Collaborative Research: Defining the role of skin microbiomes in defense against chytridiomycosis in frogs with seasonal infections

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Microbiomes are a ubiquitous part of all ecosystems including the skin. Although the idea that “good” microbes can defend against pathogens is widely accepted, it is still unclear how microbial communities provide benefits to the host under variable climates. This research will examine the defense mechanisms against a lethal skin fungus that has been associated with global amphibian declines. The studies will investigate the links between natural skin microbes and frog immunity to understand seasonal changes in disease outcomes using a species of frog that can die of infection but can survive under optimal environmental conditions. This project addresses the interplay between disease susceptibility and immunity for species that do not have a free-living tadpole stage but instead are direct-developing frogs. Considering the current changes in weather patterns, seasonality is expected to shift over time, adding more instability to host-pathogen relationships. To address how microbiomes in skin interact with the immunological response to this pathogen, the researchers will study frogs in natural populations and perform controlled laboratory experiments. The results will allow better predictions about the impact of seasonal variations on species interactions that can influence defense against emerging diseases. The researchers will develop and disseminate course materials for a college-level Disease Ecology course that integrates fundamental concepts from ecology and evolution and from the molecular level to ecosystem impacts. In addition, the researchers will work with the Florida Museum of Natural History to develop outreach travel exhibitions targeted to middle schoolers about amphibian disease ecology and microbiomes. Amphibians are globally threatened by chytridiomycosis, a fungal disease caused by Batrachochytrium dendrobatidis, and hosts often live under dynamic cycles of low and high pathogen risk. This proposal will focus on the direct-developing frog, Eleutherodactylus coqui, a species that persists in the wild with infections modulated by abiotic factors and microbial communities. The researchers will test if host immune defenses interact with skin microbiome by regulating the presence/absence of certain bacterial members, in turn influencing susceptibility to fungal infection. The researchers will assemble sets of microbial consortia (i.e., groupings of putative symbionts with different community structures) to quantify host immune defenses including constitutive immunity and adaptive responses in the field and in the lab. The proposal includes three research objectives: 1) characterize population-level seasonal consortia of skin bacteria, immune defenses in the skin secretions, and their interactions, 2) test for the redistribution of host defenses under contrasting backgrounds of bacterial diversity, and 3) measure life-stage variability in putative symbionts, host skin defenses, and resulting pathogen burden. The project will leverage individual-level data from host defenses and microbiological assays, microbiome amplicon sequencing, and functional genomics to evaluate the timing and magnitude of responses. Integrated studies of skin microbiomes seen through the lens of host skin defenses under different environmental conditions will shed light on the role of the environment, immunity, and microbiome in resistance and tolerance to disease.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.