1. ¹Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
2. ²Department of Soil Science, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
3. ³Department of Physical and Environmental Sciences, University of Toronto at Scarborough, Scarborough, Ontario, Canada
4. ⁴Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
5. ⁵Department of Statistics, University of Florida, Gainesville, FL, USA
6. ⁶Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
7. ⁷Everglades Research and Education Center and Soil and Water Science Department, University of Florida, Belle Glade, FL, USA
8. ⁸Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA

Correspondence: Professor EW Triplett, Microbiology and Cell Science, University of Florida, 1052 Museum Road, Gainesville, FL 32611-0700, USA. E-mail: ewt@ufl.edu

Received 3 April 2007; Revised 4 June 2007; Accepted 4 June 2007; Published online 5 July 2007.

Abstract

Estimates of the number of species of bacteria per gram of soil vary between 2000 and 8.3 million (Gans et al., 2005; Schloss and Handelsman, 2006). The highest estimate suggests that the number may be so large as to be impractical to test by amplification and sequencing of the highly conserved 16S rRNA gene from soil DNA (Gans et al., 2005). Here we present the use of high throughput DNA pyrosequencing and statistical inference to assess bacterial diversity in four soils across a large transect of the western hemisphere. The number of bacterial 16S rRNA sequences obtained from each site varied from 26 140 to 53 533. The most abundant bacterial groups in all four soils were the Bacteroidetes, Betaproteobacteria and Alphaproteobacteria. Using three estimators of diversity, the maximum number of unique sequences (operational taxonomic units roughly corresponding to the species level) never exceeded 52 000 in these soils at the lowest level of dissimilarity. Furthermore, the bacterial diversity of the forest soil was phylum rich compared to the agricultural soils, which are species rich but phylum poor. The forest site also showed far less diversity of the Archaea with only 0.009% of all sequences from that site being from this group as opposed to 4%–12% of the sequences from the three agricultural sites. This work is the most comprehensive examination to date of bacterial diversity in soil and suggests that agricultural management of soil may significantly influence the diversity of bacteria and archaea.