Abstract
Among terrestrial microorganisms, mushroom-forming fungi have been relatively well investigated, however the inconspicuous strains may be overlooked by conventional visual investigations causing underestimation of their phylogenetic diversity. Herein, we sought to obtain a comprehensive phylogenetic diversity profile for the early-diverging wood-decaying mushrooms Dacrymycetes, using an approach that combines fruiting-body collection, culture isolation, and environmental DNA (eDNA) metabarcoding of decaying branches. Among the 28 operational taxonomic units (OTUs) detected during a three-year investigation, 10 each were from fruiting bodies and cultured mycelia and 27 were detected as eDNA sequences. eDNA metabarcoding revealed various lineages across the Dacrymycetes phylogeny. Alternatively, fruiting-body and culture surveys uncovered only ~50% of the OTUs detected through eDNA metabarcoding, suggesting that several inconspicuous or difficult-to-isolate strains are latent in the environment. Further, eDNA and culture surveys revealed early-diverging clades that were not identified in the fruiting-body survey. Thus, eDNA and culture-based techniques can uncover inconspicuous yet phylogenetically important mushroom lineages that may otherwise be overlooked via typical visual investigations.
Highlights
IntroductionMushroom-forming fungi have been relatively well investigated, the inconspicuous strains may be overlooked by conventional visual investigations causing underestimation of their phylogenetic diversity
Among terrestrial microorganisms, mushroom-forming fungi have been relatively well investigated, the inconspicuous strains may be overlooked by conventional visual investigations causing underestimation of their phylogenetic diversity
We investigated the diversity of Dacrymycetes over one year using three methods: fruiting-body collection, culture isolation followed by DNA sequencing, and environmental DNA (eDNA) analysis of decaying branches through DNA cloning4. eDNA-cloning and culture isolation methods detected operational taxonomic units (OTUs) belonging to unknown clades in the phylogeny that were not identified among the sequences obtained via the fruiting-body survey
Summary
Mushroom-forming fungi have been relatively well investigated, the inconspicuous strains may be overlooked by conventional visual investigations causing underestimation of their phylogenetic diversity. We sought to obtain a comprehensive phylogenetic diversity profile for the early-diverging wood-decaying mushrooms Dacrymycetes, using an approach that combines fruiting-body collection, culture isolation, and environmental DNA (eDNA) metabarcoding of decaying branches. EDNA and culture-based techniques can uncover inconspicuous yet phylogenetically important mushroom lineages that may otherwise be overlooked via typical visual investigations. Two methods are generally employed for detecting fungal mycelia from environmental samples: culture isolation[6,7] and environmental DNA (eDNA) analysis[8,9,10,11]. The diversity of mushroom-forming fungi has previously been investigated using methods based on the fruiting-body, culture isolation, and/or eDNA4,21–27. These studies have revealed the unique characteristics of each method. Few studies have compared both taxonomic and phylogenetic diversities by estimating the phylogenetic positions of the OTUs obtained from simultaneous investigations using each method
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