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Background  Prokaryotic microorganisms are able to survive and proliferate in severe environmental conditions. The increasing number of complete sequences of prokaryotic genomes has provided the basis for studying the molecular mechanisms of their adaptation at the genomic level. We apply here a computer-based approach to compare the genomes and proteomes from  P. furiosus, P. horikoshii , and  P. abyssi  to identify features of their molecular evolution related to adaptation strategy to diverse environmental conditions.    Results  Phylogenetic analysis of rRNA genes from 26 Pyrococcus strains suggested that the divergence of  P. furiosus, P. horikoshii  and  P. abyssi  might have occurred from ancestral deep-sea organisms. It was demonstrated that the function of genes that have been subject to positive Darwinian selection is closely related to abiotic and biotic conditions to which archaea managed to become adapted. Divergence of the  P. furiosus  archaea might have been due to loss of some genes involved in cell motility or signal transduction, and/or to evolution under positive selection of the genes for translation machinery. In the course of  P. horikoshii  divergence, positive selection was found to operate mainly on the transcription machinery; divergence of  P. abyssi  was related with positive selection for the genes mainly involved in inorganic ion transport. Analysis of radical amino acid replacement rate in evolving  P. furiosus, P. horikoshii  and  P. abyssi  showed that the fixation rate was higher for radical substitutions relative to the volume of amino acid side-chain.    Conclusions  The current results give due credit to the important role of hydrostatic pressure as a cause of variability in the  P. furiosus, P. horikoshii  and  P. abyssi  genomes evolving in different habitats. Nevertheless, adaptation to pressure does not appear to be the sole factor ensuring adaptation to environment. For example, at the stage of the divergence of  P. horikoshii  and  P. abyssi , an essential evolutionary role may be assigned to changes in the trophic chain, namely, acquisition of a consumer status at a high ( P. horikoshii ) or low level ( P. abyssi ).

Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions