Bacterial and Archaeal Community Structure of Two Adjacent Calcite Speleothems in Kartchner Caverns, Arizona, USA

Abstract

Information concerning the bacterial and archaeal communities present on calcite speleothems in carbonate caves is of interest because the activity of these microbes has been implicated as a potential biogenic component in the formation of secondary mineral deposits. In addition, these speleothems may harbor unique, previously unidentified microbes. The current study presents a comparative analysis of the superficial bacterial and archaeal community structure of multiple stalactites from two different cave formations located in close proximity to each other in a nonhuman-impacted area of Kartchner Caverns, Arizona, USA. PCR-denaturing gradient gel electrophoresis analysis (PCR-DGGE) revealed that microbial communities sampled from stalactites of a single speleothem are more similar to each other than to the communities sampled from stalactites of an adjacent speleothem, suggesting that both bacterial and archaeal communities are speleothem-specific. SR-XRD analysis confirmed that both speleothems sampled were primarily calcite, but subtle differences were detected in the elemental composition profiles obtained from ICP-MS analysis indicating that substrate geochemistry was also speleothem-specific. PhyloChip analysis of composite samples from both speleothems revealed a broad diversity of phyla represented in the bacterial communities, while bacterial and archaeal bands sequenced from the DGGE profiles confirmed the presence of unique phylotypes not closely related ( < 96% similarity) to any sequences deposited in the GenBank database.

Keywords:

• Carbonate cave
• speleothem
• DGGE
• Community structure
• PhyloChip

ACKNOWLEDGMENTS

We express our sincere appreciation to Dr. Robert Casavant and Ginger Nolan from Arizona State Parks for their assistance in sample site selection and for the expertise that they have shared with respect to the history, geology and development of the cave. We acknowledge the assistance of Mary Kay Amistadi from the Arizona Laboratory of Emerging Contaminants who developed the nitric acid digestion protocol for the ICP-MS analysis of the stalactite samples to accommodate the small sample size. In addition, we thank Sarah Hayes and Dr. Jon Chorover from the University of Arizona, Department of Soil, Water and Environmental Science for the Synchotron-radiation X-ray diffraction (SR-XRD) mineral analysis of the stalactite samples and for their assistance in the data interpretation. Furthermore, we thank Dr. Yvette M. Piceno from the Lawrence Berkeley National Laboratory, Earth Sciences Division for the PhyloChip analysis of the bacterial communities of the speleothem samples.

This research was supported by Microbial Observatories Grant MCB0604300 from the National Science Foundation with additional funding from the Arizona State Parks Board.