Here, we describe the taxon hypothesis (TH) paradigm, which covers the construction, identification, and communication of taxa as datasets. Defining taxa as datasets of individuals and their traits will make taxon identification and most importantly communication of taxa precise and reproducible. This will allow datasets with standardized and atomized traits to be used digitally in identification pipelines and communicated through persistent identifiers. Such datasets are particularly useful in the context of formally undescribed or even physically undiscovered species if data such as sequences from samples of environmental DNA (eDNA) are available. Implementing the TH paradigm will to some extent remove the impediment to hastily discover and formally describe all extant species in that the TH paradigm allows discovery and communication of new species and other taxa also in the absence of formal descriptions. The TH datasets can be connected to a taxonomic backbone providing access to the vast information associated with the tree of life. In parallel to the description of the TH paradigm, we demonstrate how it is implemented in the UNITE digital taxon communication system. UNITE TH datasets include rich data on individuals and their rDNA ITS sequences. These datasets are equipped with digital object identifiers (DOI) that serve to fix their identity in our communication. All datasets are also connected to a GBIF taxonomic backbone. Researchers processing their eDNA samples using UNITE datasets will, thus, be able to publish their findings as taxon occurrences in the GBIF data portal. UNITE species hypothesis (species level THs) datasets are increasingly utilized in taxon identification pipelines and even formally undescribed species can be identified and communicated by using UNITE. The TH paradigm seeks to achieve unambiguous, unique, and traceable communication of taxa and their properties at any level of the tree of life. It offers a rapid way to discover and communicate undescribed species in identification pipelines and data portals before they are lost to the sixth mass extinction.

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.

Despite recent advances in understanding the microbiome of eukaryotes, little is known about microbial communities in fungi. Here we investigate the structure of bacterial communities in mushrooms, including common edible ones, with respect to biotic and abiotic factors in the boreal forest. Using a combination of culture-based and Illumina high-throughput sequencing, we characterized the bacterial communities in fruitbodies of fungi from eight genera spanning four orders of the class Agaricomycetes (Basidiomycota). Our results revealed that soil pH followed by fungal identity are the main determinants of the structure of bacterial communities in mushrooms. While almost half of fruitbody bacteria were also detected from soil, the abundance of several bacterial taxa differed considerably between the two environments. The effect of host identity was significant at the fungal genus and order level and could to considerable extent be ascribed to the distinct bacterial community of the chanterelle, representing Cantharellales – the earliest diverged group of mushroom-forming basidiomycetes. These data suggest that besides the substantial contribution of soil as a major taxa source and environmental determinant of bacterial communities in mushrooms, the structure of these communities is to a great degree affected by the identity of the host. Thus, bacteria inhabiting fungal fruitbodies may be non-randomly selected from environment based on their symbiotic functions and/or habitat requirements.

Twelve species of Hypomyces/Cladobotryum producing red pigments are reported growing in various tropical areas of the world. Ten of these are described as new, including teleomorphs for two previously known anamorphic species. In two species the teleomorph has been found in nature and in three others it was obtained in culture; only anamorphs are known for the rest. None of the studied tropical collections belongs to the common temperate species H. rosellus and H. odoratus to which the tropical teleomorphic collections had previously been assigned. Instead, taxa encountered in the tropics are genetically and morphologically distinct from the nine species of Hypomyces/Cladobotryum producing red pigments known from temperate regions. Besides observed host preferences, anamorphs of several species can spread fast on soft ephemeral agaricoid basidiomata but the slower developing teleomorphs are mostly found on polyporoid basidiomata or bark. While a majority of previous records from the tropics involve collections from Central America, this paper also reports the diversity of these fungi in the Paleotropics. Africa appears to hold a variety of taxa as five of the new species include material collected in scattered localities of this mostly unexplored continent. In examining distribution patterns, most of the taxa do not appear to be pantropical. Some species are known only from the Western Hemisphere, while others have a geographic range from southeastern Asia to Africa or Australia. The use of various morphological characters of anamorphs and teleomorphs as well as culture characteristics in species delimitation is evaluated. For detecting genetic segregation, partial sequences of the two largest subunits of the ribosomal polymerase perform the best in terms of providing informative sites and the number of well-supported groups recognised in the phylogenies. These are followed by the sequence data of the translation-elongation factor 1-alpha, while the ribosomal DNA ITS regions are of only limited use in distinguishing species and their phylogenetic relationships. Taxonomic novelties: Cladobotryum coriolopsicola (R.F. Castañeda) K. Põldmaa, comb. nov., Hypomyces aconidialis K. Põldmaa, sp. nov., Hypomyces australasiaticus K. Põldmaa, sp. nov., Hypomyces gabonensis K. Põldmaa, sp. nov., Hypomyces samuelsii K. Põldmaa, sp. nov., Hypomyces virescens G.R.W. Arnold & K. Põldmaa, sp. nov., Cladobotryum heterosporum K. Põldmaa, sp. nov., Cladobotryum indoafrum K. Põldmaa, sp. nov., Cladobotryum paravirescens K. Põldmaa, sp. nov., Cladobotryum protrusum K. Põldmaa, sp. nov., Cladobotryum tchimbelense K. Põldmaa, sp. nov.

Increasing evidence suggest that bacteria form diverse communities in various eukaryotic hosts, including fungi. However, little is known about their succession and the functional potential at different host development stages. Here we examined the effect of fruiting body parts and developmental stages on the structure and potential function of fungus-associated bacterial communities. Using high-throughput sequencing, we characterized bacterial communities and their associated potential functions in fruiting bodies from ten genera belonging to four major mushroom-forming orders and three different developmental stages of a model host species Cantharellus cibarius. Our results demonstrate that bacterial community structure differs between internal and external parts of the fruiting body but not between inner tissues. The structure of the bacterial communities showed significant variation across fruiting body developmental stages. We provide evidence that certain functional groups, such as those related to nitrogen fixation, persist in fruiting bodies during the maturation, but are replaced by putative parasites/pathogens afterwards. These data suggest that bacterial communities inhabiting fungal fruiting bodies may play important roles in their growth and development.

The degree of ecological specialization plays a crucial role in shaping the structure and functioning of communities. However, comparing specialization within and among groups of organisms is complicated by both methodological issues and conceptual and terminological inconsistencies. Environmental predictability has been considered a key determinant of specialization though empirical evidence is still limited. Fungi and their insect consumers provide a poorly studied but promising system to measure host specialization and test the predictability hypothesis. In this study, we systematically sampled mushrooms in North European boreal forest, and reared total samples of fungivores colonizing the fruitbodies. Due to the unpredictable nature of mushrooms as a resource, low levels of host specialization can be predicted for these insects, which have indeed widely been considered polyphagous. Contrary to expectations, the majority of the studied fungus gnats were found not to exploit their host taxa indiscriminately. Not only were some mushroom taxa never colonized, the infestation rate of acceptable hosts also differed in most of these fungivores. Gnat species themselves formed continua with respect to the estimates of the degree of specialization, derived from parametric individual-based analyses of presence-absence data. In most cases, host use was best explained by models in which the hosts were classified at genus level, with limited support to specialization to particular host species, families, or orders. Indeed, most of the common fungivores appeared to preferentially use various species from one or a few mushroom genera while occasionally feeding on members of other host taxa. This pattern has likely evolved as a compromise between selective forces stemming from host unpredictability and taxon-specific chemical profiles of the mushrooms. Our study highlights the multidimensional nature of ecological specialization: a high number of acceptable hosts does not preclude considerable discrimination among members of the available resource pool. Such situations can only be revealed by individual-based analyses capable of capturing differences in partner-to-partner interaction intensities.