title: Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA.
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.
authors.affiliation: Center For Microbial Ecology, Michigan State University,East Lansing, MI 48824-1325,USA.
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Center For Microbial Ecology, Michigan State University,East Lansing, MI 48824-1325,USA.
authors.forename: Mary Ellen
authors.initials: ME
authors.lastname: Davey
authors.affiliation: Center For Microbial Ecology, Michigan State University,East Lansing, MI 48824-1325,USA.
authors.forename: Jordi B
authors.initials: JB
authors.lastname: Figueras
authors.affiliation: Institute of Soil Sciences and Photosynthesis, Russia Academy of Science,Pushchino,Russia.
authors.forename: Elizaveta
authors.initials: E
authors.lastname: Rivkina
authors.affiliation: Institute of Soil Sciences and Photosynthesis, Russia Academy of Science,Pushchino,Russia.
authors.forename: David
authors.initials: D
authors.lastname: Gilichinsky
authors.affiliation: Center For Microbial Ecology, Michigan State University,East Lansing, MI 48824-1325,USA.
authors.forename: James M
authors.initials: JM
authors.lastname: Tiedje
mesh_terms: D001110:Arctic Regions; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D001483:Base Sequence; D003001:Cloning, Molecular; D003081:Cold Climate; D017931:DNA Primers; D004275:DNA, Ribosomal / Q000235:genetics; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D012329:RNA, Bacterial / Q000235:genetics; D012800:Siberia; D012988:Soil Microbiology
chemical_list: D017931:DNA Primers; D004275:DNA, Ribosomal; D012329:RNA, Bacterial