Richness and composition of macrofungi on large decaying trees in a Central European old-growth forest: a case study on silver fir (Abies alba)

Species Diversity and Community Composition of Macrofungi in the Dongling Mountains, Western Beijing, China

Macrofungi are a group of fungi with important ecological functions and economic value in forest ecosystems. In this study, the species diversity and community composition of macrofungi in different areas, vegetation types, and elevation gradients from the Lingshan Natural Scenic Area and Xiaolongmen National Forest Park of the Dongling Mountains, Western Beijing were investigated. A total of 1379 specimens were collected. All specimens were identified by morphological and molecular methods, resulting in the identification of 311 species belonging to two phyla, four classes, 18 orders, 74 families, and 147 genera. The alpha diversity analysis indicated that the alpha diversity was significantly different among different vegetation types. The Betula spp. and Populus davidiana of the Lingshan Natural Scenic Area, and Quercus liaotungensis of Xiaolongmen National Forest Park had higher macrofungal alpha diversity. The difference in alpha diversity between the two areas was not significant. The principal coordinate analysis indicated a significant difference in macrofungal community composition among different vegetation types. The fungal community composition of the two areas was also significantly different. The fungal species richness and unique species tended to increase and then decrease with increasing elevation. The species composition of neighboring elevation gradients was more similar. The macrofungal species richness and the number of unique species were not significantly affected by elevation gradient. The vegetation types with higher fungal alpha diversity in the Dongling Mountains were Betula spp., Populus davidiana, and Quercus liaotungensis, and there were abundant fungal species in deciduous broad-leaved mixed forests. Macrofungal diversity and community composition was significantly affected by vegetation type. To better protect the macrofungi, the protection of these four vegetation types in the Dongling Mountains should be strengthened in the future.

What Quality Suffices for Nanopore Metabarcoding? Reconsidering Methodology and Ectomycorrhizae in Decaying Fagus sylvatica Bark as Case Study

Nanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed to ensure reliable taxonomic unit recovery. This study aims to provide those guidelines for a fungal metabarcoding context and to apply them to a case study of ectomycorrhizae in the decaying bark of Fagus sylvatica. We introduce the eNano pipeline to test two standard metabarcoding approaches: (1) Reference-based mapping leveraging UNITE's species hypothesis system (SH approach); (2) Constructing 98% OTUs (OTU approach). Our results demonstrate that both approaches are effective with Nanopore data. When using a reference database, we recommend strict mapping criteria rather than Phred-based filtering. Leveraging the SH-system further enhances reproducibility and facilitates cross-study communication. For the 98% OTUs, filtering reads at ≥Q25 is recommended. Our case study reveals that the decay gradient is a primary determinant of community composition and that specific mycorrhizal fungi colonize decaying bark. Complementing our metabarcoding results with root tip morphotypification, we identify Laccaria amethystina and Tomentella sublilacina as key ectomycorrhizae of saplings on decaying logs. These findings demonstrate that Nanopore sequencing can provide valuable ecological insights and support its broader use in fungal metabarcoding as read quality continues to improve.

Effects of experimental canopy openness on wood-inhabiting fungal fruiting diversity across succession

While the succession of terrestrial plant communities is well studied, less is known about succession on dead wood, especially how it is affected by environmental factors. While temperate forests face increasing canopy mortality, which causes considerable changes in microclimates, it remains unclear how canopy openness affects fungal succession. Here, we used a large real-world experiment to study the effect of closed and opened canopy on treatment-based alpha and beta fungal fruiting diversity. We found increasing diversity in early and decreasing diversity at later stages of succession under both canopies, with a stronger decrease under open canopies. However, the slopes of the diversity versus time relationships did not differ significantly between canopy treatments. The community dissimilarity remained mainly stable between canopies at ca. 25% of species exclusively associated with either canopy treatment. Species exclusive in either canopy treatment showed very low number of occupied objects compared to species occurring in both treatments. Our study showed that canopy loss subtly affected fungal fruiting succession on dead wood, suggesting that most species in the local species pool are specialized or can tolerate variable conditions. Our study indicates that the fruiting of the fungal community on dead wood is resilient against the predicted increase in canopy loss in temperate forests.

Singleton-based species names and fungal rarity: Does the number really matter?

Fungi are among the least known organisms on earth, with an estimated number of species between 1.5 and 10 million. This number is expected to be refined, especially with increasing knowledge about microfungi in undersampled habitats and increasing amounts of data derived from environmental DNA sequencing. A significant proportion of newly generated sequences fail to match with already named species, and thus represent what has been referred to as fungal "dark taxa". Due to the challenges associated with observing, identifying, and preserving sporophores, many macro- and microfungal species are only known from a single collection, specimen, isolate, and/or sequence-a singleton. Mycologists are consequently used to working with "rare" sequences and specimens. However, rarity and singleton phenomena lack consideration and valorization in fungal studies. In particular, the practice of publishing new fungal species names based on a single specimen remains a cause of debate. Here, we provide some elements of reflection on this issue in the light of the specificities of the fungal kingdom and global change context. If multiple independent sources of data support the existence of a new taxon, we encourage mycologists to proceed with formal description, irrespective of the number of specimens at hand. Although the description of singleton-based species may not be considered best practice, it does represent responsible science in the light of closing the Linnean biodiversity shortfall.