The under-recognized dominance of Verrucomicrobia in soil bacterial communities

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

Research output: Contribution to journalArticlepeer-review

374 Scopus citations

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

Bibliographical note

Funding Information:
We want to thank Spencer Debenport, Rebecca McCulley, and the large number of other collaborators who helped us collect soils from all of the sites included here. We also want to thank Donna Berg-Lyons for help with the laboratory work and Joe Jones from Engencore at the University of South Carolina who conducted the pyrosequencing run. This research was funded by grants to R.K. and N.F. from the Bill and Melinda Gates Foundation , Crohn’s and Colitis Foundation of America , National Institutes of Health , National Science Foundation , and the U.S. Department of Agriculture .

Copyright:
Copyright 2011 Elsevier B.V., All rights reserved.

Keywords

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

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