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

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

Research output: Contribution to journalArticle

32 Citations (Scopus)

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.

Original languageEnglish (US)
Article number531
JournalFrontiers in Microbiology
Volume5
Issue numberOCT
DOIs
StatePublished - Jan 1 2014

Fingerprint

Metagenome
Genes
Metagenomics
Ecosystem
Phylogeography
Water
Biodiversity

All Science Journal Classification (ASJC) codes

  • Microbiology (medical)
  • Microbiology

Keywords

  • Evolution
  • Functional genes
  • N-cycle
  • Phylogenetics
  • Phylogeny
  • Phylogeography
  • Terrestrial subsurface

Cite this

Lau, Maggie C.Y. ; Cameron, Connor ; Magnabosco, Cara ; Brown, C. Titus ; Schilkey, Faye ; Grim, Sharon ; Hendrickson, Sarah ; Pullin, Michael ; Lollar, Barbara Sherwood ; van Heerden, Esta ; Kieft, Thomas L. ; Onstott, Tullis C. / of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships. In: Frontiers in Microbiology. 2014 ; Vol. 5, No. OCT.
@article{061efb12515f4c0d81115bfb98b8478a,
title = "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.",
keywords = "Evolution, Functional genes, N-cycle, Phylogenetics, Phylogeny, Phylogeography, Terrestrial subsurface",
author = "Lau, {Maggie C.Y.} and Connor Cameron and Cara Magnabosco and Brown, {C. Titus} and Faye Schilkey and Sharon Grim and Sarah Hendrickson and Michael Pullin and Lollar, {Barbara Sherwood} and {van Heerden}, Esta and Kieft, {Thomas L.} and Onstott, {Tullis C.}",
year = "2014",
month = "1",
day = "1",
doi = "https://doi.org/10.3389/fmicb.2014.00531",
language = "English (US)",
volume = "5",
journal = "Frontiers in Microbiology",
issn = "1664-302X",
publisher = "Frontiers Media S. A.",
number = "OCT",

}

Lau, MCY, Cameron, C, Magnabosco, C, Brown, CT, Schilkey, F, Grim, S, Hendrickson, S, Pullin, M, Lollar, BS, van Heerden, E, Kieft, TL & Onstott, TC 2014, 'of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships', Frontiers in Microbiology, vol. 5, no. OCT, 531. https://doi.org/10.3389/fmicb.2014.00531

of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships. / Lau, Maggie C.Y.; Cameron, Connor; Magnabosco, Cara; Brown, C. Titus; Schilkey, Faye; Grim, Sharon; Hendrickson, Sarah; Pullin, Michael; Lollar, Barbara Sherwood; van Heerden, Esta; Kieft, Thomas L.; Onstott, Tullis C.

In: Frontiers in Microbiology, Vol. 5, No. OCT, 531, 01.01.2014.

Research output: Contribution to journalArticle

TY - JOUR

T1 - of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships

AU - Lau, Maggie C.Y.

AU - Cameron, Connor

AU - Magnabosco, Cara

AU - Brown, C. Titus

AU - Schilkey, Faye

AU - Grim, Sharon

AU - Hendrickson, Sarah

AU - Pullin, Michael

AU - Lollar, Barbara Sherwood

AU - van Heerden, Esta

AU - Kieft, Thomas L.

AU - Onstott, Tullis C.

PY - 2014/1/1

Y1 - 2014/1/1

N2 - 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.

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.

KW - Evolution

KW - Functional genes

KW - N-cycle

KW - Phylogenetics

KW - Phylogeny

KW - Phylogeography

KW - Terrestrial subsurface

UR - http://www.scopus.com/inward/record.url?scp=84987846822&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84987846822&partnerID=8YFLogxK

U2 - https://doi.org/10.3389/fmicb.2014.00531

DO - https://doi.org/10.3389/fmicb.2014.00531

M3 - Article

VL - 5

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

IS - OCT

M1 - 531

ER -