The quest for biofuels fuels genome sequencing

The list of recently completed microbial genome projects (Table 1) shows further progress in sequencing genomes of poorly studied environmental bacteria. The genome of Aquifex aeolicus, sequenced 10 years ago, has been joined by genomes of two more representatives of the phylum Aquificae. The genome of Polaribacter sp. MED152, a marine member of Bacteroidetes, revealed a combination of heterotrophic metabolism with light energy capture by proteorhodopsin. In addition, six genomes from the phylum Chlorobi more than doubled the number of sequenced genomes of green sulfur bacteria. In eukaryotic genomics, important news was the release by the JGI scientists of a draft genome of the soft-rot ascomycete fungus Trichoderma reesei, also known as Hypocrea jecorina (Martinez et al., 2008). Trichoderma reesei is filamentous fungus that is widely used in biotechnology as a producer of various cellulases and hemicellulases for the hydrolysis of plant cell walls. This organism has attracted renewed interest owing to its potential use in the conversion of lignocelluloses to biofuel. The GenBank version of the draft genome of T. reesei consists of 2236 contigs, assembled into 170 scaffolds and containing ~34 Mbp of DNA, representing ~99% of the whole genome. The current assembly did not assign the scaffolds to any of the seven chromosomes of T. reesei, but allowed identification of 9129 predicted protein-coding genes (Martinez et al., 2008). Comparison of T. reesei with Fusarium graminearum (Gibberella zeae) and Neurospora crassa revealed a certain degree of synteny between these three genomes. A surprising finding was the relatively low number of glycoside hydrolases (cellulases, hemicellulases and pectinases) encoded by T. reesei genome. The authors suggest that successful utilization by T. reesei of its limited set of cellulolytic enzymes to efficiently degrade plant cell walls could be due to (i) clustering of the respective genes that ensures co-expression of the right combination of hydrolytic enzymes, and (ii) secretion of secondary metabolites (Martinez et al., 2008). Although phylogenetically unrelated to T. reesei, the g-proteobacterium Cellvibrio japonicus also encodes an efficient machinery for degrading plant cell walls that includes 130 predicted glycoside hydrolases (DeBoy et al., 2008). The current list includes two actinobacterial genomes, representing the soil bacterium Kocuria rhizophila (Takarada et al., 2008) and a new strain of the human gut symbiont Bifidobacterium longum (Lee and O’Sullivan, 2006; Lee et al., 2008). The genus Kocuria belongs to the family Micrococcineae and was separated from Micrococcus just a few years ago (Stackebrandt et al., 1995). Accordingly, K. rhizophila ATCC 9341, parental strain of the sequenced K. rhizophila DC2201, was until recently classified as Micrococcus luteus and used as a standard quality control strain in a number of applications, including testing of antimicrobial compounds (Tang and Gillevet, 2003). The genus name was assigned to honour Miroslav Kocur, Slovakian microbiologist who dedicated many years to studying M. luteus (Rosypal and Kocur, 1963; Kocur, 1986). Kocuria rhizophila is an environmental actinomycete that is often associated with plant roots. Despite its small (for a soil actinomycete) 2.7 Mbp genome, K. rhizophila appears to encode the full set of key metabolic enzymes. However, it encodes fewer proteins participating in secondary metabolism, including single genes for a non-ribosomal peptide synthetase and a polyketide synthase. The relatively high tolerance of K. rhizophila to various organic compounds correlates with the presence of a large number of genes encoding various membrane transporters, including drug efflux pumps (Takarada et al., 2008). The two newly sequenced genomes of Aquificae represent two major families in this phylum. Hydrogenobaculum sp. YO4AAS1 belongs to the family Aquificaceae, which also includes A. aeolicus, the best-characterized member of the phylum, whereas Sulfurihydrogenibium sp. YO3AOP1 belongs to the family Hydrogenothermaceae. Both are thermophilic chemolitoautotrophs, isolated from *For correspondence. E-mail [email protected]; Tel. (+1) 301 435 5910; Fax (+1) 301 435 7793. Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation. Environmental Microbiology (2008) 10(10), 2471–2475 doi:10.1111/j.1462-2920.2008.01754.x