SARD: A Novel Surveying Method to Develop Genomic Reagents

75703S Microbes play a vital role in all aspects of our lives, yet our ability to understand these processes is limited by the availability of appropriate tools. Current microbial survey methods capture only the most abundant organisms in complex communities, organisms that may represent less than 1% of the species present. This project involves the development of a new genomics tool, known as SARD (Serial Analysis of Ribosomal DNA), which enables deep surveys of complex microbial communities by creating an inventory of short DNA sequence tages representing members of the community. A particular application of the technology is the identification of bacterial species that can be used to locate hydrocarbon plumes that originate from sub-surface petroleum reservoirs. Phase I isolated a greater number of unique sequence tages than currently reside in any public database, identified clusters of sequences that correlate with propane/butane abundance, developed quantitative assays, and conducted surveys to show the geographical distributions of these sequences. In Phase II, the technology will be further developed by profiling on-shore exploratory well sites and marine samples from known reservoirs. These profiles will be further analyzed to determine the ability of this technology to accurately predict a commercially viable well. Commercial Applications and Other Benefits as described by the awardee: By creating inventories of any microbial community, the SARD profiling technology should have commercial application to petroleum and mineral exploration, pollutant detection, and clinical diagnostics. In addition, the SARD DNA sequence tages themselves represent a genomic resource that should find use as: (1) a PCR (polymerase chain reaction) primer to recover the corresponding full-length 16S rRNA gene; (2) a primer in a quantitative PCR assay to query the presence of the tage sequence in a large sample collection; (3) a fluorescently-labeled probe in fluorscent in situ hybridization (FISH) experiments; and 4) a probe on a DNA microarray for hybridization-based surveys.