title: Metagenome-Based Metabolic Reconstruction Reveals the Ecophysiological Function of Epsilonproteobacteria in a Hydrocarbon-Contaminated Sulfidic Aquifer.
abstract: The population genome of an uncultured bacterium assigned to the Campylobacterales (Epsilonproteobacteria) was reconstructed from a metagenome dataset obtained by whole-genome shotgun pyrosequencing. Genomic DNA was extracted from a sulfate-reducing, m-xylene-mineralizing enrichment culture isolated from groundwater of a benzene-contaminated sulfidic aquifer. The identical epsilonproteobacterial phylotype has previously been detected in toluene- or benzene-mineralizing, sulfate-reducing consortia enriched from the same site. Previous stable isotope probing (SIP) experiments with (13)C6-labeled benzene suggested that this phylotype assimilates benzene-derived carbon in a syntrophic benzene-mineralizing consortium that uses sulfate as terminal electron acceptor. However, the type of energy metabolism and the ecophysiological function of this epsilonproteobacterium within aromatic hydrocarbon-degrading consortia and in the sulfidic aquifer are poorly understood. Annotation of the epsilonproteobacterial population genome suggests that the bacterium plays a key role in sulfur cycling as indicated by the presence of an sqr gene encoding a sulfide quinone oxidoreductase and psr genes encoding a polysulfide reductase. It may gain energy by using sulfide or hydrogen/formate as electron donors. Polysulfide, fumarate, as well as oxygen are potential electron acceptors. Auto- or mixotrophic carbon metabolism seems plausible since a complete reductive citric acid cycle was detected. Thus the bacterium can thrive in pristine groundwater as well as in hydrocarbon-contaminated aquifers. In hydrocarbon-contaminated sulfidic habitats, the epsilonproteobacterium may generate energy by coupling the oxidation of hydrogen or formate and highly abundant sulfide with the reduction of fumarate and/or polysulfide, accompanied by efficient assimilation of acetate produced during fermentation or incomplete oxidation of hydrocarbons. The highly efficient assimilation of acetate was recently demonstrated by a pulsed (13)C2-acetate protein SIP experiment. The capability of nitrogen fixation as indicated by the presence of nif genes may provide a selective advantage in nitrogen-depleted habitats. Based on this metabolic reconstruction, we propose acetate capture and sulfur cycling as key functions of Epsilonproteobacteria within the intermediary ecosystem metabolism of hydrocarbon-rich sulfidic sediments.
authors.affiliation: Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany ; Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany.
authors.forename: Andreas H
authors.initials: AH
authors.lastname: Keller
authors.affiliation: Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany.
authors.forename: Kathleen M
authors.initials: KM
authors.lastname: Schleinitz
authors.affiliation: Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany.
authors.forename: Robert
authors.initials: R
authors.lastname: Starke
authors.affiliation: Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University Uppsala, Sweden.
authors.forename: Stefan
authors.initials: S
authors.lastname: Bertilsson
authors.affiliation: Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany.
authors.forename: Carsten
authors.initials: C
authors.lastname: Vogt
authors.affiliation: Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ Leipzig, Germany.
authors.forename: Sabine
authors.initials: S
authors.lastname: Kleinsteuber
keywords: Campylobacterales; acetate assimilation; anaerobic hydrocarbon degradation; intermediary ecosystem metabolism; niche adaptation; nitrogen fixation; rTCA cycle; sulfur cycling