The bodies of animals contain multitudes of bacteria that are sensitive to their diet and critical to their health. These unseen players are major forces in evolution, population fluctuations and the dynamics of ecosystems, but their roles are largely unknown. This project investigates the effects of animal-associated bacteria and evolutionary change in two critical ecological processes: the flow of energy from plants to herbivores, and cycling of predator and prey populations. Plankton in lakes are ideal for testing these questions as they are ubiquitous and amenable to experiments over multiple generations and evolutionary time scales. The project tests the roles of evolution and microbiome composition in the response of plankton to changes in diet and climate from the top to the bottom of the Sierra Nevada Mountains of California. Experiments and models in a classic lab system of cycling populations of invertebrates and algae will test the roles of evolution and changes in associated bacteria in food chain stability. This research explores the integral roles of host-associated microbes and genetic adaptation in the stability and resilience of populations and ecosystems facing environmental change, and their capacity to sustain delivery of vital ecosystem services like clean water and healthy fisheries. This project will expand STEM education activities for Hispanic communities and will train a postdoctoral researcher and a graduate student.

The project uses a combined approach integrating observations in nature, lab experiments and modeling to test the roles of genetic adaptation and microbiomes in the adaptive potential of populations and ecosystems. Sequencing environmental samples will reveal changes in zooplankton microbiomes from warm lakes with a low quality, terrestrial food base, to cold lakes with more nutritious algae. Microbiome transplant experiments with clones isolated from different lakes will reveal the roles of genetic adaptation and host-associated bacteria in the transfer of energy from producers to consumers. Culturing invertebrates in the presence and absence of co-adapted microbes will reveal their effect on dynamic stability of predator prey cycles, and sequencing of functional genes (metagenomics) will show how adaptive potential arises from the host’s genes vs. associated symbionts. Finally, mathematical models of lake food webs will synthesize the empirical results to explore the effects of microbiomes for top-down control of primary production by consumers and the vertical flow of energy to upper trophic levels like fish.

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)
Division of Environmental Biology (DEB)
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Andrea Porras-Alfaro
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University of California San Diego
La Jolla
United States
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