Microbial Community Structures Correlated with Geochemistry: a DNA-based Exploration Technology

Dimster-Denk, Dago¹, Matthew Ashby¹, Emmanuel Mongodin², Karen Nelson², Thomas Lorenson³ (1) Taxon Biosciences, Inc, Tiburon, CA (2) The Institute for Genomic Research, Rockville, MD (3) U.S. Geological Survey, Menlo Park, CA

The development of molecular technologies in recent years allowing for the direct detection of microbial cells without laboratory culturing is leading to a much greater understanding of the incredible species richness in the microbial world, as well as their ubiquitous distribution in the environment. Although the presence of microbes on the whole may be ubiquitous, the distribution of individuals, or sub-groups, with varying metabolic potential is not. Ultimately the local geochemistry determines which organisms are able to survive in a given ecological niche through natural selection. Therefore, a method to describe the structure of a microbial community at a given locale would provide a very sensitive biological “fingerprint” of the geochemistry of the site.

A proprietary DNA-based technology termed SARD (for Serial Analysis of Ribosomal DNA) has been developed that allows for high resolution, quantitative surveys of microbial communities. SARD surveys have been performed on a variety of near surface and sub-surface samples located both onshore and offshore. A database of more than 130,000 DNA sequences was assembled from hydrocarbon-associated samples. Two-dimensional hierarchal cluster analysis identified specific DNA sequences that are correlated with various geochemical parameters that characterize the sites. A series of quantitative assays have been developed for DNA sequences which strongly correlate to specific geochemical features. This technology allows determinations of geochemistry based on the distribution of microbial indicator species.