The under-recognized dominance of Verrucomicrobia in soil bacterial communities

Gaddy T. Bergmann, Scott T. Bates, Kathryn G. Eilers, Christian L. Lauber, James G Caporaso, William A. Walters, Rob Knight, Noah Fierer

Research output: Contribution to journalArticle

259 Citations (Scopus)

Abstract

Verrucomicrobia are ubiquitous in soil, but members of this bacterial phylum are thought to be present at low frequency in soil, with few studies focusing specifically on verrucomicrobial abundance, diversity, and distribution. Here we used barcoded pyrosequencing to analyze verrucomicrobial communities in surface soils collected across a range of biomes in Antarctica, Europe, and the Americas (112 samples), as well as soils collected from pits dug in a montane coniferous forest (69 samples). Data collected from surface horizons indicate that Verrucomicrobia average 23% of bacterial sequences, making them far more abundant than had been estimated. We show that this underestimation is likely due to primer bias, as many of the commonly used PCR primers appear to exclude verrucomicrobial 16S rRNA genes during amplification. Verrucomicrobia were detected in 180 out of 181 soils examined, with members of the class Spartobacteria dominating verrucomicrobial communities in nearly all biomes and soil depths. The relative abundance of Verrucomicrobia was highest in grasslands and in subsurface soil horizons, where they were often the dominant bacterial phylum. Although their ecology remains poorly understood, Verrucomicrobia appear to be dominant in many soil bacterial communities across the globe, making additional research on their ecology clearly necessary.

Original languageEnglish (US)
Pages (from-to)1450-1455
Number of pages6
JournalSoil Biology and Biochemistry
Volume43
Issue number7
DOIs
StatePublished - Jul 2011
Externally publishedYes

Fingerprint

Verrucomicrobia
soil bacteria
dominance (genetics)
Soil
biome
soil
ecology
Ecology
ecosystems
Ecosystem
soil horizons
montane forest
soil horizon
coniferous forest
montane forests
soil depth
Antarctica
coniferous forests
relative abundance
amplification

Keywords

  • 16S rRNA genes
  • Bacteria
  • Barcoded pyrosequencing
  • Ecological dominance
  • Oligotroph
  • Primer bias
  • Relative abundance
  • Spartobacteria
  • Subsurface horizon
  • Verrucomicrobia

ASJC Scopus subject areas

  • Soil Science
  • Microbiology

Cite this

Bergmann, G. T., Bates, S. T., Eilers, K. G., Lauber, C. L., Caporaso, J. G., Walters, W. A., ... Fierer, N. (2011). The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biology and Biochemistry, 43(7), 1450-1455. https://doi.org/10.1016/j.soilbio.2011.03.012

The under-recognized dominance of Verrucomicrobia in soil bacterial communities. / Bergmann, Gaddy T.; Bates, Scott T.; Eilers, Kathryn G.; Lauber, Christian L.; Caporaso, James G; Walters, William A.; Knight, Rob; Fierer, Noah.

In: Soil Biology and Biochemistry, Vol. 43, No. 7, 07.2011, p. 1450-1455.

Research output: Contribution to journalArticle

Bergmann, GT, Bates, ST, Eilers, KG, Lauber, CL, Caporaso, JG, Walters, WA, Knight, R & Fierer, N 2011, 'The under-recognized dominance of Verrucomicrobia in soil bacterial communities', Soil Biology and Biochemistry, vol. 43, no. 7, pp. 1450-1455. https://doi.org/10.1016/j.soilbio.2011.03.012
Bergmann, Gaddy T. ; Bates, Scott T. ; Eilers, Kathryn G. ; Lauber, Christian L. ; Caporaso, James G ; Walters, William A. ; Knight, Rob ; Fierer, Noah. / The under-recognized dominance of Verrucomicrobia in soil bacterial communities. In: Soil Biology and Biochemistry. 2011 ; Vol. 43, No. 7. pp. 1450-1455.
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