Abstract
We surveyed the diversity of soil Archaea across a large scale elevational gradient of ecosystem types, from foothills forest to alpine tundra in the Front Range of the Rocky Mountains. We used a dilution technique to sequence the single most abundant archaeal 16S rDNA sequence in each of the 40 soil cores distributed across the gradient to compare our results to those of typical 16S clone library studies.We found a greater diversity of sequences than has typically been found in clone library studies from a single site or core, identifying sequences both from the Terrestrial Group and the FFSB Group at several sites. We did not observe any significant environmental correlates with the dominant sequence type, nor was there any relationship between the spatial distance between samples and the phylogenetic similarity of the dominant sequence types. Despite using a very different methodology, our collective results are in remarkably good agreement with other studies of soil Crenarchaeota in terms of the diversity and relative abundance of sequence types identified. We are able to identify two instances of very tightly clustered sequences which we suggest are the results of global selective sweeps—one closely related to SCA1145, an abundant globally distributed group within the Terrestrial Group of Crenarchaeota, and another nested within the more basal FFSB group of sequences. We replicated our sequence results at two levels: first, by repeating the dilution and PCR processes from the same soil core DNA extraction, and second, by performing a replicate DNA extraction from the same homogenized soil core sample. Pairs of sequences produced by the dilution replicates were significantly more similar than the pairs of sequences produced by the extraction replicates, suggesting that soil Crenarchaeota exists in highly localized and discrete clonal populations.
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Acknowledgments
The authors wish to thank J. Mitton, B. Kreiser, R. Ramey, A. Martin, T. Seastedt, and B. Bowman. We also thank the Arapahoe-Roosevelt National Forest, the University of Colorado Mountain Research Station, and the Niwot Ridge LTER site for their support. Thanks to R. Gutell for secondary structure diagrams of rRNA sequences, R. Sandaa for providing sequence data, and H. Simon for providing a preprint of her manuscript. Special thanks to samiam.colorado.edu for an outstanding effort devoted to the cause of molecular phylogeny.
Funding for this research was provided by the Colorado Mountain Club, the David Paddon Memorial Scholarship of the Indian Peaks Working Group, the Beverley Sears Deans Small Grants, Sigma Xi, the Department of EPO Biology at the University of Colorado, the National Science Foundation Dissertation Improvement Grants (DEB-9972713), and the Microbial Observatories program (DEB-0084243).
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Oline, D.K., Schmidt, S.K. & Grant, M.C. Biogeography and Landscape-Scale Diversity of the Dominant Crenarchaeota of Soil. Microb Ecol 52, 480–490 (2006). https://doi.org/10.1007/s00248-006-9101-5
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DOI: https://doi.org/10.1007/s00248-006-9101-5