Use of environmental sequencing in evaluating fungal response to peatland degradation

Central European peatlands are critically endangered by climate change, eutrophication, disturbed water regime and inappropriate management. This leads to their degradation, which affects all components of these habitats including fungi, and significantly fungi participating in the carbon cycle such as saprotrophs, mycorrhizal symbionts and parasites. Nature conservation efforts focus mainly on macrofungi, especially ‘fungi important for nature conservation’ (FINC) which are rare or associated with endangered habitats. To find out whether standard environmental DNA (eDNA) sequencing methods can be used to monitor the effect of peatland degradation on FINC and fungal communities, we established pairs of plots in degraded and well-preserved parts of ten peatlands in the Třeboň Protected Landscape Area (Czech Republic). Peatland degradation was locally caused by a combination of different factors (water level and chemistry) followed by vegetation succession, whose effect on fungi was evaluated using multivariate analyses. A total of 28 FINC species were detected using macrofungal surveying, whereas 25 were found using eDNA of Sphagnum and peat (Illumina sequencing of ITS2). These two methods agreed on 13 predominantly abundant FINC species, most of which grew in both well-preserved and degraded plots. However, their sensitivity to the studied degradation could not be assessed due to the low abundance of most species. Fungal communities found on the basis of both methods (macrofungal survey, eDNA) were affected by water chemistry, whereas a significant effect of vegetation and locally expansive plants was demonstrated only in fungal communities found using macrofungal survey. Optimisation (e.g. specific primers) for local conditions leading to a better FINC capture must be carried out if eDNA is to be used in the practice of evaluating management effects on peatlands.