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

Environmental microbiology ·Vol. 4 ·No. 5 ·2002-05-00 ·Pages 277-86

Inagaki F, Sakihama Y, Inoue A, Kato C, Horikoshi K

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.

MeSH Terms

Base Sequence DNA, Bacterial/chemistry,genetics DNA, Complementary/chemistry,genetics Geologic Sediments/microbiology Molecular Sequence Data Pacific Ocean Phylogeny Polymerase Chain Reaction Polymorphism, Restriction Fragment Length Proteobacteria/chemistry,classification,genetics RNA, Ribosomal/chemistry,genetics Reverse Transcriptase Polymerase Chain Reaction Sequence Analysis, DNA

Chemicals

DNA, Bacterial DNA, Complementary RNA, Ribosomal

Authors & Affiliations

5 authors, click to expand affiliations / ORCID

Inagaki Fumio

Subground Animalcule Retrieval (SUGAR) Project, Japan Marine Science and Technology Center (JAMSTEC), Yokosuka 237-0061, Japan. [email protected]

Sakihama Yuri

Inoue Akira

Kato Chiaki

Horikoshi Koki

Article Info

Journal

Environmental microbiology

Abbr.

Environ Microbiol

ISSN

1462-2912

DOI

10.1046/j.1462-2920.2002.00294.x

[email protected]

Published

2002-05-00

Pages

277-86

Language

English

Region

England

NLM ID

100883692

Subset

Databases

GENBANK

AB069782, AB069783, AB069784, AB069785, AB069786, AB069787, AB069788, AB069789, AB069790, AB069791, AB069792, AB069793, AB069794, AB069795, AB069796, AB069797, AB069798, AB069799, AB069800, AB069801, AB069802, AB069803, AB069804, AB069805, AB069806, AB069807, AB069808, AB069809

External Links

PubMed source DOI: 10.1046/j.1462-2920.2002.00294.x View journal details

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

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