CAREER: Fungal pathogen induced dysbiosis alters microbiome assembly along host resource gradients: implications for biodiversity conservation

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Reptiles are among the most threatened species on Earth with approximately 20% of taxa at risk of extinction. This threat is likely a cumulative effect of environmental, climatic, and biotic factors, such as emerging pathogens. Recently, a fungal pathogen of snakes (Ophidiomyces ophidiicola) has been linked with population declines in the USA. This snake skin pathogen causes changes to the skin microbiome by affecting the structure and function of bacterial assemblages. The microbiome is an important component of host health and can provide disease resistance to wildlife pathogens. This research will study interactions between O. ophidiicola and skin microbiomes, with tangible conservation implications. The proposed model system will advance understanding of mechanisms that contribute to variation in microbiome communities across gradients. The researchers propose to fill a knowledge gap by testing for the effects of fungal pathogens on mechanisms of microbiome community assembly, and more generally, advance fundamental knowledge of disease ecology. Outreach activities with zoos and the Great Smoky Mountains National Park will help inform the general public about wildlife disease and the importance of skin microbiomes in biodiversity conservation. An undergraduate microbiome scientist program at Middle Tennessee State University will contribute to the training of the next generation of microbial ecologists. Dysbiosis is defined as disruption to the typical function or composition of a microbiome, potentially resulting in adverse effects to host health. The proposed work will use the snake fungal disease system to improve understanding of disease ecology, bacterial-fungal interactions and dysbiosis to skin microbiomes. This will be accomplished by studies spanning multiple scales (field, live animal, lab-based) in ecology to allow for explicit hypothesis tests, cross validation of observed ecological trends and establishment of fundamental rules governing pathogen induced dysbiosis. The researchers will test the following hypotheses, H1: Bacterial assemblages of reptile skin microbiomes are structured by interactions with fungi across space, time and host ecology. H2: Variation in microbiome α- and β-diversity are predictably altered by pathogen induced dysbiosis. H3: Taxonomic and functional variability are attributed to metabolic niche effects across a gradient of host resources and/or fungal metabolites. This research will produce a comprehensive census of bacterial and fungal microbiome diversity on reptile species with important contributions to inform experimental systems focused on microbial interactions and disease ecology.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.