title: Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla.
abstract: BD1-5, OP11, and OD1 bacteria have been widely detected in anaerobic environments, but their metabolisms remain unclear owing to lack of cultivated representatives and minimal genomic sampling. We uncovered metabolic characteristics for members of these phyla, and a new lineage, PER, via cultivation-independent recovery of 49 partial to near-complete genomes from an acetate-amended aquifer. All organisms were nonrespiring anaerobes predicted to ferment. Three augment fermentation with archaeal-like hybrid type II/III ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) that couples adenosine monophosphate salvage with CO(2) fixation, a pathway not previously described in Bacteria. Members of OD1 reduce sulfur and may pump protons using archaeal-type hydrogenases. For six organisms, the UGA stop codon is translated as tryptophan. All bacteria studied here may play previously unrecognized roles in hydrogen production, sulfur cycling, and fermentation of refractory sedimentary carbon.
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, USA.
authors.forename: Kelly C
authors.initials: KC
authors.lastname: Wrighton
authors.forename: Brian C
authors.initials: BC
authors.lastname: Thomas
authors.forename: Itai
authors.initials: I
authors.lastname: Sharon
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Miller
authors.forename: Cindy J
authors.initials: CJ
authors.lastname: Castelle
authors.forename: Nathan C
authors.initials: NC
authors.lastname: VerBerkmoes
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Wilkins
authors.forename: Robert L
authors.initials: RL
authors.lastname: Hettich
authors.forename: Mary S
authors.initials: MS
authors.lastname: Lipton
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Williams
authors.forename: Philip E
authors.initials: PE
authors.lastname: Long
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
mesh_terms: D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001421:Bacteria, Anaerobic / Q000145:classification* / Q000201:enzymology* / Q000235:genetics; D018388:Codon, Terminator / Q000235:genetics; D004269:DNA, Bacterial; D005285:Fermentation; D016680:Genome, Bacterial; D006859:Hydrogen / Q000378:metabolism*; D006864:Hydrogenase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D010802:Phylogeny; D012273:Ribulose-Bisphosphate Carboxylase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013455:Sulfur / Q000378:metabolism*; D014364:Tryptophan / Q000235:genetics
chemical_list: D019843:Archaeal Proteins; D018388:Codon, Terminator; D004269:DNA, Bacterial; D013455:Sulfur; D006859:Hydrogen; D014364:Tryptophan; D006864:Hydrogenase; D012273:Ribulose-Bisphosphate Carboxylase