Linking phylogenetic and functional diversity to nutrient spiraling in microbial mats from Lower Kane Cave (USA)

Abstract

Microbial mats in sulfidic cave streams offer unique opportunities to study redox-based biogeochemical nutrient cycles. Previous work from Lower Kane Cave, Wyoming, USA, focused on the aerobic portion of microbial mats, dominated by putative chemolithoautotrophic, sulfuroxidizing groups within the Epsilonproteobacteria and Gammaproteobacteria. To evaluate nutrient cycling and turnover within the whole mat system, a multidisciplinary strategy was used to characterize the anaerobic portion of the mats, including application of the full-cycle rRNA approach, the most probable number method, and geochemical and isotopic analyses. Seventeen major taxonomic bacterial groups and one archaeal group were retrieved from the anaerobic portions of the mats, dominated by Deltaproteobacteria and uncultured members of the Chloroflexi phylum. A nutrient spiraling model was applied to evaluate upstream to downstream changes in microbial diversity based on carbon and sulfur nutrient concentrations. Variability in dissolved sulfide concentrations was attributed to changes in the abundance of sulfide-oxidizing microbial groups and shifts in the occurrence and abundance of sulfate-reducing microbes. Gradients in carbon and sulfur isotopic composition indicated that released and recycled byproduct compounds from upstream microbial activities were incorporated by downstream communities. On the basis of the type of available chemical energy, the variability of nutrient species in a spiraling model may explain observed differences in microbial taxonomic affiliations and metabolic functions, thereby spatially linking microbial diversity to nutrient spiraling in the cave stream ecosystem.

Sustained Anthropogenic Impact in Carter Saltpeter Cave, Carter County, Tennessee and the Potential Effects on Manganese Cycling

“…Localized variations in geochemistry and nutrient availability have been shown to impact microbial community structure (Johnston et al, 2012;Barton and Jurado, 2007;Shabarova and Pernthaler, 2010) and niche diversification (Engel et al, 2010;Macalady et al, 2008). Further, the composition of cave microbial communities mediates and stabilizes biogeochemical cycling and mineralization processes within an environment (Portillo and Gonzalez, 2010;Portillo et al, 2009).…”

The Genome of Pseudomonas fluorescens Strain R124 Demonstrates Phenotypic Adaptation to the Mineral Environment

“…Given the metabolic flexibility of pseudomonads to degrade complex organic molecules in the environment, the acquisition of these genes suggests that HGT may have expanded the cellular catabolic pathways to take advantage of presumably microbial detritus within the system, allowing this organism to play a potentially important role in carbon turnover. Indeed, in a number of cave systems, geologic isolation has led to the evolution of microbial ecosystems more dependent on chemolithotrophic energy generation and bacterially derived carbon turnover than similar microbial systems in soils (62). Nonetheless, many of the genes in these genomic islands had no annotated homologs in sequence databases, suggesting that the full range of adaptations by P. fluorescens R124 remains to be elucidated, an unsurprising finding given that the sequencing of greater numbers of genomes reveals increasingly greater numbers of gene families (63).…”

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

“…Clone sequences affiliated with the genus Sphingomonas were also retrieved from all wells. From the clone libraries, Girl Scout Deep and Paradise Alley Shallow shared an OTU that was most closely related to uncultured Alphaproteobacteria (99% sequence similarity) isolated from the sulfidic Lower Kane Cave, Wyoming, USA (Engel et al, 2010). In contrast, pyrosequence results showed that Caulobacteraceae were rare (o0.3% of all pyrosequences for any sample), Sphingomonadales were only retrieved from freshwater wells and Comal Springs, and representation by Rhodospirillales or Rhizobiales families was higher (up to 12%) in all wells (Supplementary Table S3).…”