Metagenome-Based Metabolic Reconstruction Reveals the Ecophysiological Function of Epsilonproteobacteria in a Hydrocarbon-Contaminated Sulfidic Aquifer.

Andreas H. Keller,Kathleen M. Schleinitz,Robert Starke,Carsten Vogt,Sabine Kleinsteuber,Stefan Bertilsson

doi:10.3389/fmicb.2015.01396

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 13C6-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 13C2-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.

Highlights

Representatives of the Epsilonproteobacteria inhabit a broad spectrum of environments like mammalian digestive systems (Wolin et al, 1961; Engberg et al, 2000), brackish water (Brettar et al, 2006), hydrothermal sediments (Inagaki et al, 2003), or subsurface systems (Watanabe et al, 2000; Gittel et al, 2012; Hubert et al, 2012; Handley et al, 2013)
We investigated a member of the epsilonproteobacterial order Campylobacterales originating from a sulfidic, hydrocarbon-contaminated aquifer at an industrial site near Zeitz, Germany (Schirmer et al, 2006; Vogt et al, 2007; Herrmann et al, 2008)
To shed light on the ecological niche and metabolic function of Epsilonproteobacteria in hydrocarbon-rich sulfidic environments, we aimed at a metabolic reconstruction of the Zeitz epsilonproteobacterium based on genome-centric metagenomics

Summary

INTRODUCTION

Representatives of the Epsilonproteobacteria inhabit a broad spectrum of environments like mammalian digestive systems (Wolin et al, 1961; Engberg et al, 2000), brackish water (Brettar et al, 2006), hydrothermal sediments (Inagaki et al, 2003), or subsurface systems (Watanabe et al, 2000; Gittel et al, 2012; Hubert et al, 2012; Handley et al, 2013). The metabolism of Epsilonproteobacteria in anoxic hydrocarbon-contaminated subsurface systems and especially in sulfate-reducing consortia is poorly understood as they are neither known to perform dissimilatory sulfate reduction nor to degrade aromatic or aliphatic hydrocarbons They seem to be stimulated by acetate amendment in anaerobic sediments (Handley et al, 2013) or even assimilate acetate as shown by DNA stable isotope probing (SIP) with 13C2-labeled acetate (Webster et al, 2010). We investigated a member of the epsilonproteobacterial order Campylobacterales originating from a sulfidic, hydrocarbon-contaminated aquifer at an industrial site near Zeitz, Germany (Schirmer et al, 2006; Vogt et al, 2007; Herrmann et al, 2008) It was originally enriched under sulfate-reducing conditions in a syntrophic, benzenemineralizing consortium and was shown to be distantly related to the genus Sulfurovum (Kleinsteuber et al, 2008; Herrmann et al, 2010). To shed light on the ecological niche and metabolic function of Epsilonproteobacteria in hydrocarbon-rich sulfidic environments, we aimed at a metabolic reconstruction of the Zeitz epsilonproteobacterium based on genome-centric metagenomics

MATERIALS AND METHODS

RESULTS

DISCUSSION