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PMID: 9421915 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA.

Microbiology (Reading, England) ·Vol. 143 ( Pt 12) ·1997-12-00 ·Pages 3913-3919

Zhou J, Davey ME, Figueras JB, Rivkina E, Gilichinsky D, Tiedje JM

Abstract

Genomic DNA was isolated from the active layer of tundra soil collected from the Kolyma lowland, Northeast Eurasia, near the Arctic Ocean coast. The SSU (small subunit) rRNA genes were amplified with eubacterial primers from the bulk genomic community DNA and cloned into plasmid vectors. Forty-three SSU rDNA clones were obtained, and all of them had different RFLP patterns. Phylogenetic analysis based on partial sequences (about 300 bp) established with the maximum likelihood method revealed the presence of three major and several minor groups that fell into 11 of the established lines of bacteria, and one sequence that could not be assigned to any of the described groups. Most of the clones belonged to the alpha (20.9%) and delta (25.6%) subdivisions of the Proteobacteria, with lesser proportions in the beta (9.3%) and gamma (4.7%) subdivisions, groups typically isolated from soil by culture methods. Fewer than 12% of the clones belonged to Gram-positive bacteria, and 16% of the clones were related to Fibrobacter. The majority of the clones (70%) had sequences that were 5-15% different from those in the current databases, and 7% of the clones had sequences that differed by more than 20% from those in the database. The results suggest that these tundra-derived clones are very diverse in phylogeny, and that many probably reflect new genera or families. Hence, most of the tundra soil bacterial community has never been isolated and thus the physiology and function of its dominant members appears to be unknown.

MeSH Terms

Arctic Regions Bacteria/classification,genetics,isolation & purification Base Sequence Cloning, Molecular Cold Climate DNA Primers DNA, Ribosomal/genetics Genetic Variation Molecular Sequence Data Phylogeny Polymerase Chain Reaction Polymorphism, Restriction Fragment Length RNA, Bacterial/genetics Siberia Soil Microbiology

Chemicals

DNA Primers DNA, Ribosomal RNA, Bacterial

Authors & Affiliations

6 authors, click to expand affiliations / ORCID

Zhou Jizhong

Center For Microbial Ecology, Michigan State University,East Lansing, MI 48824-1325,USA.

Davey Mary Ellen

Center For Microbial Ecology, Michigan State University,East Lansing, MI 48824-1325,USA.

Figueras Jordi B

Center For Microbial Ecology, Michigan State University,East Lansing, MI 48824-1325,USA.

Rivkina Elizaveta

Institute of Soil Sciences and Photosynthesis, Russia Academy of Science,Pushchino,Russia.

Gilichinsky David

Institute of Soil Sciences and Photosynthesis, Russia Academy of Science,Pushchino,Russia.

Tiedje James M

Center For Microbial Ecology, Michigan State University,East Lansing, MI 48824-1325,USA.

Article Info

Journal

Microbiology (Reading, England)

Abbr.

Microbiology (Reading)

ISSN

1350-0872

DOI

10.1099/00221287-143-12-3913

Published

1997-12-00

Pages

3913-3919

Language

English

Region

England

NLM ID

9430468

Subset

Databases

GENBANK

AF016717, AF016718, AF016719, AF016720, AF016721, AF016722, AF016723, AF016724, AF016725, AF016726, AF016727, AF016728, AF016729, AF016730, AF016731, AF016732, AF016733, AF016734, AF016735, AF016736, AF016737, AF016738, AF016739, AF016740, AF016741, AF016742, AF016743, AF016744, AF016745, AF016746

External Links

PubMed source DOI: 10.1099/00221287-143-12-3913 View journal details

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Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA.

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