Environmental Microbiology (2004) 6(10), 1001–1004 doi:10.1111/j.1462-2920.2004.00707.x © 2004 Blackwell Publishing Ltd (No claim to original US government works) Blackwell Science, LtdOxford, UKEMIEnvironmental Microbiology 1462-2912Blackwell Publishing Ltd, 20046 1010011004MiscellaneousGenomics updateM. Y. Galperin Accepted 11 August, 2004. For correspondence. E-mail galperin@ncbi.nlm.nih.gov; Tel. (+1) 301 435 5910; Fax (+1) 301 435 7794. Genomics update The bugs that came in from the cold Michael Y. Galperin National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. In a recent episode of the popular sci-fi show ‘Stargate’, the heroes had to dig through the ice crust of the Antarctic to find an ancient artefact that could hold keys to the secrets of life on the planet. This is also a fair description of the isolation process of the most psychrophilic (cold- loving) microorganisms, harvested these days in both Arc- tic and Antarctic. One of such organisms, Desulfotalea psychrophila, which has been isolated from Arctic marine sediments near the Spitsbergen island and can grow at temperatures as low as -1.8∞C (the freezing point of sea water), had its complete genome sequence reported in the previous issue of Environmental Microbiology (Rabus et al., 2004). The authors correctly note that although most people would classify such organisms as extremo- philes, most water on this planet has near-freezing temperature, and the organisms inhabiting it play an extremely important role in the global cycles of carbon and sulfur. The D. psychrophila genome, along with genomes of several other psychrophiles that are currently being sequenced, could provide a valuable insight into the largely obscure world of life at low temperatures. Its anal- ysis has already revealed an abundance of cold-shock proteins (and of uncharacterized proteins), but failed to confirm certain earlier ideas about the adaptation mech- anisms. It is relevant to note here that mere expression in Escherichia coli of chaperonins GroES and GroEL from a psychrophilic bacterium Oleispira antarctica allowed E. coli cells to grow well at 4∞C (Ferrer et al., 2003, 2004). This might mean that bacteria actually need very few, if any, specialized adaptations to cold temperatures. Another episode of ‘Stargate’ deals with the lost city of Atlantis, preserved for millions of years on the sea bottom. This is another attractive location for microbe hunters, as, in addition to the cold temperatures, these organisms have to cope with high-pressure and high-salt environ- ments. Complete genome sequences of at least three deep-sea proteobacteria have been finished this year and the first of them, of Photobacterum profundum (also known as deep-sea eubacterium SS9), has been recently deposited in GenBank (Table 1). The genome description, which has not been published yet, promises to unveil the complexity of high-pressure adaptations. Future compar- isons of the genomes and proteomes of marine psychro- philes with those of marine hyperthermophiles, such as the bacterium Thermotoga maritima and three archaea of the genus Pyrococcus, could bring very interesting results. Two other recently sequenced genomes, Leifsonia xyli and Erwinia carotovora, add to the growing diversity of sequenced plant pathogens, which already includes seven representatives of Proteobacteria and a single one of Mollicutes. Erwinia carotovora ssp. atroseptica (official name Pectobacterium atrosepticum), the causative agent of soft rot and blackleg potato diseases, belongs to Enter- obacteriales, a group with many sequenced representa- tives, including four strains of E. coli and three of Salmonella enterica. A comparison of Erwinia genes with those of human pathogens offered a way to delineate specific adaptations to plant pathogenicity (Bell et al., 2004). As much as one-third of Erwinia genes had not been seen in enteric human pathogens; some of these were shared with other plant pathogens. The latter genes, which encoded 20 putative pectinases and seven other plant cell wall-degrading enzymes, were obvious pathoge- nicity determinants. A total of 393 genes with possible involvement in pathogenicity have been identified, as well as systems of nitrogen fixation and opine catabolism, which might be useful for Erwinia’s survival in the soil or rhizosphere. Leifsonia xyli, causing ratoon stunting disease in sugar cane, is the first plant pathogen from Actinobacteria (for- merly high G+C Gram-positive bacteria), another group rich in human pathogens. Leifsonia xyli is closely related to Tropheryma whipplei, the causative agent of the human Whipple’s disease, but has a much larger genome and encodes ª1200 extra proteins. Leifsonia xyli has a limited geographical distribution and has not been seen in Papua New Guinea, the centre of diversity of wild sugar cane. This suggests a relatively recent conversion to pathogenicity, an idea that finds support from the analysis of L. xyli genome (Monteiro-Vitorello et al., 2004). Indeed,