The contribution of environmental DNA to exploring hypogeous fungal diversity and vulnerability

Abstract Background Hypogeous fungi play important ecological roles and have significant economic value. However, the hypogeous habit of these organisms hinders our understanding of their diversity and vulnerability. Results The first comprehensive assessment of the hypogeous fungal diversity in Korea was conducted using environmental DNA metabarcoding, encompassing 643 soil samples collected from 162 nationwide grids. A total of 186 phylotypes of hypogeous fungi (representing 32 genera) were identified through phylogeny-based identification using a curated ITS reference database that comprised 3,359 sequences from 693 species (83 genera). This number largely exceeds the 30 species recorded in Korea. The environmental preference analysis revealed two distinct ecological clusters of hypogeous fungal genera, respectively vulnerable to climate warming and to soil eutrophication. Based on geographic range criteria (Area of Occupancy and Extent of Occurrence), 10 of 15 phylotypes exhibited distribution patterns consistent with Endangered or Vulnerable thresholds. Conclusions These findings reveal extensive cryptic diversity, establish baseline conservation data for hypogeous fungi, and provide a replicable methodology for global hypogeous fungal assessments in soil ecosystems.