Fish are recognized as a major global food resource, key ecological components of aquatic ecosystems, and have been valuable laboratory model organisms to study vertebrate biology. Like all animals, fish harbor rich communities of symbiotic microorganisms both upon their external body surfaces, such as the skin, and internally, such as the gut. These microbial populations play important roles in the health and fitness of their hosts by providing protection against invading pathogens, regulating immune functions, and the breakdown of environmental and dietary compounds. This project investigates the microbiota associated with two common marine fish species with contrasting feeding ecologies, the carnivorous Pacific chub mackerel and the herbivorous opaleye. Robust cultivation systems will be developed to propagate fish-associated microbes in the laboratory and analyzed using high-throughput DNA sequencing and small molecule detection methods. The data will be incorporated into a computational model to analyze and predict microbiome interactions. Thus, this research will provide an experimental framework to understand microbial contributions to fish biology and reveal the intricate interactions between microbes within the fish gut microbial ecosystem. This work has broad significance for understanding microbial activities that promote the diversity and ecology of marine fishes and can inform sustainable aquaculture practices by manipulating the fish microbiome to improve fish health and aquaculture yield. Additional benefits to society include the training of undergraduate and graduate students and the development of STEM education modules that explore the ocean microbiome.

The microbiota associated with marine fish represent an uncharted source of novel catabolic and biosynthetic pathways that impact the physiology and ecology of their hosts. This project will pioneer the development of robust in vitro bioreactor cultivation systems to replicate and propagate marine fish gut microbiota in the laboratory to assess and experimentally manipulate metabolic outputs of the fish microbiome. Classical and high-throughput cultivation methods will also be used to obtain isolates representing different fish gut microbiome functional guilds from natural samples and in vitro bioreactors. These isolates will be assembled into reproducible and experimentally tractable synthetic communities to study emergent properties of community organization and microbe-microbe interactions. Multi-omic data sets (metagenomics, metatranscriptomics, and untargeted metabolomics) will be integrated using computational modeling approaches (neural network statistical methods) to discover linkages between key microbial taxa, their enzyme diversity, metabolite production, and biotransformations within the high-fidelity bioreactor systems. The project will deliver new perspectives on microbiome dynamics in aquatic animals, setting the foundation for future microbiome-host studies and novel resources for microbial discovery.

This project is funded by the Understanding the Rules of Life: Microbiome Theory and Mechanisms Program, administered as part of NSF's Ten Big Ideas through the Division of Emerging Frontiers in the Directorate for Biological Sciences. Co-funding is provided by the Systems and Synthetic Biology Program, Division of Molecular and Cellular Biosciences, Directorate for Biological Sciences.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

National Science Foundation (NSF)
Emerging Frontiers (EF)
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Mamta Rawat
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University of California-San Diego Scripps Inst of Oceanography
La Jolla
United States
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