title: The complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome.
abstract: We reconstructed the complete 2.4 Mb-long genome of a previously uncultivated epsilonproteobacterium, Candidatus Sulfuricurvum sp. RIFRC-1, via assembly of short-read shotgun metagenomic data using a complexity reduction approach. Genome-based comparisons indicate the bacterium is a novel species within the Sulfuricurvum genus, which contains one cultivated representative, S. kujiense. Divergence between the species appears due in part to extensive genomic rearrangements, gene loss and chromosomal versus plasmid encoding of certain (respiratory) genes by RIFRC-1. Deoxyribonucleic acid for the genome was obtained from terrestrial aquifer sediment, in which RIFRC-1 comprised ∼ 47% of the bacterial community. Genomic evidence suggests RIFRC-1 is a chemolithoautotrophic diazotroph capable of deriving energy for growth by microaerobic or nitrate-/nitric oxide-dependent oxidation of S°, sulfide or sulfite or H₂oxidation. Carbon may be fixed via the reductive tricarboxylic acid cycle. Consistent with these physiological attributes, the local aquifer was microoxic with small concentrations of available nitrate, small but elevated concentrations of reduced sulfur and NH(4)(+) /NH₃-limited. Additionally, various mechanisms for heavy metal and metalloid tolerance and virulence point to a lifestyle well-adapted for metal(loid)-rich environments and a shared evolutionary past with pathogenic Epsilonproteobacteria. Results expand upon recent findings highlighting the potential importance of sulfur and hydrogen metabolism in the terrestrial subsurface.
authors.affiliation: Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA; Institute for Genomics and Systems Biology, Argonne National Laboratory, Lemont, IL, 60439, USA.
authors.forename: Kim M
authors.initials: KM
authors.lastname: Handley
authors.forename: Daniela
authors.initials: D
authors.lastname: Bartels
authors.forename: Edward J
authors.initials: EJ
authors.lastname: O'Loughlin
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Williams
authors.forename: William L
authors.initials: WL
authors.lastname: Trimble
authors.forename: Kelly
authors.initials: K
authors.lastname: Skinner
authors.forename: Jack A
authors.initials: JA
authors.lastname: Gilbert
authors.forename: Narayan
authors.initials: N
authors.lastname: Desai
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Glass
authors.forename: Tobias
authors.initials: T
authors.lastname: Paczian
authors.forename: Andreas
authors.initials: A
authors.lastname: Wilke
authors.forename: Dionysios
authors.initials: D
authors.lastname: Antonopoulos
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Kemner
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
mesh_terms: D001483:Base Sequence; D002244:Carbon / Q000378:metabolism; D020565:Epsilonproteobacteria / Q000235:genetics*; D016680:Genome, Bacterial; D019015:Geologic Sediments / Q000737:chemistry; D060587:Groundwater / Q000737:chemistry / Q000382:microbiology*; D006859:Hydrogen / Q000378:metabolism; D054892:Metagenome; D056186:Metagenomics; D010084:Oxidation-Reduction; D010957:Plasmids / Q000235:genetics; D013455:Sulfur / Q000378:metabolism
chemical_list: D013455:Sulfur; D002244:Carbon; D006859:Hydrogen