S21: A phylogenetic microarray approach to monitoring and source tracking coastal-zone pollution

Understanding the origins of fecal pollution is essential to associate health risks as well as the actions needed to remedy the problem. Towards this end, we have developed a high-density microarray system to accurately measure a broad range of bacterial and archaeal components within any ecosystem Unique regions of DNA within gene sequences of the16S small subunit of bacterial and archaeal ribosomes are used to identify specific organisms. To assist in probe design, an online tool (Greengenes, http://greengenes.lbl.gov) was developed to maintain a comprehensive set of aligned, full-length, chimera-screened 16S rRNA genes and which allows users to exchange taxonomic annotations. We are using this high-density LBNL PhyloChip microarray to measure the occurrence and activity of bacteria and archaea in coastal waters that are routinely monitored for fecal indicator bacteria. The aim is to identify fecal indicator communities that can be used as sensitive and highly specific markers of various pollutants. Fecal sources such as agricultural runoff and septic waste are placed in receiving waters to determine the survivability and activity of each of the several thousand different microbial taxa that comprise the complex microbial communities found in potential pollutants.  This approach will allow us to identify a robust set of indictor taxa whose response to changing environmental conditions, such as salinity, is better understood.