Research article

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

Debora F Rodrigues¹ , Natalia Ivanova² , Zhili He³ , Marianne Huebner⁴ , Jizhong Zhou³ and James M Tiedje¹

¹  Michigan State University, NASA Astrobiology Institute and Center for Microbial Ecology, East Lansing, MI 48824, USA

²  DOE Joint Genome Institute, Walnut Creek, CA 94598-1604, USA

³  Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA

⁴  Michigan State University, Department of Statistics and Probability, East Lansing, MI, USA

author email corresponding author email

BMC Genomics 2008, 9:547doi:10.1186/1471-2164-9-547

Published:	18 November 2008

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°C to 39°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°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, 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°C and 28°C, but at the extremities of its Arrhenius growth profile, namely -2.5°C and 39°C, several physiological and metabolic adaptations associated with stress responses were observed.