Molecular Phylogenetic Analysis of a Bacterial Community in an Oligotrophic Cave Environment

Abstract

While much work has been carried out on cave communities that obtain energy from measurable exogenous energy sources (surface organics, sulfide or nitrite), very little work has been carried out on communities that subsist in regions of nutrient scarcity. In this study we generated a 16S SSU-rDNA clone library from an oligotrophic, bacterial community that occurs on a wall in Fairy Cave, Glenwood Springs, Colorado, in the absence of observable energy sources. Thirty-eight unique phylotypes based on restriction fragment length polymorphisms were identified and sequenced. Phylogenetic analysis of the sequences revealed that these phylotypes did not correspond to any known sequence, but were related to organisms in the bacterial divisions Proteobacteria, Actinobacteria, Cytophagales and the Low G+C gram-positive bacterial relatedness group. Comparative metabolic analysis suggests that the bacterial community subsists using a complex metabolic network, with input from trace organics within the environment or fixation of atmospheric gases using lithotrophic metabolism. Community distribution of these phylotypes is unique from previous observations in caves using cultivation, suggesting that many of the species identified are sufficiently adapted to the oligotrophic lifestyle and thus remain resistant to cultivation using standard techniques. Such oligotrophic microbial communities may reflect the principal form of life in subaerial cave environments.