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.

莫哈韦沙漠龟（Gopherus agassizii）是美国西南部特有的受威胁爬行动物。导致其人口下降的因素有很多，例如人类造成的栖息地破坏和传染病，其中可能包括新出现的真菌病原体。我们分析了来自亚利桑那州西北部的两只陆龟的真菌群落，并将宿主菌群与洞穴菌群进行了比较。我们的主要目标是描述生活在莫哈韦沙漠陆龟身上的真菌群落特征，并确定洞穴土壤和陆龟真菌群落之间的群落组成和潜在病原体丰度是否存在差异。群落中的差异表明存在适应动物生态位的真菌，而土壤中很少存在，反之亦然。ITS2 扩增子的宏基因组分析揭示了底物和动物样本之间真菌群落的显着差异。陆龟样本显示出比土壤更高的α多样性，并且根据β多样性分析与土壤样本不同。我们观察到，陆龟样本中的Onygenales 潜在真菌病原体的相对丰度明显高于土壤。这些真菌生物组数据表明，存在一个独特的真菌群落占据了沙漠龟的宿主生态位，并且该群落包含相对丰度较高的潜在真菌病原体。我们认为这些真菌可能会增加沙漠龟发病率和死亡率，从而导致沙漠龟数量下降。