Molecular Phylogenetic Analysis of Archaea and Bacteria in Wind Cave, South Dakota

Abstract

The diversity of bacteria and archaea was characterized from sediments collected from Wind Cave located in Wind Cave National Park in the Black Hills of South Dakota. Wind Cave is a limestone dissolution cave with strata that started forming over 300 million years ago, making it one of the oldest in the world. Previous work suggested that the cave was largely a detritus based system ultimately dependent upon allochthonous energy and carbon from photosynthesis of the overlying vegetation, and algae growing near lights along the tour routes. In this work, we used a molecular phylogenetic approach to characterize the microbial structure and infer a corresponding ecosystem function where appropriate. Four bacterial divisions and subdivisions were found in the culture collection, which represented 14 phylotypes, whereas 12 divisions and subdivisions were identified in the clonal analysis comprising 49 phylotypes. The predominant groups were the γ-Proteobacteria and Acidobacteria. Although a few of the clones resembled sequences from other cave and subterranean systems, no cave-specific bacterial community was evident in this work. Archaeal phylotypes (20 Crenarchaeota and 2 Euryarchaeota) were detected, with a large proportion of the Crenarchaeota resembling sequences from a South African gold mine. One archaeal cluster in particular appears to be specific to the subterranean environment. Most of the microbial sequences were not related to known chemolithoautotrophs, therefore we conclude that this particular community is likely detritus based where allochthonous energy and carbon are transported into the cave by infiltrating waters.

Keywords:

• Archaea
• bacteria
• cave
• diversity
• 16S rDNA

We thank the National Science Foundation (DEB-9819525), and the U.S. National Park Service at Wind Cave National Park for supporting this work. Special thanks to Rod Horrocks, Cave Specialist at Wind Cave, for his assistance with the logistics of the cave trips, R. Horrocks and P. Heimbrook and anonymous reviewers for their comments on the manuscript. We are grateful to H. Horton, A. Ratcliffe, K. Melville, C. Pritekel, and G. Selby for field and laboratory assistance.

Notes

∗Below detection limit.