Abstract
Comparative studies on community phylogenetics and phylogeography of microorganisms living in extreme environments are rare. Terrestrial subsurface habitats are valuable for studying microbial biogeographical patterns due to their isolation and the restricted dispersal mechanisms. Since the taxonomic identity of a microorganism does not always correspond well with its functional role in a particular community, the use of taxonomic assignments or patterns may give limited inference on how microbial functions are affected by historical, geographical and environmental factors. With seven metagenomic libraries generated from fracture water samples collected from five South African mines, this study was carried out to (1) screen for ubiquitous functions or pathways of biogeochemical cycling of CH4, S, and N; (2) to characterize the biodiversity represented by the common functional genes; (3) to investigate the subsurface biogeography as revealed by this subset of genes; and (4) to explore the possibility of using metagenomic data for evolutionary study. The ubiquitous functional genes are NarV, NPD, PAPS reductase, NifH, NifD, NifK, NifE, and NifN genes. Although these eight common functional genes were taxonomically and phylogenetically diverse and distinct from each other, the dissimilarity between samples did not correlate strongly with geographical or environmental parameters or residence time of the water. Por genes homologous to those of Thermodesulfovibrio yellowstonii detected in all metagenomes were deep lineages of Nitrospirae, suggesting that subsurface habitats have preserved ancestral genetic signatures that inform the study of the origin and evolution of prokaryotes.
Highlights
Solar energy and photosynthesis together form the basis for life to thrive in most ecosystems on Earth, except where temperature is too hot for the photosynthetic machinery to operate, or where it is too deep for light or photosynthetically-derived carbon substrates to penetrate
The water samples from BE, MM and FI yielded δ18O and δ2H values that are similar to each other with an average value of −7 and −43, respectively, and all falling on the Global Meteroic Water Line (GMWL), as previously noted for BE and MM (Ward et al, 2004)
N-CYCLING PATHWAYS SELECTED BY TERRESTRIAL SUBSURFACE ENVIRONMENTS Among the genes in CH4, S, and N metabolisms being screened, the dominance of N-cycling genes in the common functional gene pool of the metagenomes implies that some N-metabolizing pathways or microorganisms with the potential to perform such processes may be preferentially selected by deep subsurface habitats
Summary
Solar energy and photosynthesis together form the basis for life to thrive in most ecosystems on Earth, except where temperature is too hot for the photosynthetic machinery to operate (e.g., geothermal springs Lau et al, 2006), or where it is too deep for light or photosynthetically-derived carbon substrates to penetrate (e.g., terrestrial deep subsurface environments Lin et al, 2006). Surveys of microbial community structure in deep subsurface sites have been carried out on different continents (Pedersen, 1997; Zhang et al, 2005; Christner et al, 2006; Gihring et al, 2006; Sahl et al, 2008; Fry et al, 2009; Itävaara et al, 2011; Dong et al, 2014), little is known about the factors governing their distribution patterns over spatial and temporal scales. Surface microbial communities display distribution patterns over large spatial scales (>103 km) as a result of geographical and/or environmental characteristics (see review in Martiny et al, 2006). Two seminal papers challenged the dogma of “everything is everywhere, but the environment selects” (Baas Becking, 1934) by showing that the geographic distance of separation better explains www.frontiersin.org
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