Fungal diversity: comparison of data from aerial and wood eDNA and visual surveys

Fungal diversity drives multiple key processes in terrestrial ecosystems, but it remains challenging to measure in the field and to monitor over time. Environmental DNA (eDNA) could provide unique insights into this diversity, once its representation and bias to capture fungal assemblages is known. We present the first comparative forest-scale fungal diversity assessment based on three approaches (full-season eDNA monitoring from air, snapshot visual surveys, and eDNA from wood) in old forests in Estonia. In addition to measuring cryptic taxonomic diversity (revealed by eDNA only), we compared eDNA derived diversity variables and habitat relationships with those derived from standard visual surveys for two fungal groups (lichens and wood basidiomycetes). Aerial eDNA provided generally consistent results: it added cryptic diversity also in visually detectable groups, also distinguished previously known habitat factors for fungal diversity. However, there were also taxon-group dependent inconsistencies and poorer detection of species of conservation concern than in visual surveys. The results imply a fungal monitoring scheme that (a) maximizes expert time for surveys including conservation targets; (b) uses aerial sampling to represent a broad range of ecosystems; (c) includes sites where both methods are used simultaneously in the same season; and (d) establishes some permanent test sites where these and other innovative methods are used over multiple seasons to exhaustively describe fungal diversity including within-species genetic diversity.