Award: OCE-1235142

This proposal explored the ecological functions of bacterial secondary metabolites as agents of chemical defense. It addressed the hypothesis that these compounds help to structure sediment microbial communities and deter predation by protistan grazers. The results add to our understanding of competitive interactions among bacteria and revealed that even among closely related strains, it is possible to distinguish between lineages that invest in growth and defense. These finding were published in the ISME Journal (Patin et al., 2015) in a paper that was awarded the 2016 Freeman Prize for the best graduate student publication at the Scripps Institution of Oceanography. While this study addressed bacteria that could be cultured, a second study addressed the effects of bacterial metabolites on the sediment community using culture independent approaches. Using next generation amplicon sequencing, it was possible to show that chemical defenses appeared to target specific taxa, including predatory bacteria. This study was published in Applied and Environmental Microbiology (Patin et al., 2016) and was selected by the editors for “in the spotlight” recognition. While the major focus of these studies was to address chemical defense, we also became aware that some of the compounds we were studying possess redox active structural features suggesting they could facilitate survival in marine sediments when oxygen was not readily available. We have submitted a manuscript on these findings to Environmental Microbiology entitled “Ecological Implications of Hypoxia-triggered shifts in Secondary Metabolism” by Gallagher et al. These studies also led us to recognize that we needed better methods to delineate ecologically relevant groups of bacteria. Using a population genomics approach, we applied various species concepts and identified secondary metabolism as a key functional trait that correlated well with phylogeny. These results have been submitted to the ISME Journal in a manuscript entitled “Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations” by Millan et al. During the course of this project, it also became apparent that there were no relevant reviews in the area of marine microbial chemical ecology. In response, we wrote a comprehensive review on the role of small molecules in mediating interactions between bacteria and other organisms. This was published in the Journal of Chemical Ecology (Weitz et al., 2013). We also became interested in the concept that the sediment bacteria we were studying may also maintain defenses against phage. We addressed this using bioinformatic approaches, which led to the publication entitled “CRISPR-Cas Systems in the Marine Actinomycete Salinispora: Linkages with Phage Defense, Microdiversity and Biogeography” (Weitz et al., 2014) in BMC Genomics. Finally, we are nearing the completion of a manuscript that describes the effects of bacterial metabolites on nematode grazing. The results demonstrate that specific compounds act as feeding deterrents and that this represents a poorly characterized function of some compounds. Collectively, these project outcomes provide important advances in our understanding of the roles of secondary metabolites in chemical defense.

The broader impact outcomes of this project included the development of a program to teach middle school students from the New Museum School in San Diego the importance of microbial diversity and healthy marine ecosystems was created. The PI’s lab hosted seven visits during the course of this award. These visits included classroom lectures followed by field exercises, such as plankton tows off the Scripps pier, and laboratory demonstrations. We established stations where students looked at plankton samples under a dissecting microscope and were shown how bacteria use antibiotics to compete in nature. These activities tied into the ultimate theme of the visits; that healthy ocean ecosystems are essential for the well being of humankind. Broader impacts also including mentoring three summer undergraduates through the NSF funded SURF program and one through the STARS program. Both programs are designed to provide meaningful research experiences for members of underrepresented groups to encouragement to pursue graduate studies in STEM fields. Two of these students have applied for admission to graduate school next fall.

Last Modified: 01/18/2017
Modified by: Paul R Jensen