐sea cold seep push‐core sediment in the Japan Trench at a depth of 5343 m were evaluated using molecular phylogenetic analyses of RNA reverse transcription‐PCR (RT‐PCR) amplified 16S crDNA fragments. A total of 137 clones of bacterial crDNA (complimentary rDNA) phylotypes (phylogenetic types) obtained at three different depths (2–4, 8–10 and 14–16 cm) were identified in partial crDNA sequencings. crDNA phylotypes from the cold seep sediment were dominantly composed of δ‐ and ɛ‐Proteobacteria (36% and 42% respectively). Phylotype analysis of crDNA clone libraries and terminal restriction fragment length polymorphism (T‐RFLP) analysis revealed that the majority of bacterial components shifted from δ‐ Proteobacteria to ɛ‐Proteobacteria with increasing depth. Among the δ‐proteobacterial crDNA clones, the sequences related to the genus Desulfosarcina were dominant. Almost all sequences of crDNA belonging to ɛ‐Proteobacteria were affiliated with the same cluster (ɛ‐CSG: ɛ‐proteobacterial cold seep group), and were closely related with rDNA sequences from deep‐sea hydrothermal vent environments.