Why Sequence an Alaskan Soil?

This project tests a new tactic for profiling microbial communities, the functional anchor approach. The strategy is to identify all clones in a library that express a certain function and then sequence them to obtain phylogenetic information about their origins. The limitation of sequence-based approaches is that genes that do not match known motifs are not recognized. By starting with a functional analysis, one can identify genes that lack homology to known ones, adding functional richness to the gene databases. Moreover, the functional approach provides a community-wide view of the diversity of genes and gene products that are involved in a given community function. For example, one might identify the diversity of molecules in a soil community that induce quorum sensing, and patterns might emerge, especially with respect to the phylogenetic origins of different mechanisms or structural classes of inducers.

Our collaborators have developed an intracellular screen in which a biosensor that detects quorum-sensing activity is located inside the same host cell as the metagenomic DNA. If the metagenomic DNA directs the synthesis of a small molecule that induces the quorum sensing biosensor, then the clone is detected by fluorescence. The JGI will sequence libraries from Alaskan soil, screened for clones that either inhibit or induce the quorum sensing biosensor.

This sequence will provide insight into the fraction of the community that shares the common feature of genes that affect quorum sensing. This work will lead to a biological profile of the soil community examined through the lens of one function. Bringing to bear the sequencing power of JGI on this project will enable researchers to obtain a good test of the use of the functional anchor approach to community analysis.

The soil to be sequenced represents one of the most complex communities on Earth. The methods developed will be applicable to communities that range in complexity. By using a subset of the data, researchers may be able to model simpler communities and functions in them.

CSP project participants: Jo Handelsman (Univ. of Wisconsin-Madison)