The sequencing and analysis of whole genomes (genomics) is a powerful tool that is being applied to many microorganisms in order to identify the distinguishing molecular features and gene content of those microorganisms. Genomic analyses allow the detection of trends that may only be apparent at the genome level rather than at the level of individual genes, due to differences resulting from genetic drift. For example, biases in amino acid abundance of the genomes of hyperthermophiles have been reported, and reflect adaptations to living at high temperatures (Singer and Hickey 2003). In addition, examination of gene content has been used to better understand the metabolic capabilities of the smallest microorganisms such as Mycoplasma geni-talium and Chlamydia (Fraser et al. 1995; Read et al. 2000). Similarly, genomics can be used to investigate cold adaptation of psychrophiles at the molecular level by analyzing amino acid composition, codon usage, and nucleotide content, and at the level of genes by examining gene content and other unique features.
To date, only ten cold-adapted microorganisms have been completely sequenced (see Table 11.1), accounting for a mere 2.5% of all microbial genomes sequenced (10 of 398). All of these cold-adapted organisms have been isolated from polar regions and have provided valuable information about cold adaptation. Comparative studies of cold adaptations in these organisms should reveal which adaptations are common to all psychrophiles and which are specific to the particular environment each psychrophile inhabits, or to the particular family of organisms they represent. The majority of these cold-adapted microorganisms have been isolated from low-temperature marine environments (water, ice, or sediment) which are distinctly different from low-temperature terrestrial environments such as permafrost. Marine environments have high solute concentrations, while terrestrial environments do not. Hence, when sea water freezes, fairly large channels of brine can be found
Department of Earth Sciences, Montana State University, P.O. Box 173480, Bozeman, MT
R. Margesin (ed.) Permafrost Soils, Soil Biology 16,
DOI: 10.1007/978-3-540-69371-0, © Springer-Verlag Berlin Heidelberg 2009
Table 11.1 Psychrophilic microorganisms whose genomes have been sequenced
Colwellia psychrerythraea Desulfotalea psychrophila Methanococcoides burtonii,
Methanogenium frigidum Polaribacter filamentus Polaribacter irgensii Pseudoalteromonas haloplanktis
TAC125 Psychrobacter arcticus 273-4,
Psychrobacter cryohalolentis K5
Arctic sea ice
Arctic marine sediment
Ace Lake, Antarctica (salinity close to sea water) Arctic surface sea water Antarctic sea water Antarctic sea water
Arctic sea ice
Methe et al. (2005) Rabus et al. (2004) Saunders et al. (2003)
Gosink et al. (1998) Gosink et al. (1998) Medigue et al. (2005)
within the ice, while liquid water in permafrost localizes to very thin films, creating a highly constrained physical environment (Rivkina et al. 2000; Bock and Eicken 2005). In addition, Siberian permafrost is a sedimentary system uniquely characterized by passage through an active layer which freezes and thaws on a seasonal basis, and subsequent burial in permanently frozen sediments that experience more stable temperatures. Consequently, genomic analysis of microorganisms isolated from permafrost may reveal unique mechanisms of cold adaptation.
Genomic analysis does not have to stop at the sequence level; complex metabolic changes at the system level can also be elucidated using postgenomic technologies. For example, microarrays can be used to study the transcriptome (all the genes expressed during specific culture conditions). Cold shock has been examined extensively using microarrays (Beckering et al. 2002; Phadtare and Inouye 2004; Gao et al. 2006); however, there are very few studies of the transcriptome during growth at low temperatures, especially at temperatures below 0°C which are essential to permafrost (Budde et al. 2006). Examination of the transcriptome enables the investigation of the underlying gene expression that results in cold adaptation, and ultimately permits the successful colonization of low-temperature environments by cold-adapted microorganisms. Here we review and summarize what has been learned about cold adaptation and active growth at temperatures below 0°C from genome sequence analysis and gene expression experiments in Psychrobacter arcticus 273-4, a model organism isolated from 20,000-30,000-year-old permafrost.
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