AUTHOR=Lau Maggie C. Y. , Cameron Connor , Magnabosco Cara , Brown C. Titus , Schilkey Faye , Grim Sharon , Hendrickson Sarah , Pullin Michael , Sherwood Lollar Barbara , van Heerden Esta , Kieft Thomas L. , Onstott Tullis C. 

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

JOURNAL=Frontiers in Microbiology

VOLUME=5

YEAR=2014

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2014.00531

DOI=10.3389/fmicb.2014.00531

ISSN=1664-302X

ABSTRACT=<p>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 CH<sub>4</sub>, 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 <italic>Nar</italic>V, NPD, PAPS reductase, <italic>Nif</italic>H, <italic>Nif</italic>D, <italic>Nif</italic>K, <italic>Nif</italic>E, and <italic>Nif</italic>N 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. <italic>Por</italic> genes homologous to those of <italic>Thermodesulfovibrio yellowstonii</italic> 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.</p>