Illumina sequencing of fungal assemblages reveals compositional shifts as a result of nutrient loading within cave sediments

Two geologically comparable epigenic caves in the upper Tennessee River Basin exhibiting widespread Mn(II) oxidation were used for this study to compare contrasting hydrologic and nutrient regimes. Using the Illumina MiSeq, fungal ITS1 amplicons were analyzed to examine baseline community structure as well as phylogenetic shifts as a result of nutrient loading within the cave sediments. At the phylum level, fungal communities in the impacted cave had a significantly greater abundance of Ascomycota, suggesting early phase decomposition of organic matter, whereas those in the near-pristine cave had a greater abundance of Basidiomycota, suggesting late phase decomposition, and more limited nutrient input. Corroborating these findings, quantifying the ratios of fungi:bacteria (0.004 ±0.027 of the impacted cave and 0.007 ±0.069 for the near-pristine cave) were at least an order of magnitude lower than what is typically reported in soils, which may be attributed to lower nutrient availability (S.K. Carmichael et al., 2013b), dearth of symbionts, or lack of leaf litter (Baldrian et al., 2012). After exposure to glucose-rich agar casts in-situ, Mn oxidation was subsequently observed, corresponding with a significant increase in the proportion of Zygomycota as well as a strong increase in cell numbers of bacteria and fungi as determined from qPCR. After nutrient exposure, data revealed an abundance of sequences related to Mortierella spp. which only accounted for 1.9% of sequences in the baseline community. Additionally, one member of this group was cultured, although, it is unclear if it is capable of Mn(II) oxidation. Our findings demonstrate that solid exogenous carbon sources can lead to increased production of Mn oxides, increases in bacterial and fungal cell numbers, as well as dramatic changes in fungal assemblages. Further, these results suggest that Mn(II) oxidation is a carbon driven process in these epigenic cave systems.