Characterizing fungal communities on Mojave desert tortoises (Gopherus agassizii) in Arizona to uncover potential pathogens

The Mojave Desert tortoise (Gopherus agassizii) is a threatened reptile endemic to the southwestern United States. There are many factors contributing to its population decline such as human-driven habitat destruction and infectious diseases, which might include emerging fungal pathogens. We analyzed the fungal communities of two tortoises from northwest Arizona and compared the host mycobiome to the burrow mycobiome. Our main goal was to characterize the fungal community living on the Mojave Desert tortoise and to determine whether there are differences in community composition and potential pathogen abundance between the soil from burrows and tortoises' mycobiome. Dissimilarities in communities would indicate that there are fungi adapted to the animal niche that are rarely present in soil and vice versa. Metagenomic analysis of ITS2 amplicons revealed significant differences in fungal communities between the substrate and samples taken from the animals. The tortoise samples show higher alpha diversity than the soil and are distinct from soil samples based on beta diversity analysis. We observed significantly greater relative abundance of potential fungal pathogens from the order Onygenales in the tortoise samples than the soil. These mycobiome data suggest that there is a unique fungal community occupying the desert tortoise host niche and this community contains a higher relative abundance of potential fungal pathogens. We argue that these fungi may pose a risk for increased morbidity and mortality among desert tortoises, which can in turn drive population decline.