title: Characterization of a bacterial community from a Northeast Siberian seacoast permafrost sample.
abstract: A combination of culture-dependent and -independent techniques was used to characterize a bacterial community, examine cold adaptation of isocitrate lyase (icl) genes, and detect genes with important ecological functions in a permafrost sample from the Bykovsky Peninsula on the Laptev Sea coast of northeast Siberia. According to the 16S rRNA gene sequence, 47 of the cultured isolates were members of the phyla Firmicutes, Proteobacteria, and Actinobacteria, with 85% of the isolates belonging to the genera Arthrobacter and Planococcus. The 16S rRNA gene clone library derived from DNA from the same permafrost sample contained sequences from the same phyla plus a few from Acidobacteria, but favored the Firmicutes at the cost of the Actinobacteria. A partial sequence of the icl gene, a proposed marker for cold adaptation, was determined for 25 isolates that grew at 0 °C. Two Psychrobacter isolates contained two of the four residues shown to be important for low-temperature activity in Colwellia maris or Colwellia psychrerythreaea. The presence in the permafrost DNA of genes with ecosystem functions was determined using geochip 2.0. The highest number of genes identified was from the categories of aromatic and natural polymer degradation genes, perhaps reflecting selection for the use of tundra vegetation-produced carbon.
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA. hinsa@grinnell.edu
authors.forename: Shannon M
authors.initials: SM
authors.lastname: Hinsa-Leasure
authors.forename: Laya
authors.initials: L
authors.lastname: Bhavaraju
authors.forename: Jorge L M
authors.initials: JL
authors.lastname: Rodrigues
authors.forename: Corien
authors.initials: C
authors.lastname: Bakermans
authors.forename: David A
authors.initials: DA
authors.lastname: Gilichinsky
authors.forename: James M
authors.initials: JM
authors.lastname: Tiedje
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000145:classification* / Q000201:enzymology / Q000235:genetics / Q000302:isolation & purification; D003080:Cold Temperature; D004269:DNA, Bacterial / Q000235:genetics; D017753:Ecosystem; D015723:Gene Library; D005798:Genes, Bacterial; D007053:Ice; D007522:Isocitrate Lyase / Q000235:genetics; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012800:Siberia; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial; D007053:Ice; D012336:RNA, Ribosomal, 16S; D007522:Isocitrate Lyase