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.

Mn(II)-oxidizing Bacteria are Abundant and Environmentally Relevant Members of Ferromanganese Deposits in Caves of the Upper Tennessee River Basin

“…1:1 in cave ferromanganese deposits is a common ratio found in deep, oligotrophic systems in the southwest United States such as Lechuguilla and Spider Caves (Northup et al 2003;Spilde et al 2005). Previous research demonstrates the role of microsite geochemistry in establishing environmental niches (Engel et al 2010;Macalady et al 2008;Rossmassler et al 2012), structuring microbial communities Goldscheider et al 2006;Shabarova and Pernthaler 2010), and influencing mineral precipitation (Frierdich et al 2011) and composition (Post 1999;White et al 2009) in subsurface karst systems. However, the role of microsite geochemistry on biomineralization in shallow, epigenic cave systems may be masked by agricultural, anthropogenic, and soil geochemical inputs.…”

Biogeographic congruency among bacterial communities from terrestrial sulfidic springs

“…Seven continental sulfidic springs in the USA were sampled from 2008–2010 to span a range of geochemical conditions, bedrock geology, and hydrological settings that overlapped or supplemented previously studied springs (e.g., Rudolph et al, 2004; Porter and Engel, 2008; Rossmassler et al, 2012) (Figure 1A, Table 1). At each spring, several grams of white, filamentous microbial mat material were collected aseptically and placed into replicate 2 ml cryogenic vials that were stored on ice during transport.…”

Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer

“…For instance, Gammaproteobacteria and Deltaproteobacteria were strongly associated with saline wells and correlated to CCA axis 1. But, Gammaproteobacteria potentially utilize sulfide and decrease alkalinity if metabolizing as chemolithoautotrophs (Rossmassler et al, 2012), and Deltaproteobacteria are well-known sulfate reducers that generate sulfide and can increase alkalinity if they metabolize chemoorganotrophically. As such, both of these groups have the potential to affect carbonate geochemistry and mineral solubility.…”