Drivers of epsilonproteobacterial community composition in sulfidic caves and springs

Abstract

Epsilonproteobacteria are widely distributed in marine, freshwater, and terrestrial environments, although most well-studied groups are from hydrothermal vents and the human intestinal tract. The environmental variables that control epsilonproteobacterial communities in sulfidic terrestrial environments, however, are poorly understood. Here, the environmental variables that influence epsilonproteobacterial community composition in geographically separated sulfidic caves and springs were determined by coarse and fine-scale approaches: denaturing gradient gel electrophoresis profiling of 23S rRNA PCR amplicons and clone library sequencing of the 16S-ITS-23S rRNA operon. Sequences retrieved from this study were not closely related to cultured representatives, indicating that existing culture collections do not adequately capture the diversity of terrestrial Epsilonproteobacteria. Comparisons of 16S-ITS-23S rRNA operon sequences from four sites revealed that some distant communities (> 8000 km) share closely related populations of Epsilonproteobacteria, while other sites have nearly clonal and phylogenetically distinct populations. Statistical evaluations of sequence data reveal that multiple environmental variables (e.g. temperature, pH, salinity, dissolved oxygen, and bicarbonate concentrations) influence Epsilonproteobacteria community composition. Locations with clonal populations tended to be from higher temperatures and intermediate dissolved oxygen concentrations. rRNA operon sequences outside of the 16S rRNA gene may be critical to recognizing environmental drivers of epsilonproteobacterial community composition.