TY - JOUR T1 - Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population JF - Frontiers in Microbiology Y1 - 2015 A1 - Labonte, Jessica M. A1 - Field, Erin K. A1 - Lau, Maggie A1 - Chivian, Dylan A1 - Van Heerden, Esta A1 - Wommack, K. Eric A1 - Kieft, Thomas L. A1 - Onstott, Tullis C. A1 - Stepanauskas, Ramunas AB - A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT) and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a three km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32 % of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs) and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment. VL - 6 N1 - PT: J; TC: 0; UT: WOS:000352551600004 JO - Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population ER - TY - JOUR T1 - Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships JF - FRONTIERS IN MICROBIOLOGY Y1 - 2014 A1 - Lau, Maggie C. Y. A1 - Cameron, Connor A1 - Magnabosco, Cara A1 - Brown, C. Titus A1 - Schilkey, Faye A1 - Grim, Sharon A1 - Hendrickson, Sarah A1 - Pullin, Michael A1 - Lollar, Barbara Sherwood A1 - Van Heerden, Esta A1 - Kieft, Thomas L. A1 - Onstott, Tullis C. KW - evolution KW - functional genes KW - N-cycle KW - phylogenetics KW - phylogeny KW - phylogeography KW - terrestrial subsurface AB - 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. VL - 5 ER -