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Appl Environ Microbiol. Nov 2012; 78(21): 7527–7537.
PMCID: PMC3485727
Abiotic Factors Shape Microbial Diversity in Sonoran Desert Soils
David R. Andrew,corresponding authorab Robert R. Fitak,ac Adrian Munguia-Vega,dh Adriana Racolta,ae Vincent G. Martinson,af and Katerina Dontsovag
aIGERT Program in Comparative Genomics, University of Arizona, Tucson, Arizona, USA
bGraduate Interdisciplinary Program in Neuroscience, University of Arizona, Tucson, Arizona, USA
cGraduate Interdisciplinary Program in Genetics, University of Arizona, Tucson, Arizona, USA
dSchool of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, USA
eDepartment of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
fCenter for Insect Sciences, University of Arizona, Tucson, Arizona, USA
gBiosphere2, University of Arizona, Tucson, Arizona, USA
hComunidad y Biodiversidad, Guaymas, Sonora, Mexico
corresponding authorCorresponding author.
Address correspondence to David R. Andrew, dandrew/at/
Received May 8, 2012; Accepted August 4, 2012.
High-throughput, culture-independent surveys of bacterial and archaeal communities in soil have illuminated the importance of both edaphic and biotic influences on microbial diversity, yet few studies compare the relative importance of these factors. Here, we employ multiplexed pyrosequencing of the 16S rRNA gene to examine soil- and cactus-associated rhizosphere microbial communities of the Sonoran Desert and the artificial desert biome of the Biosphere2 research facility. The results of our replicate sampling approach show that microbial communities are shaped primarily by soil characteristics associated with geographic locations, while rhizosphere associations are secondary factors. We found little difference between rhizosphere communities of the ecologically similar saguaro (Carnegiea gigantea) and cardón (Pachycereus pringlei) cacti. Both rhizosphere and soil communities were dominated by the disproportionately abundant Crenarchaeota class Thermoprotei, which comprised 18.7% of 183,320 total pyrosequencing reads from a comparatively small number (1,337 or 3.7%) of the 36,162 total operational taxonomic units (OTUs). OTUs common to both soil and rhizosphere samples comprised the bulk of raw sequence reads, suggesting that the shared community of soil and rhizosphere microbes constitute common and abundant taxa, particularly in the bacterial phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Bacteroidetes, Chloroflexi, and Acidobacteria. The vast majority of OTUs, however, were rare and unique to either soil or rhizosphere communities and differed among locations dozens of kilometers apart. Several soil properties, particularly soil pH and carbon content, were significantly correlated with community diversity measurements. Our results highlight the importance of culture-independent approaches in surveying microbial communities of extreme environments.
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