Project: The Chemical Ecology of Marine Sediment Bacteria

This project explores the ecological functions of bacterial secondary metabolites as agents of chemical defense. It targets marine sediments, a major and poorly explored marine biome. The aims are to test three hypotheses related to the effects of bacterial secondary metabolites on co-occurring microorganisms and protistan grazers. The focus is on the bacterial genus Salinispora, which is well defined in terms of its diversity and distributions in marine sediments, and well characterized at the genomic level and in terms of secondary metabolite production. A genetic system recently developed for these bacteria will be employed to establish links between biological activities and specific secondary metabolites. By employing a variety of innovative methodologies including imaging mass spectrometry, it will be possible for the first time to gain insight into the potential roles of Salinispora secondary metabolites in structuring marine sediment microbial communities. The results will have broad implications for our understanding of the factors that regulate the diversity and distributions of bacteria in the marine environment. They will additionally address the supplemental hypothesis that secondary metabolites represent ecotype-defining traits that delineate Salinispora species.

The hypotheses to be tested are:
H1: Secondary metabolites inhibit microbial competitors,
H2: Secondary metabolites affect bacterial community composition, and
H3: Secondary metabolites function as invertebrate feeding deterrents.

A large collection of diverse, co-occurring microbes will be tested for sensitivity to Salinispora secondary metabolites using a direct challenge assay. These types of assays are highly informative in that they can detect behavioral and morphological responses in addition to toxicity. A recently developed imaging mass spectrometry technique will be used to visualize secondary metabolites associated with any observed biological activities. The results will be linked to existing genome sequences and used to aide in compound identification. The associated pathways will be knocked out to provide experimental support for the biological activities of specific compounds.

Given that most marine bacteria are not readily cultured, these experiments will additionally address the effects of secondary metabolites on the sediment bacterial community by employing culture independent techniques. In situ growth chambers and next generation sequencing technologies will be used to test extracts and pure compounds against a natural assemblages of sediment bacteria. The results will inform future cultivation efforts and provide a more comprehensive assessment of the organisms targeted by native chemical defenses. Finally, a robust feeding assay using two model protists will be developed and used to test the roles of bacterial secondary metabolites as invertebrate feeding deterrents. In situ experiments will provide insight into the natural assemblage of invertebrates affected by these defenses. The overall results of these studies have the potential to profoundly impact our understanding of the ecological functions of microbial secondary metabolites and the extent to which these compounds affect community composition.