This is a Small Grant for Exploratory Research (SGER) award to identify and sequence metagenomic clones derived from Alaskan soil that produce biologically active small molecules. This exploratory project was stimulated by two recent events: first, the development of a rapid intracellular assay to identify clones that produce signaling molecules; and second, recently published studies of the metagenomes of the Sargasso Sea and an acid mine drainage community, respectively, that illustrate the power of obtaining vast amounts of sequence data from metagenomic sources.
Slicing complex microbial communities many ways is necessary to construct a comprehensive portrait of them. Some of the most fruitful approaches to obtain slices of microbial communities include: culturing, PCR amplification of 16S rRNA sequences, identification of phylogenetic anchors on metagenomic clones, and analysis of random end sequences of metagenomic clones. The phylogenetic anchor approach involves sequencing all clones that contain a certain phylogenetic marker. The collection of clones containing 16S rRNA phylogenetic information provides the basis for inferences from nucleotide sequence about functions performed by the organisms from which the fragments of metagenomic DNA originated. By contrast, this project will introduce the use of a functional anchor - the converse of the phylogenetic anchor approach. The function anchor approach will be used to identify all clones in a library that express a certain function and then sequence them to obtain phylogenetic information about their origins. If successful, this will become a new standard of analysis of metagenomic libraries that will provide access to new genes whose functions might not have been suspected by inspection of their sequences and phylogenetic inference about the origins of those functions. Undergraduate students will also be involved in the project, with the investigators utilizing and evaluating two different approaches to attracting and incorporating members of underrepresented groups in science.
