Bacterial Community in Ancient Siberian Permafrost as Characterized by Culture and Culture-Independent Methods

Abstract

The microbial composition of ancient permafrost sediments from the Kolyma lowland of Northeast Eurasia was examined through culture and culture-independent approaches. These sediments have been continuously frozen for 5,000 to 2-3 million years. A total of 265 Bacteria 16S rRNA gene sequences were amplified from the permafrost total-community genomic DNA and screened by amplified ribosomal 16S rRNA restriction analysis. Members of three major lineages were found: gamma-Proteobacteria (mostly Xanthomonadaceae), Actinobacteria, and Firmicutes. We also determined partial 16S rRNA gene sequences of 49 isolates from a collection of 462 aerobes isolated from these sediments. The bacteria included Actinomycetales (Arthrobacter and Microbacteriaceae); followed by the Firmicutes (Exiguobacterium and Planomicrobium); the Bacteroidetes (Flavobacterium); the gamma-Proteobacteria (Psychrobacter); and the alpha-Proteobacteria (Sphingomonas). Both culture and culture-independent approaches showed the presence of high and low G+C Gram-positive bacteria and gamma-Proteobacteria. Some of the 16S rRNA gene sequences of environmental clones matched those of Arthrobacter isolates. Two-thirds of the isolates grew at -2.5 degrees C, indicating that they are psychroactive, and all are closely related to phylogenetic groups with strains from other cold environments, mostly commonly from Antarctica. The culturable and non-culturable microorganisms found in the terrestrial permafrost provide a prototype for possible life on the cryogenic planets of the Solar System.

The role of terrestrially derived organic carbon in the coastal ocean: A changing paradigm and the priming effect

“…Similarly, functional exoenzymes of metabolically active bacteria have been found in 124,000-y-old sapropel of the eastern Mediterranean (104). Viable bacteria have also been found in some of the oldest permafrost layers in the Northern hemisphere (105). In addition to the "power" of the ever-evolving enzyme capability of microbial communities, there are physical gradients (e.g., photochemical examples mentioned previously) that also control the availability of "labile" and "recalcitrant" OC substrates.…”

Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria

“…A potential bacterial rhodopsin gene was also identified in the genome of a Grampositive bacterium Exiguobacterium sibiricum, isolated from Siberian permafrost soil (6). This extreme environment contains a unique microbial community adapted to long-term freezing, cumulative radiation, and high-water osmolarity (7,8). E. sibiricum, one of the Gram-positive microorganisms widely present in permafrost samples, can withstand a wide range of growth conditions, including the temperature from −5°C to 40°C (9).…”

Earth as a Tool for Astrobiology—A European Perspective

“…The Artic permafrost has also a high content of microorganisms (Jakosky et al 2003;Gilichinsky et al 2003;Rivkina et al 2000;Vorobyova et al 1997;Vishnivetskaya et al 2006), making both environments good analogues for the icy Moons Europa, Enceladus and Ganymede. The Arctic ice may also be used as an analogue of Mars due to the observation by the Phoenix Lander of the water ice-Martian surface interface (Smith 2009;), the low water activity and limited organic content (Deming 2002;Vishnivetskaya et al 2006).…”