Dr. Frank Stewart was awarded $540,000 in March 2015 by the Simons Foundation to investigate the microbiomes of reef fish. The Simons Foundation has made ocean processes and ecology one of their priority areas for investigation. They have initiated a Collaboration on Ocean Processes and Ecology (SCOPE) that will measure, model and experimentally manipulate a complex system representative of a broad swath of the North Pacific Ocean. This collaboration aims to advance our understanding of the biology, ecology and biogeochemistry of microbial processes that dominate the global ocean.  A central premise of SCOPE is that we must study the ocean ecosystem in situ, at a variety of levels of biological organization (e.g., genetic, biochemical, physiological, biogeochemical and ecological), and at highly resolved, nested scales of space and time in order to fully describe and model it.

By investigating fish microbiomes, Dr. Stewart hopes to better understand how bacteria interact with their hosts in the ocean. Symbiosis between microorganisms and higher eukaryotes is among the most pervasive evolutionary and ecological strategies in nature, impacting fundamental processes including speciation, ecosystem structuring, primary production, nutrient cycling, and disease.  A surge of studies exploring the commensal microbiome of the human body has identified complex networks of factors shaping microbiome acquisition, composition, and function, as well as a range of host developmental and immunological outcomes affected by microbiome activity. For most animal lineages, excluding humans, the ecology and evolution of host-associated microbiomes are almost completely unexplored.  This is true for the largest and most diverse of the vertebrate groups, the teleost fishes. In many ocean regions, notably in productive coastal zones and reefs, teleosts play vital roles in material and energy transport and ecosystem structuring.  Teleosts on coral reefs represent over 2500 fish species and engage in a complex network of ecological interactions including nutrient recycling, herbivory, corallivory, and symbiosis. Fish also serve cryptic roles as habitats for microorganisms.  Given the phylogenetic and ecological breadth of reef teleosts and the potential for host species-specificity in vertebrate microbiomes, reef fish microbiomes are hypothesized to harbor a wide diversity of uncharacterized bacterial lineages.  Such lineages may play important roles as mediators of fish nutrition and disease prevention and as inocula for free-living or coral microbiome populations.

Dr. Stewart will execute an integrated research plan over three years to sample deeply across this spectrum, combining 1) 16S rRNA gene sequencing, multivariate, and indicator analyses to identify determinants of fish gut and mucus microbiome composition, 2) quantitative metagenomic and single-amplified genome (SAG) sequencing of indicator microbes to identify shared (core) and peripheral (host-specific) functional properties, and to enable comparisons to pathways in microbiomes of other major vertebrate groups, and 3) targeted experiments to quantify acquisition and transmission dynamics of fish microbiomes. The proposed work will help to quantify connectivity between host-associated and external microbial niches, as well as identify host benefits of microbial-association, potentially including unrecognized contributions to immunity, digestion, and chemical signaling between host individuals.