Connecting the multiple dimensions of global soil fungal diversity

How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic and phylogenetic diversity of fungi and their ecological groups. We show the impact of precipitation and temperature interactions on local fungal species richness (alpha diversity) across different climates. Our findings reveal how temperature drives fungal compositional turnover (beta diversity) and phylogenetic diversity, linking them with regional species richness (gamma diversity). We integrate fungi into the principles of global biodiversity distribution and present detailed maps for biodiversity conservation and modeling of global ecological processes.

Symbiotic status alters fungal eco-evolutionary offspring trajectories

Despite host-fungal symbiotic interactions being ubiquitous in all ecosystems, understanding how symbiosis has shaped the ecology and evolution of fungal spores that are involved in dispersal and colonization of their hosts has been ignored in life-history studies. We assembled a spore morphology database covering over 26,000 species of free-living to symbiotic fungi of plants, insects and humans and found more than eight orders of variation in spore size. Evolutionary transitions in symbiotic status correlated with shifts in spore size, but the strength of this effect varied widely among phyla. Symbiotic status explained more variation than climatic variables in the current distribution of spore sizes of plant-associated fungi at a global scale while the dispersal potential of their spores is more restricted compared to free-living fungi. Our work advances life-history theory by highlighting how the interaction between symbiosis and offspring morphology shapes the reproductive and dispersal strategies among living forms.

Holarctic Species in the Pluteus podospileus Clade: Description of Six New Species and Reassessment of Old Names

We studied the taxonomy of Pluteus podospileus and similar species using morphological and molecular (nrITS, TEF1-α) data, including a detailed study of the type collections of P. inflatus var. alneus, Pluteus minutissimus f. major, and P. granulatus var. tenellus. Within the P. podospileus complex, we phylogenetically confirmed six species in Europe, five in Asia, and eight in North America. Based on our results, we recognize P. seticeps as a separate species occurring in North America, while P. podospileus is limited to Eurasia. We describe six new species and a new variety: P. absconditus, P. fuscodiscus, P. gausapatus, P. inexpectatus, P. millsii, and P. notabilis and its variety, P. notabilis var. insignis. We elevate Pluteus seticeps var. cystidiosus to species rank as Pluteus cystidiosus. Based on the holotype of P. inflatus var. alneus, collections of P. inflatus identified by Velenovský, and several modern collections, we resurrect the name P. inflatus. Based on molecular analyses of syntypes of Pluteus minutissimus f. major and a holotype of Pluteus granulatus var. tenellus, we synonymize them under P. inflatus. We also increase our knowledge about the morphology and distribution of P. cutefractus.

Automatic Fungi Recognition: Deep Learning Meets Mycology

The article presents an AI-based fungi species recognition system for a citizen-science community. The system's real-time identification too - FungiVision - with a mobile application front-end, led to increased public interest in fungi, quadrupling the number of citizens collecting data. FungiVision, deployed with a human-in-the-loop, reaches nearly 93% accuracy. Using the collected data, we developed a novel fine-grained classification dataset - Danish Fungi 2020 (DF20) - with several unique characteristics: species-level labels, a small number of errors, and rich observation metadata. The dataset enables the testing of the ability to improve classification using metadata, e.g., time, location, habitat and substrate, facilitates classifier calibration testing and finally allows the study of the impact of the device settings on the classification performance. The continual flow of labelled data supports improvements of the online recognition system. Finally, we present a novel method for the fungi recognition service, based on a Vision Transformer architecture. Trained on DF20 and exploiting available metadata, it achieves a recognition error that is 46.75% lower than the current system. By providing a stream of labeled data in one direction, and an accuracy increase in the other, the collaboration creates a virtuous cycle helping both communities.

First Evidence That Nematode Communities in Deadwood Are Related to Tree Species Identity and to Co-Occurring Fungi and Prokaryotes

Nematodes represent a diverse and ubiquitous group of metazoans in terrestrial environments. They feed on bacteria, fungi, plants, other nematodes or parasitize a variety of animals and hence may be considered as active members of many food webs. Deadwood is a structural component of forest ecosystems which harbors many niches for diverse biota. As fungi and bacteria are among the most prominent decomposing colonizers of deadwood, we anticipated frequent and diverse nematode populations to co-occur in such ecosystems. However, knowledge about their ability to colonize this habitat is still limited. We applied DNA-based amplicon sequencing (metabarcoding) of the 18S rRNA gene to analyze nematode communities in sapwood and heartwood of decaying logs from 13 different tree species. We identified 247 nematode ASVs (amplicon sequence variants) from 27 families. Most of these identified families represent bacterial and fungal feeders. Their composition strongly depended on tree species identity in both wood compartments. While pH and water content were the only wood properties that contributed to nematodes' distribution, co-occurring fungal and prokaryotic (bacteria and archaea) α- and β-diversities were significantly related to nematode communities. By exploring thirteen different tree species, which exhibit a broad range of wood characteristics, this study provides first and comprehensive insights into nematode diversity in deadwood of temperate forests and indicates connectivity to other wood-inhabiting organisms.

Molecular biogeography of the fungus-dwelling saproxylic beetle Bolitophagus reticulatus indicates rapid expansion from glacial refugia

The geographical distributions of species associated with European temperate broadleaf forests have been significantly influenced by glacial–interglacial cycles. During glacial periods, these species persisted in Mediterranean and extra-Mediterranean refugia and later, during interglacial periods, expanded northwards. The widespread saproxylic beetle Bolitophagus reticulatus depends closely on European temperate broadleaf forests. It usually develops in the tinder fungus Fomes fomentarius, a major decomposer of broadleaf-wood. We sampled B. reticulatus in sporocarps from European beech (Fagus sylvatica) and Oriental beech (Fagus orientalis) across Europe and the Caucasus region. We analysed mitochondrial gene sequences (cox1, cox2, cob) and 17 microsatellites to reconstruct the geographical distribution of glacial refugia and postglacial recolonization pathways. We found only marginal genetic differentiation of B. reticulatus, except for a significant split between populations of the Caucasus region and Europe. This indicates the existence of past refugia south of the Great Caucasus, and a contact zone with European populations in the Crimean region. Further potential refugia might have been located at the foothills of the Pyrenees and in the Balkan region. Our genetic data suggest a phalanx-wise recolonization of Europe, a reflection of the high mobility of B. reticulatus.

Detecting flying insects using car nets and DNA metabarcoding

Monitoring insects across space and time is challenging, due to their vast taxonomic and functional diversity. This study demonstrates how nets mounted on rooftops of cars (car nets) and DNA metabarcoding can be applied to sample flying insect richness and diversity across large spatial scales within a limited time period. During June 2018, 365 car net samples were collected by 151 volunteers during two daily time intervals on 218 routes in Denmark. Insect bulk samples were processed with a DNA metabarcoding protocol to estimate taxonomic composition, and the results were compared to known flying insect richness and occurrence data. Insect and hoverfly richness and diversity were assessed across biogeographic regions and dominant land cover types. We detected 15 out of 19 flying insect orders present in Denmark, with high proportions of especially Diptera compared to Danish estimates, and lower insect richness and diversity in urbanized areas. We detected 319 species not known for Denmark and 174 species assessed in the Danish Red List. Our results indicate that the methodology can assess the flying insect fauna at large spatial scales to a wide extent, but may be, like other methods, biased towards certain insect orders.

European mushroom assemblages are darker in cold climates

Thermal melanism theory states that dark-colored ectotherm organisms are at an advantage at low temperature due to increased warming. This theory is generally supported for ectotherm animals, however, the function of colors in the fungal kingdom is largely unknown. Here, we test whether the color lightness of mushroom assemblages is related to climate using a dataset of 3.2 million observations of 3,054 species across Europe. Consistent with the thermal melanism theory, mushroom assemblages are significantly darker in areas with cold climates. We further show differences in color phenotype between fungal lifestyles and a lifestyle differentiated response to seasonality. These results indicate a more complex ecological role of mushroom colors and suggest functions beyond thermal adaption. Because fungi play a crucial role in terrestrial carbon and nutrient cycles, understanding the links between the thermal environment, functional coloration and species' geographical distributions will be critical in predicting ecosystem responses to global warming.

Considerations and consequences of allowing DNA sequence data as types of fungal taxa

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.

Explaining European fungal fruiting phenology with climate variability

Here we assess the impact of geographically dependent (latitude, longitude, and altitude) changes in bioclimatic (temperature, precipitation, and primary productivity) variability on fungal fruiting phenology across Europe. Two main nutritional guilds of fungi, saprotrophic and ectomycorrhizal, were further separated into spring and autumn fruiters. We used a path analysis to investigate how biogeographic patterns in fungal fruiting phenology coincided with seasonal changes in climate and primary production. Across central to northern Europe, mean fruiting varied by approximately 25 d, primarily with latitude. Altitude affected fruiting by up to 30 d, with spring delays and autumnal accelerations. Fruiting was as much explained by the effects of bioclimatic variability as by their large-scale spatial patterns. Temperature drove fruiting of autumnal ectomycorrhizal and saprotrophic groups as well as spring saprotrophic groups, while primary production and precipitation were major drivers for spring-fruiting ectomycorrhizal fungi. Species-specific phenology predictors were not stable, instead deviating from the overall mean. There is significant likelihood that further climatic change, especially in temperature, will impact fungal phenology patterns at large spatial scales. The ecological implications are diverse, potentially affecting food webs (asynchrony), nutrient cycling and the timing of nutrient availability in ecosystems.

Fungal spore diversity reflects substrate-specific deposition challenges

Sexual spores are important for the dispersal and population dynamics of fungi. They show remarkable morphological diversity, but the underlying forces driving spore evolution are poorly known. We investigated whether trophic status and substrate associations are associated with morphology in 787 macrofungal genera. We show that both spore size and ornamentation are associated with trophic specialization, so that large and ornamented spores are more probable in ectomycorrhizal than in saprotrophic genera. This suggests that spore ornamentation facilitates attachment to arthropod vectors, which ectomycorrhizal species may need to reach lower soil layers. Elongated spore shapes are more common in saprotrophic taxa, and genera associated with above ground substrates are more likely to have allantoid (curved elongated) spores, probably to lower the risk of wash out by precipitation. Overall, our results suggest that safe arrival on specific substrates is a more important driver of evolution in spore morphology than dispersal per se.

Are ungulates in forests concerns or key species for conservation and biodiversity? Reply to Boulanger et al. (DOI: 10.1111/gcb.13899)

Increasing species richness of light demanding species in forests may not be a conservation concern if we accept a macroecological and evolutionary baseline for biodiversity. Most of the current biodiversity in Europe has evolved in the Pleistocene or earlier, and in ecosystems markedly influenced by dynamic natural processes, including grazing. Many threatened species are associated with high-light forest environments such as forest glades and edges, as these have strongly declined at least partially due to the decline of large herbivores in European forests. Hence, moderate grazing in forests should be an ecological baseline and conservation target rather than a concern.

Taxonomy of Tricholoma in northern Europe based on ITS sequence data and morphological characters

Based on molecular and morphological data we investigated the taxonomy and phylogeny of the ectomycorrhizal genus Tricholoma in northern Europe. Our phylogenetic tree confirmed the presence of at least 72 well circumscribed species within the region. Of these, three species, viz. T. boreosulphurescens, T. bryogenum and T. ilkkae are described as new to science, based on morphological, distributional, ecological and molecular data. Several other terminal branches represent putative cryptic taxa nested within classical species or species groups. Molecular type studies and/or designation of sequenced neotypes are needed in these groups, before the taxonomy can be settled. In general our phylogenetic analysis supported previous suprageneric classification systems, but with some substantial changes. Most notably, T. virgatum and allies were found to belong to sect. Tricholoma rather than sect. Atrosquamosa, while T. focale was found to be clearly nested in sect. Genuina rather than in sect. Caligata. In total, ten sections are accepted, with five species remaining unassigned. The combination of morphological and molecular data showed pileus colour, pileipellis structure, presence of clamp connections and spore size to be rather conservative characters within accepted sections, while the presence of a distinct ring, and especially host selection were highly variable within these.

Citizen science data reveal ecological, historical and evolutionary factors shaping interactions between woody hosts and wood-inhabiting fungi

Woody plants host diverse communities of associated organisms, including wood-inhabiting fungi. In this group, host effects on species richness and interaction network structure are not well understood, especially not at large geographical scales. We investigated ecological, historical and evolutionary determinants of fungal species richness and network modularity, that is, subcommunity structure, across woody hosts in Denmark, using a citizen science data set comprising > 80 000 records of > 1000 fungal species on 91 genera of woody plants. Fungal species richness was positively related to host size, wood pH, and the number of species in the host genus, with limited influence of host frequency and host history, that is, time since host establishment in the area. Modularity patterns were unaffected by host history, but largely reflected host phylogeny. Notably, fungal communities differed substantially between angiosperm and gymnosperm hosts. Host traits and evolutionary history appear to be more important than host frequency and recent history in structuring interactions between hosts and wood-inhabiting fungi. High wood acidity appears to act as a stress factor reducing fungal species richness, while large host size, providing increased niche diversity, enhances it. In some fungal groups that are known to interact with live host cells in the establishment phase, host selectivity is common, causing a modular community structure.

Dataset on species incidence, species richness and forest characteristics in a Danish protected area

The data presented in this article are related to the research article entitled "Restoring hydrology and old-growth structures in a former production forest: Modelling the long-term effects on biodiversity" (A. Mazziotta, J. Heilmann-Clausen, H. H.Bruun, Ö. Fritz, E. Aude, A.P. Tøttrup) [1]. This article describes how the changes induced by restoration actions in forest hydrology and structure alter the biodiversity value of a Danish forest reserve. The field dataset is made publicly available to enable critical or extended analyses.

A fungal perspective on conservation biology

Hitherto fungi have rarely been considered in conservation biology, but this is changing as the field moves from addressing single species issues to an integrative ecosystem-based approach. The current emphasis on biodiversity as a provider of ecosystem services throws the spotlight on the vast diversity of fungi, their crucial roles in terrestrial ecosystems, and the benefits of considering fungi in concert with animals and plants. We reviewed the role of fungi in ecosystems and composed an overview of the current state of conservation of fungi. There are 5 areas in which fungi can be readily integrated into conservation: as providers of habitats and processes important for other organisms; as indicators of desired or undesired trends in ecosystem functioning; as indicators of habitats of conservation value; as providers of powerful links between human societies and the natural world because of their value as food, medicine, and biotechnological tools; and as sources of novel tools and approaches for conservation of megadiverse organism groups. We hope conservation professionals will value the potential of fungi, engage mycologists in their work, and appreciate the crucial role of fungi in nature.

Population evidence of cryptic species and geographical structure in the cosmopolitan ectomycorrhizal fungus, Tricholoma scalpturatum

Tricholoma scalpturatum is an ectomycorrhizal fungus that forms symbioses with roots of diverse trees and shrubs. It is commonly encountered in a wide range of habitats, across temperate ecosystems. A previous study has revealed a high genetic diversity at a local scale, and ruderal abilities. To examine genetic structure at a large geographical scale, a total of 164 basidiocarps were collected from 30 populations located in Western Europe, from Spain to Scandinavia. These samples were analyzed by three molecular methods with different levels of resolution: inter-simple sequence repeats (ISSRs), restriction fragment length polymorphisms (RFLPs) in the rDNA internal transcribed spacer (ITS), and ITS sequence analysis. Considerable genetic variation was found, and the morphospecies was separated into two genetic groups that were distinct from each other. The ISSR data and the relatively low percentage value (96%) of shared sequence polymorphisms in the ITS between isolates from the two groups, strongly suggest cryptic species and long-lasting separation. No geographical exclusion was detected for these two widely distributed taxa. However, high estimates of population differentiation were observed in each group, including between populations less than a few kilometers apart. This result provides evidence for limited gene flow and/or founding effects. It also indicates that T. scalpturatum does not constitute a random mating population, and the hypothesis of endemism cannot be excluded for this cosmopolitan wind-dispersed fungus.

Inhibition and stimulation effects in communities of wood decay fungi: exudates from colonized wood influence growth by other species

The effects of exudates from uncolonized and from partly decayed beech wood on the extension rates of 16 later stage decay fungi were investigated. The partly decayed wood had been colonized by the pyrenomycete Eutypa spinosa, or the basidiomycetes Fomes fomentarius, Stereum hirsutum, and Trametes versicolor, all known as common early decay agents in European beech forests. Sterilized wood pieces were placed onto 0.5% malt agar, opposite to small agar plugs containing the test fungi. The latter showed very variable and species-specific growth responses to the various wood types. The presence of uncolonized wood stimulated extension rates in many species, whereas the four previously decayed wood types had variable stimulatory or inhibitory effects. Wood decayed by S. hirsutum resulted in reduced extension rate, delayed growth, or total inhibition in the majority of species, thus it is suggested that this species uses secondary metabolites in a defensive strategy. A single species was, however, stimulated in the presence of S. hirsutum-decayed wood. In contrast, the presence of wood decayed by F. fomentarius was stimulatory to 45% of the species. The other previously decayed wood types generally resulted in more variable responses, depending upon species. The results are discussed in an ecological context and it is suggested that the exudates from the partly decayed wood that are responsible for the reported effects may function as infochemicals, structuring microbial communities in wood.