title: Molecular phylogenetic analyses of reverse-transcribed bacterial rRNA obtained from deep-sea cold seep sediments.
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 delta- and epsilon-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 delta- Proteobacteria to epsilon-Proteobacteria with increasing depth. Among the delta-proteobacterial crDNA clones, the sequences related to the genus Desulfosarcina were dominant. Almost all sequences of crDNA belonging to epsilon-Proteobacteria were affiliated with the same cluster (epsilon-CSG: epsilon-proteobacterial cold seep group), and were closely related with rDNA sequences from deep-sea hydrothermal vent environments.
authors.affiliation: Subground Animalcule Retrieval (SUGAR) Project, Japan Marine Science and Technology Center (JAMSTEC), Yokosuka 237-0061, Japan. inagaki@jamstec.go.jp
authors.forename: Fumio
authors.initials: F
authors.lastname: Inagaki
authors.forename: Yuri
authors.initials: Y
authors.lastname: Sakihama
authors.forename: Akira
authors.initials: A
authors.lastname: Inoue
authors.forename: Chiaki
authors.initials: C
authors.lastname: Kato
authors.forename: Koki
authors.initials: K
authors.lastname: Horikoshi
mesh_terms: D001483:Base Sequence; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D019015:Geologic Sediments / Q000382:microbiology*; D008969:Molecular Sequence Data; D010140:Pacific Ocean; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D020560:Proteobacteria / Q000737:chemistry / Q000145:classification* / Q000235:genetics; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D018076:DNA, Complementary; D012335:RNA, Ribosomal