Microbial Ecology

, Volume 65, Issue 2, pp 371–383 | Cite as

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

  • Marianyoly Ortiz
  • Julia W. Neilson
  • William M. Nelson
  • Antje Legatzki
  • Andrea Byrne
  • Yeisoo Yu
  • Rod A. Wing
  • Carol A. Soderlund
  • Barry M. Pryor
  • Leland S. PiersonIII
  • Raina M. Maier
Environmental Microbiology


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.


Bacterial Community Proteobacteria Actinobacteria Operational Taxonomic Unit Drip Water 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



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.

Supplementary material

248_2012_143_MOESM1_ESM.doc (276 kb)
ESM 1 (DOC 276 kb)


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Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  • Marianyoly Ortiz
    • 1
  • Julia W. Neilson
    • 1
  • William M. Nelson
    • 2
  • Antje Legatzki
    • 1
  • Andrea Byrne
    • 1
  • Yeisoo Yu
    • 3
  • Rod A. Wing
    • 3
  • Carol A. Soderlund
    • 2
  • Barry M. Pryor
    • 3
  • Leland S. PiersonIII
    • 4
  • Raina M. Maier
    • 1
  1. 1.Department of Soil, Water and Environmental ScienceUniversity of ArizonaTucsonUSA
  2. 2.BIO5 InstituteUniversity of ArizonaTucsonUSA
  3. 3.Department of Plant SciencesUniversity of ArizonaTucsonUSA
  4. 4.Department of Plant Pathology and MicrobiologyTexas A&M UniversityCollege StationUSA

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