Illumina Sequencing of Fungal Assemblages Reveals Compositional Shifts as a Result of Nutrient Loading Within Cave Sediments

This study compared fungal communities in two southern Appalachian caves: Carter Saltpeter Cave (CSPC, an anthropogenically-impacted cave) and Daniel Boone Caverns (DBC, a near-pristine cave). The impacted cave had an order of magnitude greater cell numbers estimated via qPCR, significantly greater ACE and Chao1 diversity and was dominated by Ascomycota common in early phase decomposition, likely due to carbon input from shallow soil sources. Fungal assemblages in more pristine DBC samples were dominated by Basidomycota found in deeper soil horizons or in late phase decomposition in other studies, suggesting more oligotrophic conditions. Average fungal to bacterial ratios (0.004 and 0.007, calculated as gene copy numbers per gram wet weight via qPCR) were roughly an order of magnitude below those reported for soils, likely due to nutrient-limitation. In situ carbon addition resulted in growth of fungal mycelia followed by increased Mn(II)-oxidation. A comparison of the fungal communities before and after the 10 week manipulation indicated that Mn(II) oxide enrichment both increased the quantity of fungal and bacterial cells (estimated via qPCR) and decreased overall fungal diversity. Overall, results demonstrate that anthropogenic carbon sources can dramatically influence the diversity and quantity of fungi, impact microbial community function, and can stimulate Mn(II)-oxidation.