Ecology, Physiology and Metabolism of Cold-adapted Microorganisms from the Siberian Permafrost
"In our solar system, seven out of nine planets, including Earth, are considered to be cold. Even though cold temperatures are lethal to many microorganisms, some successfully colonize cold habitats. I studied the distribution, abundance and diversity of two cold-adapted genera, Exiguobacterium and Psychrobacter. Total microbial community DNA extracted from 54 sediment and soil samples from Siberia, Antarctica, Michigan, Iowa, Brazil, Puerto Rico and Hawaii was analyzed with specific primer sets for each genus by quantitative real-time PCR and by 16S rRNA gene clone libraries. Both genera were more commonly found and have higher densities in polar regions, but they were also detected in some temperate and tropical sites. The later was more likely the case when physicochemical conditions such as salinity, K and pH were similar to their polar habitat conditions. Exiguobacterium isolates obtained from the Siberian permafrost were analyzed using a polyphasic approach, and yielded a new species, Exiguobacterium sibiricum. The genome of the type strain of the new E. sibiricum species was sequenced by the DOE Joint Genome Institute. The genome is approximately 3 Mb in size, has a GC content of 47.7% and includes 2,978 putative protein-encoding genes (CDS). I used the genome and transcriptome analysis along with the organism's known physiology to better understand its thermal adaptation. A total of about 27%, 3.2% and 5.2% of E. sibiricum strain 255-15 DS spotted on the DNA microarray yielded differentially expressed genes in cells grown at -2.5°C, 10°C and 39°C, respectively, when compared to cells grown at 28°C. The hypothetical and unknown genes represented 10.6%, 0.89% and 2.3% of the CDS differentially expressed when grown at -2.5°C 10°C and 39°C versus 28°C. The transcriptome analyses showed that E. sibiricum is constitutively adapted to cold temperatures since little differential gene expression was observed at growth temperatures of 0°C and 28°C, but at the extremities of its Arrhenius growth profile, namely -2.5°C and 39°C, much more differential gene expression occurred. The genes that responded were more typically associated with stress response. I showed that Exiguobacterium and Psychrobacter are more prevalent in but not restricted to cold, polar environments, and that this ecology is consistent with the Exiguobacterium's transcriptional response, i.e., little differential gene expression between 10°C and 28°C."--Leaves [iii-iv]