Sergei Põlme’s research while affiliated with University of Tartu and other places

Journal impact factors were devised to qualify and compare university library holdings but are frequently repurposed for use in ranking applications, research papers, and even individual applicants in mycology and beyond. The widely held assumption that mycological studies published in journals with high impact factors add more to systematic mycology than studies published in journals without high impact factors nevertheless lacks evidential underpinning. The present study uses the species hypothesis system of the UNITE database for molecular identification of fungi and other eukaryotes to trace the publication history and impact factor of sequences uncovering new fungal species hypotheses. The data show that journal impact factors are poor predictors of discovery potential in systematic mycology. There is no clear relationship between journal impact factor and the discovery of new species hypotheses for the years 2000–2021. On the contrary, we found journals with low, and even no, impact factor to account for substantial parts of the species hypothesis landscape, often discovering new fungal taxa that are only later picked up by journals with high impact factors. Funding agencies and hiring committees that insist on upholding journal impact factors as a central funding and recruitment criterion in systematic mycology should consider using indicators such as research quality, productivity, outreach activities, review services for scientific journals, and teaching ability directly rather than using publication in high impact factor journals as a proxy for these indicators.

The Deliverable discusses the critical role of soil in supporting terrestrial ecosystems, agriculture, and global climate regulation. It highlights that a significant portion of European soils are currently unhealthy, which has far-reaching consequences, including risks to human health, the environment, and the economy. Soil degradation affects food security, water quality, climate change, and biodiversity. It also emphasizes the importance of soil monitoring in Europe to ensure sustainable land management, preserve biodiversity, and mitigate environmental challenges. Healthy soils are essential for agriculture, food security, and climate resilience. The European Union (EU) recognizes the importance of soil health in addressing the food needs of a growing global population increasing the need for improved soil monitoring. It also discusses the role of advanced remote sensing technologies in soil monitoring and mentions initiatives and projects focused on soil biodiversity and ecosystem functioning. This Deliverable highlights the showcase in soil restoration and climate change mitigation that is aimed at developing soil essential biodiversity variables to test the capacity of current datasets and monitoring frameworks to provide relevant information on the distribution and future trends of key soil biodiversity variables. The development process also stakeholder engagement in the context of selecting essential biodiversity variables (EBVs). Two main approaches were used: a working group involving researchers and targeted meetings with institutional stakeholders. Key meetings were held with stakeholders from organizations such as the European Environmental Agency, the Joint Research Center, and German soil and biodiversity monitoring agencies. These meetings aimed to gather input and insights on the selection of EBVs. The stakeholder engagement process revealed three key points: i) the importance of using readily available and open data to ensure data continuity and promote transparency and accessibility (this includes data from sources like the European Soil Data Centre (ESDAC) and GBIF, as well as point data from the LUCAS sampling framework); ii) the need for diversity in modeling approaches, incorporating multiple data sources and levels of expertise (the goal is to showcase the potential use of existing information and allow various stakeholders to identify their roles in producing soil-based EBVs for different functions or ecosystem services); and iii) the importance of including climate and land use prediction data in modeling frameworks when possible. Overall, the stakeholder engagement process emphasized the significance of data accessibility, diverse modeling approaches, and the incorporation of relevant future data in the selection and development of essential biodiversity variables. Furthermore, the Deliverable discusses the existing gap in the EU's legal framework concerning soil management and highlights the proposed Soil Monitoring Law as a comprehensive framework to address this gap. The outcomes of this Deliverable align with several EU environmental policy initiatives, such as the EU Biodiversity Strategy for 2030, the Zero Pollution Action Plan, the Circular Economy Action Plan, and the Chemicals Strategy for Sustainability. Finally, it proceeds with the selection of essential biodiversity variables (EBVs) for soil-related monitoring within the EuropaBON initiative. Three primary soil-related EBVs have been chosen: 'Functional Composition of soil biota' and 'Community Biomass of soil microbes' and ‘Taxonomic diversity’. These EBVs belong to the 'Community Composition' class within the 'Terrestrial' realm category.

Extreme climatic events and related disturbances such as hurricanes are increasingly altering forest ecosystems. How these events impact forest fungal communities is poorly characterized. We examined the effect of a hurricane on mycorrhizal community structure and potential interspecific fungal interactions, inferred from OTU co-occurrences. We characterized the root fungal communities of dual-mycorrhizal plants from nine plots during two consecutive years after a category four hurricane impacted the coastal Mexican Pacific tropical forest in Jalisco. Presence-abundance matrices were used to calculate properties of mycorrhizal networks including nestedness and modularity, and to infer patterns of co-occurrence. One year after the hurricane there was a loss of links between plants and fungi. Increased network modularity and connectivity were observed after two years. We also found that disturbance changed arbuscular mycorrhizal fungal network structure more strongly than ectomycorrhizal fungal networks. Fungal guilds changed their putative interspecific interactions, from mutual exclusion in the first year to a significant increase in co-occurrence of plant pathogens, saprotrophs, and en-dophytes in the second year. Our results suggest that in the short term, rhizospheric interactions can be resilient to hurricanes, but fungal guilds may have divergent responses.

Partner specificity is a well‐documented phenomenon in biotic interactions, yet the factors that determine specificity in plant‐fungal associations remain largely unknown. By utilizing composite soil samples, we identified the predictors that drive partner specificity in both plants and fungi, with a particular focus on ectomycorrhizal associations. Fungal guilds exhibited significant differences in overall partner preference and avoidance, richness, and specificity to specific tree genera. The highest level of specificity was observed in root endophytic and ectomycorrhizal associations, while the lowest was found in arbuscular mycorrhizal associations. The majority of ectomycorrhizal fungal species showed a preference for one of their partner trees, primarily at the plant genus level. Specialist ectomycorrhizal fungi were dominant in belowground communities in terms of species richness and relative abundance. Moreover, all tree genera (and occasionally species) demonstrated a preference for certain fungal groups. Partner specificity was not related to the rarity of fungi or plants or environmental conditions, except for soil pH. Depending on the partner tree genus, specific fungi became more prevalent and relatively more abundant with increasing stand age, tree dominance, and soil pH conditions optimal for the partner tree genus. The richness of partner tree species and increased evenness of ectomycorrhizal fungi in multi‐host communities enhanced the species richness of ectomycorrhizal fungi. However, it was primarily the partner‐generalist fungi that contributed to the high diversity of ectomycorrhizal fungi in mixed forests.

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.

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.

Introduction Traditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. Methods We sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. Results Large-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. Discussion eDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.

Partner specificity is a well-known phenomenon in biotic interactions, but little is known about biotic and abiotic factors that determine specificity in plant-fungal associations. Using PacBio sequencing of soils from monospecific and mixed forest stands, we determined the predictors driving partner specificity in both ectomycorrhizal plants and fungi. Fungal guilds differed strongly in the patterns of partner preference and avoidance, and specificity to particular tree genera. Specialist ectomycorrhizal fungi dominated in belowground communities, and most species preferred one of their partner trees - mostly at the plant genus level. Furthermore, all tree genera (sometimes species) displayed preference towards certain fungal groups. Partner specificity was unrelated to rarity of fungi or plants or environmental conditions except soil pH. Depending on partner taxon, specificity in fungi tended to increase with dominance and optimal pH of the partner tree genus and stand age. Partner tree richness and increased evenness of ectomycorrhizal fungi in multi-host communities promotes species richness. However, mainly partner-generalist fungi contribute to the high diversity in mixed forests. Our results further suggest that reforestation with mixed tree species promotes soil biodiversity, and that besides conserving mixed forests, protection of old pure stands may be particularly important for conserving partner-specific ectomycorrhizal fungi.

Fungal metabarcoding of substrates such as soil, wood, and water is uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside the scope of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of some in the mycological community – that the current situation is satisfactory and that no change is needed to “the code” – and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. The present authors hope for a revitalized and deepened discussion on DNA-based typification, because to us it seems harmful and counter-productive to intentionally deny the overwhelming majority of extant fungi a formal standing under the International Code of Nomenclature for algae, fungi, and plants.

Fungal metabarcoding of substrates such as soil, wood, and water are uncovering an unprecedented number of fungal species that do not seem to produce tangible morphological structures and that defy our best attempts at cultivation, thus falling outside of the ambit of the International Code of Nomenclature for algae, fungi, and plants. The present study uses the new, ninth release of the species hypotheses of the UNITE database to show that species discovery through environmental sequencing vastly outpaces traditional, Sanger sequencing-based efforts in a strongly increasing trend over the last five years. Our findings challenge the present stance of the mycological community - that 'the code' works fine and that these complications will somehow sort themselves out given enough time and a following wind - and suggest that we should be discussing not whether to allow DNA-based descriptions (typifications) of species and by extension higher ranks of fungi, but what the precise requirements for such DNA-based typifications should be. We submit a tentative list of such criteria for further discussion. However, the present authors fear that no waves of change will be lapping the shores of mycology for the foreseeable future, leaving the overwhelming majority of extant fungi without formal names and thus scientific and environmental agency. It is not clear to us who benefits from that, but neither fungi nor mycology are likely to be on the winning side.