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.

Isolation and Characterization of Bacteria from Ancient Siberian Permafrost Sediment

“…In Siberian permafrost samples, they represented 1%–30% of viable isolates [67] or were not at all detected [68]. This was also the case in our study.…”

“…Firmicutes and Actinobacteria generally represent a high proportion of the bacterial permafrost community and accounted for 45% of Siberian isolates [67]; Arthrobacter ( Actinobacteria ) and Planococcus ( Firmicutes ) accounted for 85% of cultured isolates from a northeast Siberian permafrost sample [68]. In our study, the majority of the identified bacterial isolates could be attributed to Actinobacteria : Arthrobacter phenanthrenivorans , previously isolated from creosote oil-polluted soil [69], and Subtercola frigoramans , so far only found in cold groundwater [70].…”

“…The high percentage of high G + C Gram-positive, non-spore-forming bacteria (such as Actinobacteria ) among ancient permafrost isolates has been attributed to their adaptation to frozen environments, to their metabolic activity at low temperatures, to their ability to form dormant cells, to their efficient DNA repair mechanisms, and to the fact that they are more easily cultured [3,66,68]. In contrast, the dominance of spore-forming bacterial genera in Canadian permafrost was attributed to the ability of this microbial group to survive as spores rather than vegetative cells [63].…”

Ancient permafrost staphylococci carry antibiotic resistance genes

“…The bacteria also included Actinomycetales (Arthrobacter and Microbacteriaceae), followed by Firmicutes ( Exiguobacterium and Planomicrobium ), Bacteroidetes ( Flavobacterium ), Gammaproteobacteria ( Psychrobacter ), and Alphaproteobacteria ( Sphingomonas ). Both culture and culture-independent approaches showed the presence of high and low guanine and cytosine (G+C)-content Gram-positive bacteria and Gammaproteobacteria [15,39]. …”

Isolation and phylogenetic classification of culturable psychrophilic prokaryotes from the Collins glacier in the Antarctica

“…Extreme environments are often rich in microorganisms with high potential to be used in biotechnological applications. For instance, psychrophilic microorganisms as source of cold-active enzymes have received considerable research attention (Garcia-Echauri et al 2009;Hinsa-Leasure et al 2010). Although major advances have been made in the last decade, our knowledge on the microbial ecology, their interactions, physiology, metabolism, enzymology, and genetics in this fascinating microbial group of extremophilic microorganisms is still limited.…”