Some bacteria degrade explosives, others prefer boiling methanol

The list of completely sequenced microbial genomes, released in August and September of 2007 (Table 1), is relatively short. Still, it includes some remarkable environmental microorganisms, such as the sulfur-reducing crenarchaeon Ignicoccus hospitalis, host of the smallest archaeon Nanoarchaeum equitans, the soil bacterium Bacillus pumilus isolated from a supposedly sterile environment of the spacecraft assembly facility in Pasadena, California, a marine bacterium that degrades nitramine explosives and two enterobacteria that are commonly found in soil and water habitats but can also infect humans, particularly newborns, causing sepsis and neonatal meningitis. The largest of the recently sequenced genomes comes from the early-diverging amitochondrial eukaryote Giardia lamblia (Morrison et al., 2007). Like most other eukaryotic genomes, it has been released in a draft form that consists of 306 contigs, representing 5 chromosomes of G. lamblia. In accordance with earlier reports, G. lamblia encodes a simplified archaeal-like DNA replication machinery, a yeast-like machinery for transcription synthesis and RNA processing and a limited set of largely bacterial-like metabolic enzymes. Since G. lamblia is an intestinal parasite, its primitive features could be equally well rationalized as either an ancestral state of the eukaryotic cell or as a result of a later adaptation to the parasitic lifestyle. So, although the genome of G. lamblia is certainly an important step towards understanding the origin and early evolution of the eukaryotic cell, genomes of other early-diverging eukaryotes would be needed to allow meaningful comparative analysis. Ignicoccus hospitalis, isolated from a submarine hydrothermal vent to the north of Iceland and originally described as Ignicoccus sp. KIN4/I, is an interesting organism in its own right. It is an obligately anaerobic hyperthermophilic chemolitoautotroph that uses CO2 as a source of carbon and derives energy from reducing elemental sulfur with H2 as the sole electron donor (Paper et al., 2007). It belongs to a recently described genus that forms a deeply branching lineage within the crenarchaeal family Desulfurococcaceae (Huber et al., 2000) and has an outer membrane (Näther and Rachel, 2004) and an unusual pathway of autotrophic CO2 fixation (Jahn et al., 2007). Still, Ignicoccus never attracted as much attention as the tiny (~400 nm) coccoidal cells of Nanoarchaeum equitans found on its surface. Based on its unique 16S rRNA sequence and the extremely small size of its genome (less than 0.5 Mbp), N. equitans was assigned to a separate phylum of archaea, the Nanoarchaeota (Huber et al., 2002). Subsequent genome sequencing revealed an extremely reduced genome of only 491 kb with 536 protein-coding genes (Waters et al., 2003). These genes encoded the components of information processing and DNA repair machinery, but not enzymes of lipid, cofactor, amino acid, or nucleotide biosynthesis. These observations showed that N. equitans must acquire most of its biosynthetic precursors from its host and cannot exist without it, establishing its interaction with I. hospitalis as a kind of symbiotic or parasitic relationship. Although the lack of the core metabolic genes suggested that N. equitans was a highly evolved organism, adapted to the parasitic lifestyle, an analysis of its ribosomal genes supported its deep branching at the base of the archaeal phylogenetic tree (Huber et al., 2003; Waters et al., 2003). Subsequent analysis led some researchers to position N. equitans near the root of the universal Tree of Life (Di Giulio, 2007), while others argued that it simply belongs to a fast-evolving lineage within the Euryarchaeota (Brochier et al., 2005; Makarova and Koonin, 2005). The genome of I. hospitalis is expected to shed light on the mechanisms and evolutionary history of its association with N. equitans. In addition, it should show whether I. hospitalis acquired any of its metabolic genes through lateral gene transfer from N. equitans. However, for a better resolution of ancestral archaeal phylogeny, we should probably wait for the upcoming release by the JGI of the genome of *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 (2007) 9(12), 2905–2910 doi:10.1111/j.1462-2920.2007.01480.x