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PMID: 19129864 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses.

The ISME journal ·Vol. 3 ·No. 4 ·2009-04-00 ·Pages 442-53

Jones RT, Robeson MS, Lauber CL, Hamady M, Knight R, Fierer N

Abstract

Acidobacteria are ubiquitous and abundant members of soil bacterial communities. However, an ecological understanding of this important phylum has remained elusive because its members have been difficult to culture and few molecular investigations have focused exclusively on this group. We generated an unprecedented number of acidobacterial DNA sequence data using pyrosequencing and clone libraries (39,707 and 1787 sequences, respectively) to characterize the relative abundance, diversity and composition of acidobacterial communities across a range of soil types. To gain insight into the ecological characteristics of acidobacterial taxa, we investigated the large-scale biogeographic patterns exhibited by acidobacterial communities, and related soil and site characteristics to acidobacterial community assemblage patterns. The 87 soils analyzed by pyrosequencing contained more than 8600 unique acidobacterial phylotypes (at the 97% sequence similarity level). One phylotype belonging to Acidobacteria subgroup 1, but not closely related to any cultured representatives, was particularly abundant, accounting for 7.4% of bacterial sequences and 17.6% of acidobacterial sequences, on average, across the soils. The abundance of Acidobacteria relative to other bacterial taxa was highly variable across the soils examined, but correlated strongly with soil pH (R=-0.80, P<0.001). Soil pH was also the best predictor of acidobacterial community composition, regardless of how the communities were characterized, and the relative abundances of the dominant Acidobacteria subgroups were readily predictable. Acidobacterial communities were more phylogenetically clustered as soil pH departed from neutrality, suggesting that pH is an effective habitat filter, restricting community membership to progressively more narrowly defined lineages as pH deviates from neutrality.

MeSH Terms
Bacteria/classification,genetics,isolation & purification Biodiversity Cluster Analysis Hydrogen-Ion Concentration Molecular Sequence Data Phylogeny Sequence Analysis, DNA/methods Sequence Homology Soil/analysis Soil Microbiology
Chemicals
Soil
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Jones Ryan T
Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA. Ryan.Jones@colorado.edu
Robeson Michael S
Lauber Christian L
Hamady Micah
Knight Rob
Fierer Noah
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Article Info
Journal
The ISME journal
Abbr.
ISME J
ISSN
1751-7370
DOI
10.1038/ismej.2008.127
Email
ryan.jones@colorado.edu
Published
2009-04-00
Epub
2009-00-08
Pages
442-53
Language
English
Region
England
NLM ID
101301086
PMCID
PMC2997719
Subset
IM
Grants
NIGMS NIH HHS · T32 GM065103 · United States
NIGMS NIH HHS · T32 GM065103-08 · United States
NIGMS NIH HHS · T32GM065103 · United States
Databases
GENBANK
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FJ166355, FJ166356, FJ166357, FJ166358, FJ166359, FJ166360, FJ166361, FJ166362, FJ166363, FJ166364, FJ166365, FJ166366, FJ166367, FJ166368, FJ166369, FJ166370, FJ166371, FJ166372, FJ166373, FJ166374, FJ166375, FJ166376, FJ166377, FJ166378, FJ166379, FJ166380, FJ166381, FJ166382, FJ166383, FJ166384, FJ166385, FJ166386, FJ166387, FJ166388, FJ166389, FJ166390, FJ166391, FJ166392, FJ166393, FJ166394, FJ166395, FJ166396, FJ166397, FJ166398, FJ166399, FJ166400, FJ166401, FJ166402, FJ166403, FJ166404, FJ166405, FJ166406, FJ166407, FJ166408, FJ166409, FJ166410, FJ166411, FJ166412, FJ166413, FJ166414, FJ166415, FJ166416, FJ166417, FJ166418, FJ166419, FJ166420, FJ166421, FJ166422, FJ166423, FJ166424, FJ166425, FJ166426, FJ166427, FJ166428, FJ166429, FJ166430, FJ166431, FJ166432, FJ166433, FJ166434, FJ166435, FJ166436, FJ166437, FJ166438, FJ166439, FJ166440, FJ166441, FJ166442, FJ166443, FJ166444, FJ166445, FJ166446, FJ166447, FJ166448, FJ166449, FJ166450, FJ166451, FJ166452, FJ166453, FJ166454, FJ166455, FJ166456, FJ166457, FJ166458, FJ166459, FJ166460, FJ166461, FJ166462, FJ166463, FJ166464, FJ166465, FJ166466, FJ166467, FJ166468, FJ166469, FJ166470, FJ166471, FJ166472, FJ166473, FJ166474, FJ166475, FJ166476, FJ166477, FJ166478, FJ166479, FJ166480, FJ166481, FJ166482, FJ166483, FJ166484, FJ166485, FJ166486, FJ166487, FJ166488, FJ166489, FJ166490, FJ166491, FJ166492, FJ166493, FJ166494, FJ166495, FJ166496, FJ166497, FJ166498, FJ166499, FJ166500, FJ166501, FJ166502, FJ166503, FJ166504, FJ166505, FJ166506, FJ166507, FJ166508, FJ166509, FJ166510, FJ166511, FJ166512, FJ166513, FJ166514, FJ166515, FJ166516, FJ166517, FJ166518, FJ166519, FJ166520, FJ166521, FJ166522, FJ166523, FJ166524, FJ166525, FJ166526, FJ166527, FJ166528, FJ166529, FJ166530, FJ166531, FJ166532, FJ166533, FJ166534, FJ166535, FJ166536, FJ166537, FJ166538, FJ166539, FJ166540, FJ166541, FJ166542, FJ166543, FJ166544, FJ166545, FJ166546, FJ166547, FJ166548, FJ166549, FJ166550, FJ166551, FJ166552, FJ166553, FJ166554
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PubMed source DOI: 10.1038/ismej.2008.127 PMC Full Text View journal details
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