Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships.
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.
Department of Geosciences, Princeton University Princeton, NJ, USA.
Maggie C Y
MC
Lau
National Center for Genome Resources Santa Fe, NM, USA.
Connor
C
Cameron
Department of Geosciences, Princeton University Princeton, NJ, USA.
Cara
C
Magnabosco
Department of Computer Science and Engineering and Department of Microbiology and Molecular Genetics, Michigan State University East Lansing, MI, USA.
C Titus
CT
Brown
National Center for Genome Resources Santa Fe, NM, USA.
Faye
F
Schilkey
The Marine Biological Laboratory Woods Hole, MA, USA.
Sharon
S
Grim
Department of Chemistry, New Mexico Tech Socorro, NM, USA.
Sarah
S
Hendrickson
Department of Chemistry, New Mexico Tech Socorro, NM, USA.
Michael
M
Pullin
Department of Earth Sciences, University of Toronto Toronto, ON, Canada.
Barbara
B
Sherwood Lollar
Department of Biotechnology, University of Free State Bloemfontein, South Africa.
Esta
E
van Heerden
Department of Biology, New Mexico Tech Socorro, NM, USA.
Thomas L
TL
Kieft
Department of Geosciences, Princeton University Princeton, NJ, USA.
Tullis C
TC
Onstott
N-cycle; evolution; functional genes; phylogenetics; phylogeny; phylogeography; terrestrial subsurface