Fungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water.
We provide rough phylogenetic ...placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat, Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH.
This study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.
Molecular methods are increasingly used to identify species that lack conspicuous macro‐ or micromorphological characters. Taxonomic and ecological research teams barcode large numbers of collected ...voucher specimens annually. In this study we assessed the efficiency of long‐read high throughput sequencing (HTS) as opposed to the traditionally used Sanger method for taxonomic identification of multiple vouchered fungal specimens. We also evaluated whether this method can provide reference information about intraindividual gene polymorphism. We developed a workflow based on a test set of 423 basidiomycete specimens (representing 195 species), the PacBio HTS method, and ribosomal rRNA operon internal transcribed spacer (ITS) and 28S rRNA gene (LSU) markers. The PacBio HTS had a higher success rate than Sanger sequencing at a comparable cost. Species identification based on PacBio reads was usually straightforward, because the dominant operational taxonomic unit (OTU) typically represented the targeted organism. The PacBio HTS also enabled us to detect widespread polymorphism within the ITS marker. We conclude that multiplex DNA barcoding of the fungal ITS and LSU markers using PacBio HTS is a useful tool for taxonomic identification of large amounts of collected voucher specimens at a competitive price. Furthermore, PacBio HTS accurately recovers various alleles and paralogues, which can provide crucial information for species delimitation and population‐level studies.
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Information about the diversity of tropical microbes, including fungi is relatively scarce. This study addresses the diversity, spatial distribution and host preference of ectomycorrhizal fungi ...(EcMF) in a neotropical rainforest site in North East Ecuador. DNA sequence analysis of both symbionts revealed relatively low richness of EcMF as compared with the richness of temperate regions that contrasts with high plant (including host) diversity. EcMF community was positively autocorrelated up to 8.5+/-1.0-m distance-roughly corresponding to the canopy and potentially rooting area of host individuals. Coccoloba (Polygonaceae), Guapira and Neea (Nyctaginaceae) differed by their most frequent EcMF. Two-thirds of these EcMF preferred one of the host genera, a feature uncommon in boreal forests. Scattered distribution of hosts probably accounts for the low EcMF richness. This study demonstrates that the diversity of plants and their mycorrhizal fungi is not always related and host preference among EcMF can be substantial outside the temperate zone.
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• Soil fungi represent a major component of below-ground biodiversity that determines the succession and recovery of forests after disturbance. However, their successional trajectories and driving ...mechanisms following wildfire remain unclear.
• We examined fungal biomass, richness, composition and enzymes across three soil horizons (Oe, A1 and A2) along a near-complete fire chronosequence (1, 2, 8, 14, 30, 49 and c. 260 yr) in cold-temperate forests of the Great Khingan Mountains, China. The importance of soil properties, spatial distance and tree composition were also tested.
• Ectomycorrhizal fungal richness and β-glucosidase activity were strongly reduced by burning and significantly increased with ‘time since fire’ in the Oe horizon but not in the mineral horizons. Time since fire and soil C : N ratio were the primary drivers of fungal composition in the Oe and A1/A2 horizons, respectively. Ectomycorrhizal fungal composition was remarkably sensitive to fire history in the Oe horizon, while saprotroph community was strongly affected by time since fire in the deeper soil horizon and this effect emerged 18 years after fire in the A2 horizon.
• Our study demonstrates pronounced horizon-dependent successional trajectories following wildfire and indicates interactive effects of time since fire, soil stoichiometry and spatial distance in the reassembly of below-ground fungal communities in a cold and fire-prone region.
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The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology ...studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.
Soil microbiome has a pivotal role in ecosystem functioning, yet little is known about its build-up from local to regional scales. In a multi-year regional-scale survey involving 1251 plots and ...long-read third-generation sequencing, we found that soil pH has the strongest effect on the diversity of fungi and its multiple taxonomic and functional groups. The pH effects were typically unimodal, usually both direct and indirect through tree species, soil nutrients or mold abundance. Individual tree species, particularly
Pinus sylvestris
,
Picea abies
, and
Populus x wettsteinii
, and overall ectomycorrhizal plant proportion had relatively stronger effects on the diversity of biotrophic fungi than saprotrophic fungi. We found strong temporal sampling and investigator biases for the abundance of molds, but generally all spatial, temporal and microclimatic effects were weak. Richness of fungi and several functional groups was highest in woodlands and around ruins of buildings but lowest in bogs, with marked group-specific trends. In contrast to our expectations, diversity of soil fungi tended to be higher in forest island habitats potentially due to the edge effect, but fungal richness declined with island distance and in response to forest fragmentation. Virgin forests supported somewhat higher fungal diversity than old non-pristine forests, but there were no differences in richness between natural and anthropogenic habitats such as parks and coppiced gardens. Diversity of most fungal groups suffered from management of seminatural woodlands and parks and thinning of forests, but especially for forests the results depended on fungal group and time since partial harvesting. We conclude that the positive effects of tree diversity on overall fungal richness represent a combined niche effect of soil properties and intimate associations.
Recent studies have detected strong phylogenetic signals in tree-fungus associations for diseased leaves and mycorrhizal symbioses. However, the extent of plant phylogenetic constraints on the ...free-living soil mycobiome remains unknown, especially at broad geographic scales. Here, 343 soil samples were collected adjacent to individual tree trunks, representing 58 woody plant species located in five mountain forests of eastern China. Integrating plant species identity and phylogenetic information, we aimed to unravel the relative contributions of phylogenetic relationships among tree species, abiotic environmental filtering, and geographic isolation to the geographic distribution of soil mycobiome. We found that the community dissimilarities of total fungi and each dominant guild (viz. saprotrophs, plant pathogens, and ectomycorrhizal fungi) significantly increased with increasing plant phylogenetic distance. Plant phylogenetic eigenvectors explained 11.4% of the variation in community composition, whereas environmental and spatial factors explained 24.1% and 7.2% of the variation, respectively. The communities of ectomycorrhizal fungi and plant pathogens were relatively more strongly affected by plant phylogeny than those of saprotrophs (13.7% and 10.4% vs. 8.5%). Overall, our results demonstrate how plant phylogeny, environment, and geographic space contribute to forest soil fungal distributions and suggest that the influence of plant phylogeny on fungal association may differ by guilds.
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Tree species identity is one of the key factors driving ectomycorrhizal (EcM) fungal richness and community composition in boreal and temperate forest ecosystems, but little is known about the ...influence of tree species combinations and their neighborhood effects on EcM communities. To advance our understanding of host plant effects on EcM fungi, the roots of silver birch, Scots pine, and Norway spruce were analyzed using high-throughput sequencing across mature boreal forest exploratory plots of monocultures and two- and three-species mixtures in Finland. Our analyses revealed that tree species identity was an important determinant of EcM fungal community composition, but tree species richness had no significant influence on EcM fungal richness and community composition. We found that EcM fungal community composition associated with spruce depends on neighboring tree species. Our study suggests that at a regional-scale tree species identity is the primary factor determining community composition of root-associated EcM fungi alongside with tree species composition effects on EcM fungal community of spruce in mixed stands.
Global species richness patterns of soil micro‐organisms remain poorly understood compared to macro‐organisms. We use a global analysis to disentangle the global determinants of diversity and ...community composition for ectomycorrhizal (EcM) fungi—microbial symbionts that play key roles in plant nutrition in most temperate and many tropical forest ecosystems. Host plant family has the strongest effect on the phylogenetic community composition of fungi, whereas temperature and precipitation mostly affect EcM fungal richness that peaks in the temperate and boreal forest biomes, contrasting with latitudinal patterns of macro‐organisms. Tropical ecosystems experience rapid turnover of organic material and have weak soil stratification, suggesting that poor habitat conditions may contribute to the relatively low richness of EcM fungi, and perhaps other soil biota, in most tropical ecosystems. For EcM fungi, greater evolutionary age and larger total area of EcM host vegetation may also contribute to the higher diversity in temperate ecosystems. Our results provide useful biogeographic and ecological hypotheses for explaining the distribution of fungi that remain to be tested by involving next‐generation sequencing techniques and relevant soil metadata.
See also the Perspective by Kennedy et al
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Ectomycorrhizal (ECM) symbiosis is a widespread plant nutrition strategy in Australia, especially in semiarid regions. This study aims to determine the diversity, community structure and host ...preference of ECM fungi in a Tasmanian wet sclero-phyll forest. Ectomycorrhizal fungi were identified based on anatomotyping and rDNA internal transcribed spacer (ITS)-large subunit (LSU) sequence analysis using taxon-specific primers. Host tree roots were identified based on root morphology and length differences of the chloroplast trnL region. A total of 123 species of ECM fungi were recovered from root tips of Eucalyptus regnans (Myrtaceae), Pomaderris apetala (Rhamnaceae) and Nothofagus cunninghamii (Nothofagaceae). The frequency of two thirds of the most common ECM fungi from several lineages was significantly influenced by host species. The lineages of Cortinarius, Tomentella-Thelephora, Russula-Lactarius, Clavulina, Descolea and Laccaria prevailed in the total community and their species richness and relative abundance did not differ by host species. This study demonstrates that strongly host-preferring, though not directly specific, ECM fungi may dominate the below-ground community. Apart from the richness of Descolea, Tulasnella and Helotiales and the lack of Suillus-Rhizopogon and Amphinema-Tylospora, the ECM fungal diversity and phylogenetic community structure is similar to that in the Holarctic realm.
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