@article {23,
	title = {Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population},
	journal = {Frontiers in Microbiology},
	volume = {6},
	year = {2015},
	note = {PT: J; TC: 0; UT: WOS:000352551600004},
	pages = {349-349},
	abstract = {A major fraction of Earth{\textquoteright}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.},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2015.00349},
	author = {Labonte, Jessica M. and Field, Erin K. and Lau, Maggie and Chivian, Dylan and Van Heerden, Esta and Wommack, K. Eric and Kieft, Thomas L. and Onstott, Tullis C. and Stepanauskas, Ramunas}
}
@article { ISI:000359186200001,
	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},
	month = {OCT 31},
	type = {Article},
	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.},
	keywords = {evolution, functional genes, N-cycle, phylogenetics, phylogeny, phylogeography, terrestrial subsurface},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2014.00531},
	author = {Lau, Maggie C. Y. and Cameron, Connor and Magnabosco, Cara and Brown, C. Titus and Schilkey, Faye and Grim, Sharon and Hendrickson, Sarah and Pullin, Michael and Lollar, Barbara Sherwood and Van Heerden, Esta and Kieft, Thomas L. and Onstott, Tullis C.}
}
