Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

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.

A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust

“…DNA extraction and sequencing DNA was extracted from the MNY filter as described in Lau et al, (2014). The DNA sample was sent to the Marine Biological Laboratory (MBL, Woods Hole, MA, USA) for whole-genome library prep using NuGen Ultralow Ovation system that included 18 cycles of PCR amplification of all adaptor-viable molecules (http://nugen.com).…”

“…Samples for cation and anion analysis were collected using the protocols described in Lau et al (2014). Mineral solubility, dissolved species activity, partial pressures and free energy of microbial reactions were calculated using the geochemical modeling program, The Geochemist's Workbench version 8.0 (Bethke, 2008).…”

Metagenomics of extreme environments

“…Analysis of water samples retrieved from ultra-deep South African mines showed the ubiquitous presence of known variants of nitrogen cycling genes such as NarV, NPD, PAPS reductase, NifH, NifD, NifK, NifE, and NifN. Interestingly, the authors found no significant correlation in these samples to geographical or subsurface environmental parameters [61]. …”

“…Some key insights into nitrogen cycling processes in subsurface habitats have been gained via the application of metagenome sequencing [61]. Analysis of water samples retrieved from ultra-deep South African mines showed the ubiquitous presence of known variants of nitrogen cycling genes such as NarV, NPD, PAPS reductase, NifH, NifD, NifK, NifE, and NifN.…”

Workshop to develop deep-life continental scientific drilling projects

“…2) (Stevens and McKinley, 1995;Chapelle et al, 2002;Sleep et al, 2004;Lin et al, 2006;Chivian et al, 2008). A wide diversity of bacteria and archaea has been detected in the continental subsurface, with the majority of these appearing to be indigenous and adapted to subterranean life (Heim, 2011;Colwell and D'Hondt, 2013;Lau et al, 2014). These microbes are active, albeit at slow metabolic rates, and thus are important in the biogeochemical cycling of carbon (Head et al, 2003), nitrogen , and other biologically relevant, redox-sensitive elements .…”