Genome Analysis of a Member of the Uncultured Phylum Riflebacteria Revealed Pathways of Organotrophic Metabolism and Dissimilatory Iron Reduction

摘要

The candidate phylum Riflebacteria was described based on analysis of genomes assembled from the metagenomes of various anaerobic ecosystems; however, to date, no member of Riflebacteria has been isolated in a pure culture. In this work, the genome of a new member of Riflebacteria was obtained from the metagenome of the microbial community of a deep subsurface thermal aquifer in Western Siberia. Phylogenetic analysis indicates that this bacterium, designated Ch46, represents a new genus of the phylum Riflebacteria, distinct from the previously described Candidatus Ozemobacter. The genome of Ch46 was found to encode putatively secreted alpha-amylases and various sugar and peptide transporters. Reconstruction of central metabolic pathways suggests that Ch46 is an anaerobic organotroph capable of fermenting sugars and proteinaceous substrates. The bacterium lacks the genes of the known pathways of autotrophic carbon fixation, as well as the aerobic respiratory chain. The transmembrane ion gradient can be generated by an Rnf complex, as well as by a sodium-transporting NADH-quinone oxidoreductase. The presence of multiheme c-type cytochromes indicates the possibility of dissimilatory Fe(III) reduction. The pathways of dissimilatory reduction of sulfate, nitrate, nitrite, arsenate, and sulfur were not detected. In the subsurface aquifer, Riflebacteria probably utilize starch and similar polysaccharides, as well as low-molecular-weight organic compounds. Based on the results of phylogenetic and genomic analysis, it is proposed to classify the novel bacterium as 'Candidatus Rifleibacterium amylolyticum.'