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Applied and Environmental Microbiology, August 2009, p. 5111-5120, Vol. 75, No. 15
0099-2240/09/$08.00+0     doi:10.1128/AEM.00335-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale{triangledown} ,{dagger}

Christian L. Lauber,1* Micah Hamady,2 Rob Knight,3 and Noah Fierer1,4

Cooperative Institute for Research in Environmental Sciences, University of Colorado, UCB 216, Boulder, Colorado 80309,1 Department of Computer Science, University of Colorado, UCB 430, Boulder, Colorado 80309,2 Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, Colorado 80309,3 Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, Colorado 803094

Received 10 February 2009/ Accepted 1 June 2009

Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

* Corresponding author. Mailing address: University of Colorado at Boulder, CIRES, 216 UCB, Boulder, CO 80309-0216. Phone: (303) 492-2099. Fax: (303) 492-1149. E-mail: Christian.lauber{at}colorado.edu

{triangledown} Published ahead of print on 5 June 2009.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, August 2009, p. 5111-5120, Vol. 75, No. 15
0099-2240/09/$08.00+0     doi:10.1128/AEM.00335-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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