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.
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.
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.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Summary
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 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.
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•The mechanisms of concerted evolution may insufficiently homogenize the rDNA array.•Alleles persist in the ITS regions at low frequencies, and may be undetectable by Sanger ...Sequencing.•ITS gene relatedness and gene flow in Boletus edulis does not correlate with genomic relatedness.•Significant inbreeding may allow fixation of novel ITS alleles, creating false signals of gene flow.•ITS barcoding for identification of population boundaries and complex species resolution is suspect.
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.
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.
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.
Setting aside overmature planted forests is currently seen as an option for preserving species associated with old-growth forests, such as those with dispersal limitation. Few data exist, however, on ...the utility of set-aside plantations for this purpose, or the value of this habitat type for biodiversity relative to old-growth semi-natural ecosystems. Here, we evaluate the contribution of forest type relative to habitat characteristics in determining species richness and composition in seven forest blocks, each containing an ancient old-growth stand (>1000yrs) paired with a set-aside even-aged planted stand (ca. 180yrs). We investigated the functionally important yet relatively neglected ectomycorrhizal fungi (EMF), a group for which the importance of forest age has not been assessed in broadleaved forests. We found that forest type was not an important determinant of EMF species richness or composition, demonstrating that set-aside can be an effective option for conserving ancient EMF communities. Species richness of above-ground EMF fruiting bodies was principally related to the basal area of the stand (a correlate of canopy cover) and tree species diversity, whilst richness of below-ground ectomycorrhizae was driven only by tree diversity. Our results suggest that overmature planted forest stands, particularly those that are mixed-woods with high basal area, are an effective means to connect and expand ecological networks of ancient old-growth forests in historically deforested and fragmented landscapes for ectomycorrhizal fungi.
•Ectomycorrhizal fungi richness was similar in ancient and overmature planted forest.•Community composition was also similar across the forest types.•Fungal fruit body richness was positively related to basal area and tree diversity.•Below-ground ectomycorrhizae richness was positively related to tree diversity.
Fungi comprise approximately 20% of all eukaryotic species and are connected to virtually all life forms on Earth. Yet, their diversity remains contentious, their distribution elusive, and their ...conservation neglected. We aim to flip this situation by synthesizing current knowledge. We present a revised estimate of 2-3 million fungal species with a "best estimate" at 2.5 million. To name the unknown >90% of these by the end of this century, we propose recognition of species known only from DNA data and call for large-scale sampling campaigns. We present an updated global map of fungal richness, highlighting tropical and temperate ecoregions of high diversity. We call for further Red List assessments and enhanced management guidelines to aid fungal conservation. Given that fungi play an inseparable role in our lives and in all ecosystems, and considering the fascinating questions remaining to be answered, we argue that fungi constitute the next frontier of biodiversity research.
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