Metagenomics and Ecology

Small-molecule discovery by functional metagenomics has concentrated on antibiotics, which are of interest for their pharmaceutical applications as well as for their roles in ecosystem function. Traditional antibiotic screens for molecules that inhibit bacterial growth have led to the discovery of antibiotics in metagenomic libraries. The exigent questions in microbial ecology focus on how microorganisms form symbioses with eukaryotes, compete and communicate with other microorganisms, and acquire nutrients and produce energy. Ecological hypotheses are difficult to test in microorganisms that cannot be cultured or for which there are no genetic tools; however, functional genomics coupled with chemical ecology can yield informative answers. Chemical ecology involves the identification of small molecules with biological activity and proposed ecological function. The following sections explore the discovery of small molecules in metagenomic libraries and postulate the ecological functions of these molecules in the organisms producing them.