ECIMMEE Project: Reef Fish Microbiomes: Models for Bacteria-Host Interaction in the Ocean
Animals harbor diverse and abundant microbial communities (microbiomes) that influence key aspects of host health, development, and behavior. The ecology and evolution of microbiomes remain almost completely unexplored for the largest and most diverse of the vertebrate groups, the teleost fishes. Coral reefs in particular support one of the richest assortments of fish among the major ocean ecosystems, with over 2500 species spanning a striking diversity of niches, reproductive and parental care strategies, and diet types. Reef fish microbiomes are hypothesized to harbor a wide diversity of uncharacterized bacterial lineages with potentially important roles as mediators of fish nutrition and disease prevention and as reservoirs for free-living or coral microbiome populations. The overarching goal of this project is to characterize the reef fish microbiome as a model for understanding microbe-animal interactions in the ocean. The research involves a combination of field sampling and laboratory experiments to understand the diversity of the reef fish microbiome and its relationship to host ecology and development, genomic analyses to identify key physiological properties and novel members of the microbiome, and experiments to quantify transmission routes of fish microbiomes and potential microbiome effects on fish behavior. This integrated approach will help identify connections between fish-associated and other microbial niches on reefs, as well as benefits of microbial-association, potentially including unrecognized contributions to fish immunity, digestion, and chemical signaling between individuals.
Frank Stewart is a marine microbiologist with broad interests in the genetic and metabolic diversity of ocean bacteria. His lab uses the tools of genomics and molecular biology to understand how marine microbes respond to environmental change and to symbiotic interactions with other organisms. In particular, research in the lab explores the diversity, evolution, and function of symbioses between bacteria and marine animals. This work targets diverse interactions, including those between deep-sea invertebrates and intracellular bacteria, as well as those within multi-species microbiomes on the surfaces and in the guts of reef corals and fish. The lab employs genomic and meta-omic methods to study these associations, often in collaboration with biogeochemists and ecologists. A second major research theme in the lab seeks to understand how declines in ocean oxygen content, due in part to climate change, affect microbial diversity and elemental cycling. This work focuses on major low-oxygen water masses in the Gulf of Mexico and the eastern Pacific Ocean, and involves a combination of oceanographic sampling, community genomics, biogeochemistry, and bioinformatics.
Dr. Stewart is an assistant professor in the School of Biology at Georgia Tech. He received a B.A. in Biology from Middlebury College and a Ph.D. in Organismic and Evolutionary Biology from Harvard University. He worked as a Postdoctoral Fellow at MIT before moving to Georgia Tech in 2011. He is a recipient of a Sloan Research Fellowship in Ocean Sciences and a Faculty Early Career Development Award from NSF.