Comparative genomics of skin microbiota from B. dendrobatidis infected amphibians from Cordillera Vilcanota, Peru

Abstract

The amphibian pathogen Batrachochytrium dendrobatidis is causing rapid global amphibian declines. Chytridiomycosis, the disease caused by this pathogen, leads to the thickening of the keratinized layer of skin ultimately restricting epidermal respiration, hydration, and thermoregulation. Infection with this pathogen has also been shown to decrease the abundance of protective bacteria within the amphibians microbiome. Two species of frog, Telmatobius marmoratus and Pleurodema marmoratum, found in the Cordillera Vilcanota, Peru were the basis of our study. Living at an altitude between 4,362-5,400 meters these frogs are the highest recorded in the world. Their infection with chytrid makes this the highest recorded case of chytrid globally as well. Population monitoring has shown that the declines in these two frog species are not uniform. Although both infected, T. marmoratus showed steep declines in population, while P. marmoratum was stable throughout the study. We used high-throughput nanopore-based sequencing to address the feasibility of completing whole genome sequencing of Bd from skin swab samples stored in the preservative buffer Prepman Ultra. We also used sequencing results to compare microbial communities between the two species of frogs. Our findings concluded that the collection and storage method of our samples were not adequate for whole genome sequencing. It was also found that there were clear differences between the microbial communities of the frog species. These findings ultimately support the idea that infection with Bd has the ability to drive down levels of protective bacteria leading to potential dysbiosis.