Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach

Abstract

Background: Many microorganisms have a wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments, however not many have been fully explored over their entire growth temperature range through a holistic view of its physiology, genome, and transcriptome. We used Exiguobacterium sibiricum strain 255-15, a psychrotrophic bacterium from 3 million year old Siberian permafrost that grows from -5 degrees C to 39 degrees C to study its thermal adaptation.

Results: The E. sibiricum genome has one chromosome and two small plasmids with a total of 3,015 protein-encoding genes (CDS), and a GC content of 47.7%. The genome and transcriptome analysis along with the organism's known physiology was used to better understand its thermal adaptation. A total of 27%, 3.2%, and 5.2% of E. sibiricum CDS spotted on the DNA microarray detected differentially expressed genes in cells grown at -2.5 degrees C, 10 degrees C, and 39 degrees C, respectively, when compared to cells grown at 28 degrees C. The hypothetical and unknown genes represented 10.6%, 0.89%, and 2.3% of the CDS differentially expressed when grown at -2.5 degrees C, 10 degrees C, and 39 degrees C versus 28 degrees C, respectively.

Conclusion: The results show that E. sibiricum is constitutively adapted to cold temperatures stressful to mesophiles since little differential gene expression was observed between 4 degrees C and 28 degrees C, but at the extremities of its Arrhenius growth profile, namely -2.5 degrees C and 39 degrees C, several physiological and metabolic adaptations associated with stress responses were observed.

Figure 1

Metabolic pathway reconstruction of Exiguobacterium sibiricum 255-15 based on genome content.

Figure 2

Negatively stained electron micrograph of E. sibiricum strain 255-15 grown at -2.5°C. Exopolysaccharide and no flagella are observed.

Figure 3

Arrhenius plot of E. sibiricum 255-15 growth rates in 1/2 TSB. The first phase of the biphasic response is in gray and the second phase is in black, each with its respective trend lines and R² values.

Figure 4

Comprehensive schematic thermal adaptation of E. sibiricum strain 255-15 gene expression results at its extreme growth temperatures. The left part of the figure summarizes the gene expression results of E. sibiricum grown at -2.5°C, when compared to 28°C, 10°C, and 39°C; and the right side does the same for E. sibiricum grown at 39°C compared to the other temperatures.

Figure 5

Venn diagram of all differentially expressed genes at the indicated temperatures.

Figure 6

Classification of all genes differentially expressed at the indicated temperatures based on COGs categories.

Figure 7

Secondary structure prediction of two alpha-amylases (Exig_1739 and Exig_2537). E = extended strand and H = alpha-helix.

Figure 8

Negatively stained electron micrograph of E. sibiricum strain 255-15 grown at 10°C. Flagella are observed.