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Background  The phylum  Verrucomicrobia  is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the  Verrucomicrobia , strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia.    Results  We report the complete genome sequence of strain V4, the first one from a representative of the  Verrucomicrobia . Isolate V4, initially named " Methylokorus infernorum " (and recently renamed  Methylacidiphilum infernorum ) is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of  M. infernorum  was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C 1 -utilization pathways compared to other known methylotrophs. The  M. infernorum  genome does not encode tubulin, which was previously discovered in bacteria of the genus  Prosthecobacter , or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping  Planctomycetes ,  Verrucomicrobia  and  Chlamydiae  into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the  M. infernorum  lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of  M. infernorum  shows apparent adaptations for existence under extremely acidic conditions including a major upward shift in the isoelectric points of proteins.    Conclusion  The results of genome analysis of  M. infernorum  support the monophyly of the PVC superphylum.  M. infernorum  possesses a streamlined genome but seems to have acquired numerous genes including those for enzymes of methylotrophic pathways  via  horizontal gene transfer, in particular, from  Proteobacteria .    Reviewers  This article was reviewed by John A. Fuerst, Ludmila Chistoserdova, and Radhey S. Gupta.

biology direct

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia