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Profiling Bacterial Diversity and Taxonomic Composition on Speleothem Surfaces in Kartchner Caverns, AZ

  • Environmental Microbiology
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Abstract

Caves are relatively accessible subterranean habitats ideal for the study of subsurface microbial dynamics and metabolisms under oligotrophic, non-photosynthetic conditions. A 454-pyrotag analysis of the V6 region of the 16S rRNA gene was used to systematically evaluate the bacterial diversity of ten cave surfaces within Kartchner Caverns, a limestone cave. Results showed an average of 1,994 operational taxonomic units (97 % cutoff) per speleothem and a broad taxonomic diversity that included 21 phyla and 12 candidate phyla. Comparative analysis of speleothems within a single room of the cave revealed three distinct bacterial taxonomic profiles dominated by either Actinobacteria, Proteobacteria, or Acidobacteria. A gradient in observed species richness along the sampling transect revealed that the communities with lower diversity corresponded to those dominated by Actinobacteria while the more diverse communities were those dominated by Proteobacteria. A 16S rRNA gene clone library from one of the Actinobacteria-dominated speleothems identified clones with 99 % identity to chemoautotrophs and previously characterized oligotrophs, providing insights into potential energy dynamics supporting these communities. The robust analysis conducted for this study demonstrated a rich bacterial diversity on speleothem surfaces. Further, it was shown that seemingly comparable speleothems supported divergent phylogenetic profiles suggesting that these communities are very sensitive to subtle variations in nutritional inputs and environmental factors typifying speleothem surfaces in Kartchner Caverns.

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Acknowledgments

We would like to express our appreciation to Robert Casavant and Ginger Nolan for their assistance during speleothem selection and sampling in Kartchner Caverns. Also, we want to thank Nick Sisneros for his assistance with 454 pyrosequencing. Funding for this work was supplied by the National Science Foundation Microbial Observatory grant MCB0604300.

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Authors and Affiliations

  1. Department of Soil, Water and Environmental Science, University of Arizona, Shantz Bldg Room 429, 1177 E. 4th Street, Tucson, AZ, 85721-0038, USA

    Marianyoly Ortiz, Julia W. Neilson, Antje Legatzki, Andrea Byrne & Raina M. Maier

  2. BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA

    William M. Nelson & Carol A. Soderlund

  3. Department of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA

    Yeisoo Yu, Rod A. Wing & Barry M. Pryor

  4. Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA

    Leland S. Pierson III

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  1. Marianyoly Ortiz
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Correspondence to Raina M. Maier.

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Ortiz, M., Neilson, J.W., Nelson, W.M. et al. Profiling Bacterial Diversity and Taxonomic Composition on Speleothem Surfaces in Kartchner Caverns, AZ. Microb Ecol 65, 371–383 (2013). https://doi.org/10.1007/s00248-012-0143-6

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