Abstract
BackgroundBacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage environments (AMD), acid-rock drainage environments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these environments, their role in biogeochemical cycling is poorly understood.ResultsHere we report draft genomes of five species of the Sulfobacillus genus (AMDSBA1-5) reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (Iron Mountain, CA). Three of these species (AMDSBA2, AMDSBA3, and AMDSBA4) have no cultured representatives while AMDSBA1 is a strain of S. benefaciens, and AMDSBA5 a strain of S. thermosulfidooxidans. We analyzed the diversity of energy conservation and central carbon metabolisms for these genomes and previously published Sulfobacillus genomes. Pathways of sulfur oxidation vary considerably across the genus, including the number and type of subunits of putative heterodisulfide reductase complexes likely involved in sulfur oxidation. The number and type of nickel-iron hydrogenase proteins varied across the genus, as does the presence of different central carbon pathways. Only the AMDSBA3 genome encodes a dissimilatory nitrate reducatase and only the AMDSBA5 and S. thermosulfidooxidans genomes encode assimilatory nitrate reductases. Within the genus, AMDSBA4 is unusual in that its electron transport chain includes a cytochrome bc type complex, a unique cytochrome c oxidase, and two distinct succinate dehydrogenase complexes.ConclusionsOverall, the results significantly expand our understanding of carbon, sulfur, nitrogen, and hydrogen metabolism within the Sulfobacillus genus.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1107) contains supplementary material, which is available to authorized users.
Highlights
Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage environments (AMD), acid-rock drainage environments (ARD), as well as in industrial bioleaching operations
In addition to illuminating the metabolic potential of a strain of S. benefaciens, and three other novel Sulfobacillus spp., this work provides one of the first genome-inferred reconstructions of Gram-positive, acidophilic sulfur oxidation pathways, and highlights both conserved and divergent metabolisms found in organisms of the Sulfobacillus genus
Based on phylogenetic trees of concatenated protein alignments and EMIRGE-generated 16S rRNA genes, AMDSBA5 was classified as a strain of S. thermosulfidooxidans (99.7% 16S rRNA gene similarity), AMDSBA1 was classified as a strain of S. benefaciens (100% 16S rRNA gene similarity), and AMDSBA3 was shown to related to be most closely related to S. acidophilus strains (97.2% 16S rRNA gene similarity, Figure 2A and B, Additional file 2: Table S1)
Summary
Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage environments (AMD), acid-rock drainage environments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these environments, their role in biogeochemical cycling is poorly understood. Each is a facultative anaerobe capable of assimilation of organic and inorganic forms of carbon, deriving energy from aerobic oxidation of iron and various sulfur species (e.g., tetrathionate and elemental sulfur), as well as from ferric iron respiration [10,11,14,15], and possibly fermentation [15]. In addition to illuminating the metabolic potential of a strain of S. benefaciens, and three other novel Sulfobacillus spp., this work provides one of the first genome-inferred reconstructions of Gram-positive, acidophilic sulfur oxidation pathways, and highlights both conserved and divergent metabolisms found in organisms of the Sulfobacillus genus
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