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Fungal diversity drives key processes in terrestrial ecosystems, but remains challenging to measure in the field and to monitor over time. In particular, we lack methods capable of describing both the regional biotas and fungal related conservation values, such as habitats for rare and threatened fungi. Environmental DNA (eDNA) could serve this purpose, once its validity to capture fungal assemblage properties is established. Using three approaches (full‐season eDNA sampling from air, snapshot visual surveys, and eDNA sampling from dead wood), we present the first comparative assessment of fungal diversity at forest stand scale. The focus was on two well‐known fungal groups (lichens and wood inhabiting basidiomycetes) in old hemiboreal forests. Aerial eDNA revealed regional‐scale cryptic diversity not detected in visual surveys, particularly among lichens and including species of conservation concern. However, at the local population scale, both aerial eDNA and eDNA sampled from dead wood often missed visually detected species. In particular, eDNA sampled from dead wood performed only as a supplementary source of species data. The methods differed in detecting the spatial covariance of wood fungal and lichen diversity, with the combined (most complete) dataset indicating the strongest congruence. Synthesis and applications. Neither eDNA approaches nor visual surveys were able to detect full diversity of local fungi and all species of specific conservation value. However, there is clear merit in combined use of these methods, particularly in pairing aerial eDNA with visual observation‐based surveys on selected taxon groups. This approach can be especially valuable in fungal groups that have challenging taxonomy, inhabit partly inaccessible microhabitats, or have overall high diversity (such as lichens). [ABSTRACT FROM AUTHOR]

Molecular methods are increasingly used to identify species that lack conspicuous macro‐ or micromorphological characters. Taxonomic and ecological research teams barcode large numbers of collected voucher specimens annually. In this study we assessed the efficiency of long‐read high throughput sequencing (HTS) as opposed to the traditionally used Sanger method for taxonomic identification of multiple vouchered fungal specimens. We also evaluated whether this method can provide reference information about intraindividual gene polymorphism. We developed a workflow based on a test set of 423 basidiomycete specimens (representing 195 species), the PacBio HTS method, and ribosomal rRNA operon internal transcribed spacer (ITS) and 28S rRNA gene (LSU) markers. The PacBio HTS had a higher success rate than Sanger sequencing at a comparable cost. Species identification based on PacBio reads was usually straightforward, because the dominant operational taxonomic unit (OTU) typically represented the targeted organism. The PacBio HTS also enabled us to detect widespread polymorphism within the ITS marker. We conclude that multiplex DNA barcoding of the fungal ITS and LSU markers using PacBio HTS is a useful tool for taxonomic identification of large amounts of collected voucher specimens at a competitive price. Furthermore, PacBio HTS accurately recovers various alleles and paralogues, which can provide crucial information for species delimitation and population‐level studies. [ABSTRACT FROM AUTHOR]

Questions: In production forest landscapes, threatened species are increasingly confined to fragments of natural forest. Protecting such fragments is a priority to halt further biological degradation, but its effectiveness depends on external impacts on the fragments. In this study, we ask: how does woody vegetation in protected old-forest fragments vary depending on management of their adjacent areas, also in combination with natural site conditions? What are the management impacts on habitat quality of the fragments in the long term? Location: Pinus-dominated and Picea mixed-wood forests in Estonia (hemiboreal Europe). Methods: Forest structure and microclimate were measured at the edge and interior of protected old-forest fragments. Woody vegetation layers, shrub species composition, coarse woody debris, and presence of cut stumps were measured in 107 fragments (adjacent to clearcuts, partial cuts, and unthinned production forests) and in 20 control stands embedded within natural forest. Air temperature and humidity were measured at the edges vs the interior of mixed-woods. Edge age effects were explored along 80 years of post-harvest chronosequences. Results: All edge types studied had multiple, partly forest-type-specific, external effects on stand structure. Some clear-cutting effects on woody layers reversed in later decades, but there was also persistent impoverishment of deadwood pools of the fragments probably related to unreported tree removal. There was a likely indirect pathway of edge effects through overstorey loss, and shrub cover was reduced in the long term. Exotic species were rare. Edges at clear-cut stands influenced humidity regimes rather than temperature regimes. Conclusions: The moderate external effects on stand structure were tightly linked to low overstorey mortality and a lack of exotic species across the forest landscapes studied. Changes in these key factors constitute risks for the future. Protecting setasides from occasional tree cutting, and establishing forest buffers around small fragments and as a precautionary strategy are current priorities in these forest landscapes. [ABSTRACT FROM AUTHOR]