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Only two Coccoloba-associated xerocomoid boletes with smooth basidiospores are currently known from the Dominican Republic, namely Boletus ruborculus and Xerocomus coccolobae. A multilocus phylogenetic analysis of four gene markers (ITS, LSU, RPB2, TEF1) reveals that B. ruborculus forms an autonomous clade in the Boletaceae corresponding to a novel genus, which is introduced here as Tropicoboletus gen. nov., whereas X. coccolobae is confirmed as a member of Xerocomus s. str. Tropicoboletus is sister to subfamily Xerocomoideae in the combined RPB2/TEF1 Boletaceae-wide analysis. Accurate morphological descriptions of the two species based on well-annotated samples are provided, accompanied by color photographs of fresh specimens in habitat and line drawings of their main anatomical features. The holotype collections of B. ruborculus and X. coccolobae were successfully sequenced and re-examined anatomically. The distribution range of Tropicoboletus ruborculus comb. nov. is extended from the original locality in Puerto Rico to the Dominican Republic and Mexico where its presence is reported for the first time. Similarly, the Dominican collections of X. coccolobae represent the first documented occurrence of this species for the Island of Hispaniola. Based on molecular and morphological evidence, we conclude that the Belizean species Xerocomus olivaceus is conspecific with X. coccolobae and is therefore reduced into synonymy. In addition, the holotypes of Xerocomus caeruleonigrescens, Xerocomus cuneipes, and Xerocomus pseudoboletinus var. pini-caribaeae were microscopically re-studied, although their exact taxonomic placement remains unresolved in the absence of any phylogenetic inference. Molecular investigation of a paratype of Boletus guadelupae resulted in a conspecificity with the recently described Singerocomus atlanticus from Brazil, extending the biogeographic coverage of Singerocomus to the Caribbean. Accordingly, the new combination Singerocomus guadelupae is proposed and S. atlanticus is synonymized. Finally, a putative novel Xerocomus s. str. species is discovered from the Dominican Republic but not formally described for the time being due to the paucity of material available.

Globally, forests are impacted by atmospheric nitrogen (N) deposition, affecting their structure and functioning above and below ground. All trees form mutualistic root symbioses with mycorrhizal fungi. Of the two kinds of mycorrhizal symbioses of trees, the ectomycorrhizal (EcM) symbiosis is much more sensitive to N enrichment than the arbuscular mycorrhizal (AM) symbiosis. Due to increasing N deposition, significant declines in the richness and abundance of EcM fungal species and shifts in community composition and functional traits have been recorded. Under increasing N deposition, ectomycorrhizal forests usually show enhanced foliar mass fractions of N, reduced foliar mass fractions of phosphorus (P), and, consequently, an increasing imbalance in the foliar N:P stoichiometry, ultimately impacting tree performance. The question has been raised of whether, under conditions of high N deposition, EcM trees can select EcM fungi that are both tolerant to high N availability and efficient in the acquisition of P, which could to some extent mitigate the negative impact of N deposition on nutrient balances. Here we evaluate the literature for mechanisms through which certain EcM fungi could increase P acquisition under increased N loading. We find very little evidence that under N enrichment, EcM fungi that have on average higher P efficiency might be selected and thereby prevent or delay tree N:P imbalances. However, methodological issues in some of these studies make it imperative to treat this conclusion with caution. Considering the importance of avoiding tree N:P disbalances under N enrichment and the need to restore EcM forests that have suffered from long-term excess N loading, further research into this question is urgently required.

Truffles are highly demanded edible fungi. They belong to the genus Tuber and have very high economic value, with Tuber magnatum being one of the most expensive and gastronomically used. This study evaluates the potential of five introduce tree species as mycorrhizal hosts for T. magnatum in Chile. Seeds from Quercus cerris, Q. robur and Corylus avellana were harvested from adult trees. Cuttings from Populus nigra and Salix caprea were harvested in the field and asexually propagated under greenhouse conditions. After two months, they were transplanted to 260 cc pots containing sterilized composted pine bark. A spore suspension (106 spores/plant) of T. magnatum was injected directly into plant roots. Three months after inoculation we observed spore germination and the presence of mycelium around the roots in some seedlings. After seven months, we observed mycorrhizae from T. magnatum only in Q. cerris, Q. robur and C. avellana, characterized by their epidermoid mantle and awl-shaped, bristle-like cystidia. The identification the mycorrhizal structures was confirmed by sequencing of the nuclear ITS- rDNA region. This study provide the first advances for the domestication of this highly valuable truffle in Chile and South America and the successful mycorrhized plants could be used in further field assays. Some Quercus, Populus and Salix species have been used as ornamental plants and are naturalized in Chile for over 100 years. Additionally, hazelnut (Corylus avellana) is currently grown in the country under intensive silviculture. These tree species could act as a non-intentional host for truffles, dispersed from production sites.

Alpine habitats are one of the most vulnerable ecosystems to environmental change, however, little information is known about the drivers of plant-fungal interactions in these ecosystems and their resilience to climate change. We investigated the influence of the main drivers of ectomycorrhizal (EM) fungal communities along elevation and environmental gradients in the alpine zone of the European Alps and measured their degree of specialisation using network analysis. We sampled ectomycorrhizas of Dryas octopetala, Bistorta vivipara and Salix herbacea, and soil fungal communities at 28 locations across five countries, from the treeline to the nival zone. We found that: (1) EM fungal community composition, but not richness, changes along elevation, (2) there is no strong evidence of host specialisation, however, EM fungal networks in the alpine zone and within these, EM fungi associated with snowbed communities, are more specialised than in other alpine habitats, (3) plant host population structure does not influence EM fungal communities, and (4) most variability in EM fungal communities is explained by fine-scale changes in edaphic properties, like soil pH and total nitrogen. The higher specialisation and narrower ecological niches of these plant-fungal interactions in snowbed habitats make these habitats particularly vulnerable to environmental change in alpine ecosystems.

Madagascar is known for its high diversity and endemism of Fauna and Flora, which makes it particularly interesting for research on diversity and evolution. Fungi, however, have been largely overlooked, and whether fungi exhibit the same patterns as animals and plants has yet to be further examined.We collected fungal sporocarps and ectomycorrhizal (EcM) roots during opportunistic surveys in five forests in Madagascar and generated a dataset of fungal Internal Transcribed Spacer (ITS) DNA sequences. We analysed them together with all publicly available fungal ITS DNA sequences. We identified 620 Operational Taxonomic Units (OTUs) from Madagascar, 10% of which contained only sequences from our surveys. We found 292 OTUs belonging to EcM species with /russula-lactarius, /boletus, /tomentella-telephora, /cortinarius and /amanita as the most abundant EcM lineages. Overall, sixty percent of all the fungi and 81% of the EcM species found are endemic to Madagascar. Lastly, we conducted a phylogenetic analysis using all the OTUs in Amanitaceae, Boletaceae and Russulaceae families to elucidate their relative timing of arrival in Madagascar. We found that the EcM species from Madagascar in the three families diverged recently (less than 34 mya), long after the separation of India and Madagascar (88 mya), which is consistent with a dispersal mediated process of arrival on the island. Our study provides the first comprehensive view of the current state of knowledge of EcM fungi in Madagascar represented by molecular data useful for ecological and evolutionary studies.

Most trees form symbioses with ectomycorrhizal fungi (EMF) which influence access to growth-limiting soil resources. Mesocosm experiments repeatedly show that EMF species differentially affect plant development, yet whether these effects ripple up to influence the growth of entire forests remains unknown. Here we tested the effects of EMF composition and functional genes relative to variation in well-known drivers of tree growth by combining paired molecular EMF surveys with high-resolution forest inventory data across 15 European countries. We show that EMF composition was linked to a three-fold difference in tree growth rate even when controlling for the primary abiotic drivers of tree growth. Fast tree growth was associated with EMF communities harboring high inorganic but low organic nitrogen acquisition gene proportions and EMF which form contact versus medium-distance fringe exploration types. These findings suggest that EMF composition is a strong bio-indicator of underlying drivers of tree growth and/or that variation of forest EMF communities causes differences in tree growth. While it may be too early to assign causality or directionality, our study is one of the first to link fine-scale variation within a key component of the forest microbiome to ecosystem functioning at a continental scale., The ISME Journal, 16 (5), ISSN:1751-7362, ISSN:1751-7370

The resilience of forests is compromised by human-induced environmental influences pushing them towards tipping points and resulting in major shifts in ecosystem state that might be difficult to reverse, are difficult to predict and manage, and can have vast ecological, economic and social consequences. The literature on tipping points has grown rapidly, but almost exclusively based on aquatic and aboveground systems. So far little effort has been made to make links to soil systems, where change is not as drastically apparent, timescales may differ and recovery may be slower. Predicting belowground ecosystem state transitions and recovery, and their impacts on aboveground systems, remains a major scientific, practical and policy challenge. Recently observed major changes in aboveground tree condition across European forests are probably causally linked to ectomycorrhizal (EM) fungal changes belowground. Based on recent breakthroughs in data collection and analysis, we apply tipping point theory to forests, including their belowground component, focusing on EM fungi; link environmental thresholds for EM fungi with nutrient imbalances in forest trees; explore the role of phenotypic plasticity in EM fungal adaptation to, and recovery from, environmental change; and propose major positive feedback mechanisms to understand, address and predict forest ecosystem tipping points.

Ectomycorrhizal fungi are central members of the forest fungal community, forming symbiosis with most trees in temperate and boreal forests, enhancing plant access to limiting soil nutrients. Decades of greenhouse studies have shown that specific mycorrhizal fungi enhance tree seedlings growth and nutrient uptake rates, and that these effects are sustained when seedlings are out-planted into regenerating forests. Whether these relationships scale up to affect the growth of mature trees and entire forests harboring diverse fungal communities remains unknown. In this study, we combined a continental set of European forest inventory data from the ICP forest network with molecular ectomycorrhizal fungal community surveys to identify features of the mycorrhizal mycobiome linked to forest productivity. We found that ectomycorrhizal fungal community composition was a key predictor of tree growth, and this effect was robust to statistically accounting for climate, nitrogen deposition, soil inorganic nitrogen availability, soil pH, and forest stand characteristics. Furthermore, ectomycorrhizal fungi with greater genomic investment in energy production and inorganic nitrogen metabolism, but lower investment in organic nitrogen acquisition, were linked to faster tree growth. Lastly, we sampled soils from fast and slow growing forests and introduced their microbiomes into a sterilized growth medium to experimentally isolate microbiome effects on tree development. Consistent with our observational analysis, tree seedling growth was accelerated when inoculated with microbiomes from fast vs. slow growing forests. By linking molecular community surveys and long-term forest inventory data in the field, and then pairing this with a microbiome manipulation study under controlled conditions, this work demonstrates an emerging link between the forest microbiome and dominant European tree growth rates.

Altres ajuts: COST Actions BIOLINK (FP1305) and KEYSOM (ES 1406). Jorge Curiel Yuste received funding by the Basque Government through the BERC 2018-2021 program. The relatively poor simulation of the below-ground processes is a severe drawback for many ecosystem models, especially when predicting responses to climate change and management. For a meaningful estimation of ecosystem production and the cycling of water, energy, nutrients and carbon, the integration of soil processes and the exchanges at the surface is crucial. It is increasingly recognized that soil biota play an important role in soil organic carbon and nutrient cycling, shaping soil structure and hydrological properties through their activity, and in water and nutrient uptake by plants through mycorrhizal processes. In this article, we review the main soil biological actors (microbiota, fauna and roots) and their effects on soil functioning. We review to what extent they have been included in soil models and propose which of them could be included in ecosystem models. We show that the model representation of the soil food web, the impact of soil ecosystem engineers on soil structure and the related effects on hydrology and soil organic matter (SOM) stabilization are key issues in improving ecosystem-scale soil representation in models. Finally, we describe a new core model concept (KEYLINK) that integrates insights from SOM models, structural models and food web models to simulate the living soil at an ecosystem scale.

Social Impact Statement Positive interactions between people and nature inspire behaviours that are in harmony with biodiversity conservation and also afford physical and mental health benefits. Since most people live in towns and cities, urban greenspaces are key points of influence for conservation, but also provide diverse ecosystem services. City trees are a foundation for biodiversity in urban ecosystems, and their belowground interactions with mycorrhizal fungi and aboveground interactions with pollinators must be central to urban ecosystem planning. Messaging about biodiversity must be clearer to avoid unintended negative outcomes from conservation actions such as low diversity tree planting and unsustainable levels of urban beekeeping Summary Trees are a foundation for biodiversity in urban ecosystems and therefore must be able to withstand global change and biological challenges over decades and even centuries to prevent urban ecosystems from deteriorating. Tree quality and diversity should be prioritized over simply numbers to optimize resilience to these challenges. Successful establishment and renewal of trees in cities must also consider belowground (e.g., mycorrhizas) and aboveground (e.g., pollinators) interactions to ensure urban ecosystem longevity, biodiversity conservation and continued provision of the full range of ecosystem services provided by trees. Positive interactions with nature inspire people to live more sustainable lifestyles that are consistent with stopping biodiversity loss and to participate in conservation actions such as tree‐planting and supporting pollinators. Interacting with nature simultaneously provides mental and physical health benefits to people. Since most people live in cities, here we argue that urban ecosystems provide important opportunities for increasing engagement with nature and educating people about biodiversity conservation. While advocacy on biodiversity must communicate in language that is relevant to a diverse audience, over‐simplified messaging, may result in unintended negative outcomes. For example, tree planting actions typically focus on numbers rather than diversity while the call to save bees has inspired unsustainable proliferation of urban beekeeping that may damage wild bee conservation through increased competition for limited forage in cities and disease spread. Ultimately multiple ecosystem services must be considered (and measured) to optimize their delivery in urban ecosystems and messaging to promote the value of nature in cities must be made widely available and more clearly defined.

In autumn 2016, symptoms of cobweb disease were observed on cultivated Pleurotus ostreatus crops in Spain. Based on morphological and genetic analyses, the causal agent of cobweb was identified as Cladobotryum mycophilum. Two cropping trials, inoculated with C. mycophilum, were set up to evaluate the pathogenicity of this causal agent of cobweb. Two different inoculation methods were used: (i) an agar plug was taken from the growing edge of a C. mycophilum isolate and placed in the centre of each hole in the block of P. ostreatus substrate (IP), and (ii) spraying each hole with a conidial suspension (ISC). In both trials, there were significant differences in disease incidence between the controls and the inoculated samples, but there were no significant differences between the two inoculation treatments. Between 75 and 87.5% of the blocks of the IP treatments and 100% of the blocks of the ISC treatments showed cobweb symptoms. Cladobotryum mycophilum was consistently re-isolated from the inoculated blocks (100%). These findings suggest that C. mycophilum can equally cause cobweb disease in A. bisporus, P. eryngii, and P. ostreatus mushroom crops.

Almost all orchid species depend on association with fungal partners. These fungal species facilitate orchid seed germination and promote growth and possibly stress tolerance in adult plants, both in the field and laboratory conditions. Codonorchis lessonii is a terrestrial orchid, endemic to southern Chile and Argentina with a currently unknown conservation status. Previous studies have reported Rhizoctonia-like fungi associated with C. lessonii in Argentina, but their fungal partners in Chilean populations are unknown. This study aims to characterize and isolate the mycorrhizal fungi associated with adult individuals of C. lessonii from three different populations in Central-South Chile. Root sections showing pelotons were used for the isolation and identification of the fungal taxa. Radial fungal growth was measured for all mycelial isolates. The presence of binucleate cells placed all isolates within the families Ceratobasidiaceae and Tulasnellaceae and the identification was confirmed by molecular analysis. Fungal isolates belonging to Ceratobasidiaceae grew at a higher rate than those from Tulasnellaceae. Phylogenetic analyses showed that different fungal partners associate with this orchid, suggesting relatively low specificity. The isolation and identification of the fungal partners of C. lessonii could help understand its ecology and contribute in future restoration and propagation initiatives for the species.

The plantation and management of sweet chestnut (Castanea sativa Mill.) orchards is a common and traditional land use system in many areas of Europe that offers the advantage of simultaneous production of nuts and timber. During the last decades, sweet chestnut has declined dramatically in many regions because of the profound social changes in rural areas coupled with pathogen attacks. Truffles, the hypogeous ascocarps of the ectomycorrhizal genus Tuber, are currently cultivated using host trees inoculated with these fungi for improving production in truffle orchards. The production of good forestry quality chestnut seedlings inoculated with European truffles in nurseries is essential for multi-cropping plantation establishment, but so far, it has not been implemented in agroforestry practices. Moreover, it is necessary to assess the physiological condition of the seedlings due to the high calcium amendment needed for the growth of Tuber spp. mycelium that can become toxic for the host plants. In this study, seedlings of C. sativa were inoculated with Tuber aestivum and its ecotypes T. uncinatum, T. brumale, and T. macrosporum and were grown in a greenhouse using culture conditions favorable for the production of high-quality plants for forestry purposes. At the end of the assay, levels of root colonization and morphological and physiological parameters of the seedlings were measured. The colonization of C. sativa with T. aestivum, its ecotype T. uncinatum, and T. brumale was successful, and the seedlings showed normal growth. Inoculation protocols with T. macrosporum need to be improved. Tuber species formed well-developed ectomycorrhizae on C. sativa in nursery conditions.

Concerted evolution of the ribosomal DNA array has been studied in numerous eukaryotic taxa, yet is still poorly understood. rDNA genes are repeated dozens to hundreds of times in the eukaryotic genome (Eickbush and Eickbush, 2007) and it is believed that these arrays are homogenized through concerted evolution (Zimmer et al., 1980; Dover, 1993) preventing the accumulation of intragenomic, and intraspecific, variation. However, numerous studies have reported rampant intragenomic and intraspecific variation in the rDNA array (Ganley and Kobayashi, 2011; Naidoo et al., 2013; Hughes and Petersen, 2001; Lindner and Banik, 2011; Li et al., 2013; Lindner et al., 2013; Hughes et al., 2018), contradicting our current understanding of concerted evolution. The internal transcribed spacers (ITS) of the rDNA cistron are the most commonly used DNA barcoding region in Fungi (Schoch et al., 2012), and rely on concerted evolution to homogenize the rDNA array leading to a "barcode gap" (Puillandre et al., 2012). Here we show that in Boletus edulis Bull., ITS intragenomic variation persists at low allele frequencies throughout the rDNA array, this variation does not correlate with genomic relatedness between populations, and rDNA genes may not evolve in a strictly concerted fashion despite the presence of unequal recombination and gene conversion. Under normal assumptions, heterozygous positions found in ITS sequences represent hybridization between populations, yet through allelic mapping of the rDNA array we found numerous heterozygous alleles to be stochastically introgressed throughout, presenting a dishonest signal of gene flow. Moreover, despite the signal of gene flow in ITS, our organisms were highly inbred, indicating a disconnect between true gene flow and barcoding signals. In addition, we show that while the mechanisms of concerted evolution are ongoing in pseudo-heterozygous individuals, they are not fully homogenizing the ITS array. Concerted evolution of the rDNA array may insufficiently homogenize the ITS gene, allowing for misleading signals of gene flow to persist, vastly complicating the use of the ITS locus for DNA barcoding in Fungi.

International audience; Biodiversity of ecosystems is an important driver for the supply of ecosystem services to people. Soils often have a larger biodiversity per unit surface area than what can be observed aboveground. Here, we present what is to our knowledge, the most extensive literature-based key-word assessment of the existing information about the relationships between belowground biodiversity and ecosystem services in European forests. The belowground diversity of plant roots, fungi, prokaryota, soil fauna, and protists was evaluated in relation to the supply of Provisioning, Regulating, Cultural, and Supporting Services. The soil biota were divided into 14 subgroups and the ecosystem services into 37 separate services. Out of the 518 possible combinations of biotic groups and ecosystem services, no published study was found for 374 combinations (72%). Of the remaining 144 combinations (28%) where relationships were found, the large majority (87%) showed a positive relationship between biodiversity of a belowground biotic group and an associated ecosystem service. However, for the majority of the combinations (102) there were only three or fewer studies. The percentage of cases for which a relationship was detected varied strongly between ecosystem service categories with 23% for Provisioning, 8% for Regulating, 40% for Cultural, and 48% for Supporting Services. We conclude that (1) soil biodiversity is generally positively related to ecosystem services in European forests; (2) the links between soil biodiversity and Cultural or Supporting services are better documented than those relating to Provisioning and Regulating services; (3) there is a huge knowledge gap for most possible combinations of soil biota and ecosystem services regarding how a more biodiverse soil biota is associated with a given ecosystem service. Given the drastically increasing societal demand for knowledge of the role of biodiversity in the functioning of ecosystems and the supply of ecosystem services, we strongly encourage the scientific community to conduct well-designed studies incorporating the belowground diversity and the functions and services associated with this diversity.

In 2010, symptoms of cobweb disease were observed on cultivated Pleurotus eryngii crops in Spain. Based on morphological and genetic analyses, the causal agent of cobweb was identified as Cladobotryum mycophilum. Pathogenicity tests on fruit bodies were performed using conidial suspensions of three C. mycophilum isolates. The causal agent was re-isolated in 80–85 % of the fruit bodies inoculated internally and 15–40 % of those fruit bodies inoculated on the cap surface. The results pointed to a certain resistance of the P. eryngii cap surface to the mycelium of C. mycophilum. Two cropping trials inoculated with C. mycophilum were set up to evaluate the pathogenicity of the causal agent of cobweb in two casings. At the end of the growth cycle, 50–60 % of the inoculated blocks cased with mineral soil, and 20–33 % of the inoculated blocks cased with black peat showed cobweb symptoms. This difference in the appearance of the disease and its aggressiveness may be partly explained by different electrical conductivity values of the casing materials used. In vitro sensitivity of the C. mycophilum isolates and P. eryngii strains against four fungicides (chlorothalonil, prochloraz-Mn, thiabendazole and thiophanate-methyl) was assessed in radial growth experiments on fungicide-amended media. The most effective fungicides for inhibiting the in vitro growth of C. mycophilum were prochloraz-Mn and chlorothalonil, while prochloraz-Mn was also the most selective fungicide between P. eryngii and C. mycophilum, and chlorothalonil was the most toxic fungicide against the P. eryngii mycelium.

Ectomycorrhizal (EcM) fungi are essential for the establishment of woody perennial plants in the European Alps. From continental to local scales, environmental conditions and plant host characteristics can predict EcM community structure and composition. However, it is unclear whether EcM communities of congeneric host species and their hybrids are differentially structured at local scales. We aimed to i) characterize EcM communities of Salix helvetica, Salix purpurea and their hybrids and ii) elucidate the abiotic and biotic factors affecting EcM communities in hybrid zones. We analysed the EcM communities associated with willows in a glacier valley by combining molecular identification of fungi from individual ectomycorrhizas and from soil. We detected diverse EcM fungi forming non-modular and unnested networks, but we did not find significant differences in the overall EcM fungal community richness or composition among parental species and hybrids. Nevertheless, individual fungi differed regarding host preference. Our results demonstrate that in a sub-alpine hybrid zone with heterogeneous geomorphology, host genotype was not a strong predictor of overall EcM fungal community, but it influenced the occurrence of particular fungi.

Psilocybin is a psychoactive compound with clinical applications produced by dozens of mushroom species1. There has been a longstanding interest in psilocybin research with regard to treatment for addiction2, depression3, and end-of-life suffering4. However, until recently very little was known about psilocybin biosynthesis and its ecological role. Here we confirm and refine recent findings5 about the genes underpinning psilocybin biosynthesis, discover that there is more than one psilocybin biosynthesis cluster in mushrooms, and we provide the first data directly addressing psilocybin’s ecological role. By analysing independent genome assemblies for the hallucinogenic mushrooms Psilocybe cyanescens and Pluteus salicinus we recapture the recently discovered psilocybin biosynthesis cluster5,6 and show that a transcription factor previously implicated in its regulation is actually not part of the cluster. Further, we show that the mushroom Inocybe corydalina produces psilocybin but does not contain the established biosynthetic cluster, and we present an alternative cluster. Finally, a meta-transcriptome analysis of wild-collected mushrooms provides evidence for intra-mushroom insect gene expression of flies whose larvae grow inside Psilocybe cyanescens. These larvae were successfully reared into adults. Our results show that psilocybin does not confer complete protection against insect mycophagy, and the hypothesis that it is produced as an adaptive defense compound may need to be reconsidered.

Explaining the large-scale diversity of soil organisms that drive biogeochemical processes—and their responses to environmental change—is critical. However, identifying consistent drivers of belowground diversity and abundance for some soil organisms at large spatial scales remains problematic. Here we investigate a major guild, the ectomycorrhizal fungi, across European forests at a spatial scale and resolution that is—to our knowledge—unprecedented, to explore key biotic and abiotic predictors of ectomycorrhizal diversity and to identify dominant responses and thresholds for change across complex environmental gradients. We show the effect of 38 host, environment, climate and geographical variables on ectomycorrhizal diversity, and define thresholds of community change for key variables. We quantify host specificity and reveal plasticity in functional traits involved in soil foraging across gradients. We conclude that environmental and host factors explain most of the variation in ectomycorrhizal diversity, that the environmental thresholds used as major ecosystem assessment tools need adjustment and that the importance of belowground specificity and plasticity has previously been underappreciated.

The enormity of the breadth and depth of specimens held within the world's biological collections offers unparalleled opportunities to capture genomic data from across the entire range of known biological diversity. Such a task would take many lifetimes to complete if we could rely only on fresh samples. High-throughput sequencing provides a technical solution to the long-term problems of recalcitrant and degraded DNA typical of museum specimens, suggesting that we may be on the verge of a major collections-based revolution. Although the potential is great, the feasibility of using preserved collections for large-scale, taxonomically comprehensive phylogenomic studies remains unknown. In the present study, we demonstrate the continued relevance of fungarium collections in the genomic era by analyzing a genomic dataset composed of 39 genomes representing 26 family-level clades, including 14 newly generated draft genomes derived from short-read shotgun sequencing of preserved specimens, frozen and freeze-dried material, representing most of the known families of Agaricales. We predicted homologues of 210 putative single copy genes in the newly generated draft genome assemblies, of which 208 were used for phylogenetic reconstruction. Our analyses resulted in a robust and, for the first time, fully supported phylogeny of the Agaricales, enabling the recognition of seven suborders and providing a resource for testing hypotheses of the evolution of mushrooms. Our analysis of optimal combinations of ranked genes using an information theory-based method provides guidance on gene selection for future studies, enabling efficient application of high-throughput sequencing techniques toward unlocking the potential of collections-based research in the genomic era.

Historical datasets of living communities are important because they can be used to document creeping shifts in species compositions. Such a historical data set exists for alpine fungi. From 1941 to 1953, the Swiss geologist Jules Favre visited yearly the region of the Swiss National Park and recorded the occurring fruiting bodies of fungi >1 mm (so-called “macrofungi”) in the alpine zone. Favre can be regarded as one of the pioneers of alpine fungal ecology not least because he noted location, elevation, geology, and associated plants during his numerous excursions. However, some relevant information is only available in his unpublished field-book. Overall, Favre listed 204 fungal species in 26 sampling sites, with 46 species being previously unknown. The analysis of his data revealed that the macrofungi recorded belong to two major ecological groups, either they are symbiotrophs and live in ectomycorrhizal associations with alpine plant hosts, or they are saprotrophs and decompose plant litter and soil organic matter. The most frequent fungi were members of Inocybe and Cortinarius, which form ectomycorrhizas with Dryas octopetala or the dwarf alpine Salix species. The scope of the present study was to combine Favre's historical dataset with more recent data, either with the “SwissFungi” database or with data from major studies of the French and German Alps, and with the data from novel high-throughput DNA sequencing techniques of soils from the Swiss Alps. Results of the latter application revealed, that problems associated with these new techniques are manifold and species determination remains often unclear. At this point, the fungal taxa collected by Favre and deposited as exsiccata at the “Conservatoire et Jardin Botaniques de la Ville de Genève” could be used as a reference sequence dataset for alpine fungal studies. In conclusion, it can be postulated that new improved databases are urgently necessary for the near future, particularly, with regard to investigating fungal communities from alpine regions using new techniques.

Since the nineteenth century, Myriostoma has been regarded as a monotypic genus with a widespread distribution in north temperate and subtropical regions. However, on the basis of morphological characters and phylogenetic evidence of DNA sequences of the internal transcribed spacer (ITS) regions and the large subunit nuclear ribosomal RNA gene (LSU), four species are now delimited: M. areolatum comb. & stat. nov., M. calongei sp. nov., M. capillisporum comb. & stat. nov., and M. coliforme. Myriostoma coliforme is typified by selecting a lectotype (iconotype) and a modern sequenced collection as an epitype. The four species can be discriminated by a combination of morphological characters, such as stomatal form, endoperidial surface texture, and basidiospore size and ornamentation., The authors would like to express their thanks to the CoordenacËão de AperfeicËoamento de Pessoal de NõÂvel Superior (CAPESÐBrazil) for the PhD scholarships awarded to Julieth de Oliveira Sousa and Donis S. Alfredo in 2014/2015 and to the Conselho Nacional de Desenvolvimento CientõÂfico e TecnoloÂgico (CNPqÐBrazil, Projeto Pesquisador Visitante Especial PVE/407474/2013±7 and Projecto de Pesquisa em Biodiversidade do Semiarido PPBio/457476/ 2012±5; MarõÂa P. MartõÂn and Iuri G. Baseia) for the scholarship of scientific initiation awarded to Luana Conrado. Natural England (Species Recovery Programme) is thanked for funding part of the sequencing work carried out in England. The first author would like to thank Bianca Silva and Judcleidson Cavalcante for their help with the Brazilian field expedition. Bart Buyck is thanked for granting permission for specimen loans from the Herbarium of the MuseÂum national d'Histoire naturelle (MNHNÐParis), and Mikael Jeppson for loan of the sample MJ8714. Thanks to M. Teresa Telleria and Margarita Dueñas from the Real JardõÂn BotaÂnico-CSIC (Madrid, Spain) for continuously supporting the study of gasteroid fungi and thanks to Paul M. Kirk (RBG, Kew) for nomenclatural advice. Thanks to Sandra Nogal-Prata forMyriostoma areolatum Fig 2A and 2B. The authors would also like to thank MarõÂa Conejero (RBG, Kew) and Yolanda Ruiz (RJB, Madrid) for technical support with the SEM images.

Orchids are obligate mycoheterotrophic plants, relying on fungal nutrient resources to grow for their entire life or until they develop into photosynthetic seedlings. In Chile, orchids are represented by 7 genera and 63 species, 27 of which are endemic. Some Chilean species are considered endangered or rare, but many are insufficiently known. This study aims to isolate, culture, and identify fungal species found in symbiosis with the endemic Chilean orchids Chloraea collicensis Kraenzl. and Chloraea gavilu Lindl. for their potential to be used in future conservation programs. Roots of both species of orchids were collected in the field and those presenting pelotons were firstly cultured in agar-water and thereafter sub-cultured in potato dextrose agar media. Fungal colony growth was measured under the dissecting microscope. Fungal isolates from C. gavilu showed a higher growth rate than isolates from C. collicensis and could be used as inoculum for seed germination in further studies. Isolated colonies showed morphological characteristics of the form genus Rhizoctonia and presented two nuclei per cell. The ITS-nrDNA sequences confirmed their morphological identification as species of Tulasnella.

Change history: In the HTML version of this Article, author 'Filipa Cox' had no affiliation in the author list, although she was correctly associated with affiliation 3 in the PDF. In addition, the blue circles for 'oak' were missing from Extended Data Fig. 1. These errors have been corrected online.

Lentinula edodes, known as shiitake, is the main cultivated edible mushroom worldwide, representing about 22% of the world’s output, with China being the major producer. In 2017 symptoms of cobweb were observed on cultivated shiitake mushrooms in Castilla-La Mancha (Spain), affecting more than 30% of the blocks of pasteurized substrate. Cobweb appeared at the end of the crop cycle as circular white patches over the surface of the blocks of substrate and fruitbodies. The fine grey-white mycelium rapidly covered pinheads, stalks, pileus and gills, eventually resulting in the decomposition of the entire fruitbody. The mycelium can colonize the surface of the substrate completely and may turn reddish brown. To isolate the parasitic fungus, infected tissues of L. edodes were plated onto potato dextrose agar (PDA). Fungal colonies consisted of white, cottony, aerial mycelium that spread rapidly on the PDA, changing from white to yellow and finally, pink, as the red pigment spread into the agar. The conidiogenou...

Relative quantification of DNA from Tuber melanosporum mycelia was performed by conventional and real-time PCR in soil from trees in three truffle orchards of different ages to determine: (1) whether burn appearance is related to the amount of T. melanosporum mycelium in soil, and (2) whether productivity onset and truffle production are related to (a) the amount of T. melanosporum mycelium in soil, (b) tree height and diameter, (c) burn extension and (d) surface rock cover. The burn seems to appear only after a certain amount of mycelium has formed. Precociously productive trees presented higher quantities of mycelium than nonproductive trees in the productivity onset study, while highly productive trees presented less quantities of mycelium than nonproductive trees in the productivity study. Trees with high but not excessive surface rock cover showed greater truffle production. Larger trees tended to display a burn earlier than smaller trees.

Chloraea cuneata es una orquidea endemica de Chile en Peligro Critico de Extincion. Se aislaron e identificaron hongos orquidioides a partir de pelotones ubicados en celulas corticales de sus raices pertenecientes al genero-forma Rhizoctonia, teleomorfo Thanatephorus (multinucleado), los que podrian ser usados en iniciativas de conservacion.

Our objectives were (i) to develop a molecular method to detect mycelia of Tuber melanosporum (black truffle) in soil and (ii) to test for mycelial distribution around two truffle-bearing Quercus ilex trees in a truffle orchard. Isolation of total DNA from soil was performed, followed by PCR amplification with T. melanosporum-specific primers and restriction analysis. To address the detection sensitivity level, soil samples were inoculated with known amounts of gleba of T. melanosporum. The detection limit was Z11.4 mg of hyphae g 1 of soil. Mycelium was detected primarily within the area defined by the truffle burn and within the top 35 cm of the soil in all directions from the trees.

Key message The ICP Forests network can be a platform for large-scale mycorrhizal studies. Mapping and monitoring of mycorrhizas have untapped potential to inform science, management, conservation and policy regarding distributions, diversity hotspots, dominance and rarity, and indicators of forest changes. Context A dearth of information about fungi at large scales has severely constrained scientific, forest management, fungal conservation and environmental policy efforts worldwide. Nonetheless, fungi fulfil critical functional roles in our changing environments and represent a considerable proportion of terrestrial biodiversity. Mycorrhizal fungi are increasingly viewed as a major functional guild across forest ecosystems, and our ability to study them is expanding rapidly. Aims This study aimed to discuss the potential for starting a mycorrhizal monitoring programme built upon the existing forest monitoring network, raise questions, propose hypotheses and stimulate further discussion. Results An overview of the state-of-the-art regarding forest ectomycorrhizal ecology raises questions and recommendations for scaling up mycorrhizal assessments aimed at informing a variety of stakeholders, with a new focus on conservation and policy. Conclusion Fungal research and conservation are areas that can be informed by ICP Forests and may lead to useful spin-offs; research linked to long-term forest monitoring plots will enhance the relevance of science and conservation.

Accurate diagnosis of the components of our food and a standard lexicon for clear communication is essential for regulating global food trade and identifying food frauds. Reliable identification of wild collected foods can be particularly difficult, especially when they originate in under-documented regions or belong to poorly known groups such as Fungi. Porcini, one of the most widely traded wild edible mushrooms in the world, are large and conspicuous and they are used as a food both on their own and in processed food products. China is a major exporter of porcini, most of it ending up in Europe. We used DNA-sequencing to identify three species of mushroom contained within a commercial packet of dried Chinese porcini purchased in London. Surprisingly, all three have never been formally described by science and required new scientific names. This demonstrates the ubiquity of unknown fungal diversity even in widely traded commercial food products from one of the most charismatic and least overlooked groups of mushrooms. Our rapid analysis and description makes it possible to reliably identify these species, allowing their harvest to be monitored and their presence tracked in the food chain.

Accurate diagnosis of the components of our food and a standard lexicon for clear communication is essential for regulating global food trade and identifying food frauds. Reliable identification of wild collected foods can be particularly difficult, especially when they originate in under-documented regions or belong to poorly known groups such as Fungi. Porcini, one of the most widely traded wild edible mushrooms in the world, are large and conspicuous and they are used as a food both on their own and in processed food products. China is a major exporter of porcini, most of it ending up in Europe. We used DNA-sequencing to identify three species of mushroom contained within a commercial packet of dried Chinese porcini purchased in London. Surprisingly, all three have never been formally described by science and required new scientific names. This demonstrates the ubiquity of unknown fungal diversity even in widely traded commercial food products from one of the most charismatic and least overlooked groups of mushrooms. Our rapid analysis and description makes it possible to reliably identify these species in the food chain, leading to an improved ability to regulate their harvest and trade, and to monitor potential adverse health effects from their consumption.

Ectomycorrhizal fungi are major ecological players in temperate forests, but they are rarely used in measures of forest condition because large-scale, high-resolution, standardized and replicated belowground data are scarce. We carried out an analysis of ectomycorrhizas at 22 intensively monitored long-term oak plots, across nine European countries, covering complex natural and anthropogenic environmental gradients. We found that at large scales, mycorrhizal richness and evenness declined with decreasing soil pH and root density, and with increasing atmospheric nitrogen deposition. Shifts in mycorrhizas with different functional traits were detected; mycorrhizas with structures specialized for long-distance transport related differently to most environmental variables than those without. The dominant oak-specialist Lactarius quietus, with limited soil exploration abilities, responds positively to increasing nitrogen inputs and decreasing pH. In contrast, Tricholoma, Cortinarius and Piloderma species, with medium-distance soil exploration abilities, show a consistently negative response. We also determined nitrogen critical loads for moderate (9.5–13.5 kg N/ha/year) and drastic (17 kg N/ha/year) changes in belowground mycorrhizal root communities in temperate oak forests. Overall, we generated the first baseline data for ectomycorrhizal fungi in the oak forests sampled, identified nitrogen pollution as one of their major drivers at large scales and revealed fungi that individually and/or in combination with others can be used as belowground indicators of environmental characteristics. Ectomycorrhizal fungi are major ecological players in temperate forests but they are rarely used in measures of forest condition because large-scale, high-resolution, standardized and replicated belowground data is scarce. We carried out an analysis of ectomycorrhizas at 22 intensively-monitored long-term oak plots, across nine European countries, covering complex natural and anthropogenic environmental gradients. We found that at large scales mycorrhizal richness and evenness declined with decreasing soil pH and root density, and with increasing atmospheric nitrogen deposition. Shifts in mycorrhizas with different functional traits were detected; mycorrhizas with structures specialized for long-distance transport related differently to most environmental variables than those without. The dominant oak-specialist Lactarius quietus, with limited soil exploration, responds positively to increasing N inputs and decreasing pH. In contrast, Tricholoma, Cortinarius and Piloderma species, with medium-distance soil exploration, show a consistently negativeresponse. We also determined N critical loads for moderate (9.5 – 13.5 kg N ha-1 yr-1) and drastic (17 kg N ha-1 yr-1) changes in belowground mycorrhizal root communities in temperate oak forests. Overall, we generated the first baseline data for ectomycorrhizal fungi in the oak forests sampled, identified nitrogen pollution as one of their major drivers at large scales, and revealed fungi that individually and/or in combination with others can be used as belowground indicators of environmental characteristics.

The high cost and restricted availability of black truffle spore inoculum for controlled mycorrhiza formation of host trees produced for truffle orchards worldwide encourage the search for more efficient and sustainable inoculation methods that can be applied globally. In this study, we evaluated the potential of the nurse plant method for the controlled inoculation of Quercus cerris and Quercus robur with Tuber melanosporum by mycorrhizal networks in pot cultures. Pine bark compost, adjusted to pH 7.8 by liming, was used as substrate for all assays. Initially, Q. robur seedlings were inoculated with truffle spores and cultured for 12 months. After this period, the plants presenting 74 % mycorrhizal fine roots were transferred to larger containers. Nurse plants were used for two treatments of two different nursling species: five sterilized acorns or five 45-day-old, axenically grown Q. robur or Q. cerris seedlings, planted in containers around the nurse plant. After 6 months, colonized nursling plant root tips showed that mycorrhiza formation by T. melanosporum was higher than 45 % in the seedlings tested, with the most successful nursling combination being Q. cerris seedlings, reaching 81 % colonization. Bulk identification of T. melanosporum mycorrhizae was based on morphological and anatomical features and confirmed by sequencing of the internal transcribed spacer region of the ribosomal DNA of selected root tips. Our results show that the nurse plant method yields attractive rates of mycorrhiza formation by the Perigord black truffle and suggest that establishing and maintaining common mycorrhizal networks in pot cultures enables sustained use of the initial spore inoculum.

Although successful cultivation of the black truffle (Tuber melanosporum) has inspired the establishment of widespread truffle orchards in agricultural lands throughout the world, there are many unknowns involved in proper management of orchards during the 6-10 years prior to truffle production, and there are conflicting results reported for fertilizer treatments. Here, we systematically evaluate the combined effects of nitrogen, phosphorous, and potassium with different doses of each element, applied to either foliage or roots, on plant growth parameters and the mycorrhizal status of outplanted 3-year-old seedlings in five experimental Quercus ilex-T. melanosporum orchards. Fertilization did not significantly improve seedling aboveground growth, but the plants treated with the fertilizer 12-7-7 applied to the roots (HNr) displayed longer field-developed roots. Only the fertilizer with the highest dose of K (10-6-28) applied to the foliage (HKf) increased the probability of fine root tip colonization by T. melanosporum in field-developed roots. However, the plants treated with the same fertilizer applied to the soil (HKr) presented the highest probability for colonization by other competing mycorrhizal soil fungi. Potassium seems to have an important role in mycorrhizal development in these soils. Apart from T. melanosporum, we found 14 ectomycorrhizal morphotypes, from which seven were identified to species level, three to genus, two to family, and two remained unidentified by their morphological characteristics and DNA analyses.

At the interface between plants and soils, ectomycorrhizal (ECM) fungi explore soils, acquire resources, transfer resources to plants, and acquire carbon from plants. Mycorrhizas enhance plant survival, nutrition and growth and play key roles in ecosystems processes such as decomposition, nutrient cycling, soil carbon storage, productivity and sustainability. Mycorrhizas are critical for plant colonization of new soils (e.g. mine spoils, volcanic deposits, glacial moraines). ECM diversity ensures plant reestablishment after disturbance and can enhance survival and growth of trees in reforestation. ECM fungi can promote fine root development as well as produce antibiotics, hormones and vitamins. Mycorrhizal associations may help protect roots from pathogens and moderate effects of heavy metals and toxins. Many environmental problems may be alleviated by mycorrhizas – problems such as pollution, erosion, soil degradation, climate change, degradation of natural resources, and poor land use management. Mycorrhizal abilities to carry out important functions are linked to diversity. ECM diversity is large and documented in many ecosystems, particularly coniferous ecosystems (Gehring et al. 1998; Goodman and Trofymow 1998; Kranabetter and Wylie 1998; van der Heijden et al. 1998; Stendell et al. 1999; Bidartondo et al. 2000). This ECM diversity has been based on surveys of fruiting bodies, but is now based on more recent methods – morphotyping (microscopic observations) and phylotyping (molecular characterization). An advantage of fruiting body surveys is ease of collection and identification based on morphology; a disadvantage is the assumption that fungi fruiting in an area also form ectomycorrhizas on nearby roots. Clearly identification of ectomycorrhizas on roots is preferable. However there are difficulties in ECM identification – complex sampling design and

International audience; We describe the distribution and the ecology of three Armillaria species observed in silver fir (Abies alba) forests of the Pyrenees.* We surveyed the presence and abundance of Armillaria above and belowground in 29 stands. Isolates were identified by the PCR-RFLP pattern of the IGS-1 region of their ribosomal DNA. We measured several ecological and management parameters of each stand in order to describe Armillaria infected sites.* Armillaria cepistipes was the most abundant of three species observed. Armillaria gallica was dominant in soils with a higher pH and at lower elevations. Armillaria ostoyae seemed to be more frequent in stands where A. alba recently increased its dominance relative to other forest tree species. Thinning activities correlated with an increased abundance of Armillaria belowground. In 83% of the stands the same Armillaria species was observed above and belowground.* It seems that in a conifer forest, A. cepistipes can be more frequent than A. ostoyae, a virulent conifer pathogen. Since logging is related to a higher abundance of Armillaria in the soil, the particular Armillaria species present in a given stand could be considered an additional site factor when making management decisions.; Nous décrivons la distribution et l'écologie de trois espèces d'Armillaria sur le sapin blanc (Abies alba) dans les forêts pyrénéennes* Nous avons recherché la présence d'Armillaire au dessus du sol et dans le sol dans 29 peuplements. Les isolats ont été identifiés par RFLP-PCR de la région IGS-1 de leur ADN ribosomal. Plusieurs paramètres écologiques et de gestion ont été mesurés dans chacun des peuplements, pour caractériser les sites infestés.* Armillaria cepistipes était la plus abondante des trois espèces observées. Armillaria gallica dominait dans les sols de basse altitude et à pH élevé. Armillaria ostoyae a semblé plus fréquent dans les peuplements où la dominance relative d'A. alba avait récemment augmenté par rapport aux autres espèces forestières. L'activité d'éclaircies était corrélée à l'augmentation d'Armillaire dans le sol. La même espèce d'Armillaria a été observée au dessus du sol et dans le sol, dans 83 % des peuplements.* Il apparaît que, en forêt de conifères, A. cepistipes peut être plus fréquent qu' A. ostoyae, pathogène virulent des conifères. Puisque les coupes forestières sont reliées à une plus grande abondance d'Armillaire dans le sol, la présence d'une espèce particulière d'Armillaria dans un peuplement donné pourrait être un paramètre stationnel supplémentaire à considérer lors de décisions de gestion.