The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference dataset, and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g., Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term “species hypothesis” (SH) for the taxa discovered in clustering on different similarity tresholds (97-99%). An automatically or manually designated sequence is chosen to represent each such species hypothesis. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, e.g., local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new web-based sequence management system in UNITE.This article is protected by copyright. All rights reserved.
... Sequencing was performed at Macrogen Europe BV (Amsterdam, The Netherlands), using the available Standard-Seq service. The sequences along with their metadata were uploaded in PlutoF, a data management and publishing platform , and made available via the UNITE database . The UNITE species hypotheses (SH) served as the basis for species identification by choosing an appropriate distance threshold value  in each case ( Table 2). ...
Immature stages of insects are vulnerable to various antagonists, including pathogens. While the abiotic factors affecting pathogen prevalence in insect populations are reasonably well documented, much less is known about relevant ecological interactions. We studied the probability of the larvae of three lepidopteran species to die from fungal infection as a function of insect species and food plants in central Argentina. Local free-growing food plants were used to feed the lepidopteran larvae. The prevalence of entomopathogenic fungi remained low (about 5%), which is a value well consistent with observations on similar systems in other regions. Eight fungal species recorded, primarily belonging to Fusarium and Aspergillus, add evidence to the reconsideration of the nutritional modes in these genera in distinguishing the role of some species (complexes) to cause insect infections. Food plant species were found to have a substantial effect on the prevalence of entomopathogenic fungi. This was especially clear for the most abundant fungal species, a representative of the Fusarium fujikuroi complex. Feeding on a particular plant taxon can thus have a specific fitness cost. Compared to the data collected from Northern Europe, the Argentinian assemblages from the families Aspergillaceae and Nectriaceae overlapped at the genus level but did not share species. It remains to be confirmed if this level of divergence in the composition of assemblages of entomopathogenic fungi among distant regions represents a global pattern.
... The OTUs obtained from the ITS gene were aligned on the UNITE database (version7. 2 https://unite.ut.ee/) and the lowest similarity was set to 0.8 (Koljalg et al., 2014). In order to analyze the microbial communities at the same sequencing depth, the lowest sequencing number was randomly selected per sample of which 24,477 sequences were selected for bacterial 16S rRNA gene and 27,192 sequences for fungal ITS gene. ...
The excessive application of phosphorus (P) fertilizer is becoming a major agricultural problem, which reduces the utilization rate of the P fertilizer and degrades soil quality. The following five P fertilizer treatments were investigated to know how they affect soil properties, enzyme activity, bacterial and fungal community structure. 1) no P fertilizer (P0); 2) farmers’ traditional P fertilization scheme (FP); 3) 30% reduction in P fertilizer application (P1, microbial blended fertilizer as base fertilizer); 4) 30% reduction in P fertilizer application (P2, diammonium phosphate as starting fertilizer); 5) 30% reduction in P fertilizer application (P3, microbial inoculum seed dressing). The P fertilizer reduction combined with microbial fertilizer significantly increased soil organic matter (SOM), total phosphorus (TP), available phosphorus (AP) available potassium (AK) contents, and acid phosphatase activity (ACP), however, soil urease activity was significantly reduced. Moreover, the P fertilizer reduction combined with microbial fertilizer significantly increased the relative abundance of a potential beneficial genus (i.e., Bacillus, Pseudomonas, Penicillium, and Acremonium) and potentially pathogenic genus (i.e., Fusarium, Gibberella, and Drechslera). The structural equation model (SEM) revealed that different P fertilizer reduction systems had significant indirect effects on bacterial and fungal community structures. The results suggested that the P fertilizer reduction combined with microbial fertilizer systems regulated the pathogenic and beneficial genus which created a microbial community that is favorable for maize growth. Moreover, the findings highlighted the importance of soil properties in determining the soil bacterial and fungal community structure.
... The taxonomy of the 16S rRNA gene sequence was analyzed by the ribosomal database project (RDP) Classifier algorithm against the Silva (SSU123) 16S rRNA database with 70% confidence threshold (Cole et al. 2009;Gurevich et al. 2013;Klindworth et al. 2013). The taxonomy of each ITS gene sequence was analyzed by Unite (Release 6.0) (Koljalg et al. 2013). Alpha rarefaction was performed in QIIME (version 1.7.0) using Chao1 to estimate species abundance (Caporaso et al. 2010). ...
Higher alcohols (HAs) are abundant compounds that provide important flavors in Huangjiu, but they also cause hangover. Previous studies have shown the production of HAs to be related to yeast, but the correlations between HAs and other microorganisms are rarely reported. In this study, we detected changes in levels of HAs and microbial dynamics during the Huangjiu fermentation process. Relationships were characterized using Pearson’s correlation coefficient. The functional core HA-producing bacteria were selected by bidirectional orthogonal partial least squares (O2PLS). The result showed that 2-methyl-1-propanol, phenethyl alcohol and 3-methyl-1-butanol were the principle HAs present at high levels. Lactococcus and Saccharomyces were predominant at the genus level of bacteria and fungi, respectively. A total of 684 correlations between HAs and microorganisms were established. Five genera were screened as functional core HA-producing bacteria. Our findings might provide some new inspiration for controlling the content of HAs, enhancing international prestige and market expansion of Huangjiu.
... The raw gene sequencing reads were quality filtered, demultiplexed by Trimmomatic, and merged by Fast Length Adjustment of Short reads (FLASH, v1.2.11) in accordance with the following criteria (Bao, 2000). Operational taxonomic units (OTUs) with 97% similarity cutoff (Kõljalg et al., 2013) were clustered using UPARSE (version 7.1) 1 , and chimeric sequences were identified and removed. We assessed the taxonomy of each representative OTU sequence using RDP Classifier 2 against the 16S rRNA database and ITS database (e.g., Silva SSU128) with a confidence threshold of 0.7 (Magoc and Salzbera, 2011;Yu et al., 2019). ...
Soil microbes play a crucial role in a forest ecosystem. However, whether the distribution of bacteria and fungi in different forest succession stages is random or following ecological specialization remains to be further studied. In the present study, we characterized soil bacterial and fungal communities to determine their distribution preference, with different succession communities in a temperate mountain forest. The Kruskal–Wallis method was used to analyze structural differences between bacterial and fungal communities in different succession processes. The specificity of soil microbial distribution in a secondary forest was studied by network analysis. The torus-translation test was used to analyze the species distribution preference of soil microbes in different succession stages. Results showed that the species composition of soil bacteria and fungi differed significantly in different succession processes. The modularity index of fungi (0.227) was higher than that of bacteria (0.080). Fungi (54.47%) had specific preferences than bacteria (49.95%) with regard to forests in different succession stages. Our work suggests that the distribution pattern of most soil microbes in a temperate mountain forest was not random but specialized in temperate mountain forests. Different microbes showed different distribution preferences. Fungi were more sensitive than bacteria during secondary succession in a temperate mountain forest. In addition, microbe–environment relations varied during secondary succession. Our results provided new insight into the mechanism through which complex soil microbial communities responded to changes in forest community succession.
The species of Hebeloma have been little studied in Mexico, but have received attention as edibles and in trials to enhance production of edible fungi and tree growth through inoculation of seedlings with ectomycorrhizal fungi. Here we describe three new species of Hebeloma that are currently known only from Mexico. These species belong to separate sections of the genus: H. ambustiterranum is a member of H. sect. Hebeloma, H. cohaerens belongs to H. sect. Theobromina, while H. magnicystidiatum belongs to H. sect. Denudata. All three species were collected from subtropical pine-oak woodland; all records of H. cohaerens came from altitudes above 2500 m. Hebeloma ambustiterranum is commonly sold in the local markets of Tlaxcala as a prized edible mushroom. An additional nine species are reported from Mexico, of which eight are new records for the country: H. aanenii , H. eburneum , H. excedens , H. ingratum , H. neurophyllum , H. sordidulum , H. subaustrale and H. velutipes . First modern descriptions of H. neurophyllum and H. subaustrale , originally described from the USA, are given here.
Soil erosion and deposition are general ecological processes that have been widely described in terms of their effects on the physical and chemical properties of soil. However, their effects on soil microbes remain unclear, especially how microbial communities respond to erosion–deposition in soils with different organic carbon levels. A long-term field experiment was conducted to examine the effects of erosion and deposition on soil microbial communities across full slopes with different organic carbon levels on the Loess Plateau of China. The results showed that erosion reduced soil bacterial alpha diversity, weakened bacterial network complexity while deposition increased bacterial alpha diversity, and enhanced the complexity of the bacterial network. However, both erosion and deposition caused a decrease in fungal alpha diversity and network complexity. There was a weak reverse cooperative covariation relationship between bacterial and fungal alpha diversity. There was a higher bacterial and fungal diversity at the eroded and depositional sites with high soil organic carbon (SOC) level than low and medium SOC levels. An increase in the SOC level effectively strengthened the network complexity of bacteria and fungi at the eroded and depositional sites.. Erosion-deposition and SOC levels significantly increased variation in bacterial community structure. In contrast, the fungal community structure only differed at the eroded and depositional sites at high SOC levels. The key factors driving variation in bacterial community structure in soil properties were not significantly affected by SOC levels. Conversely, key factors resulting in differences in fungal community structure were regulated by the SOC level. Our results demonstrate that erosion–deposition reconstruct the bacterial community and weakens the fungal community, organic carbon regulate soil microbial communities and functions by controlling earth surface processes induced by erosion–deposition.
Moso bamboo (Phyllostachys pubescens) has an extremely fast growth rate and major carbon sequestration potential. However, little information is available on the dynamics of soil C accumulation and fungi communities related to different management practices. Here, we investigated changes in the soil organic carbon (SOC) fractions and fungal communities of a Moso bamboo plantation under three different management practices (M0: undisturbed; M1: extensively managed; and M2: intensively managed). Compared with M0, SOC levels were reduced by 41.2% and 71.5% in M1 and M2, respectively; furthermore, four SOC fractions (C1: very labile; C2: labile; C3: less labile; and C4: nonlabile) and the carbon management index (CMI) were also significantly reduced by plantation management. These practices further altered fungal communities, for example, by increasing Basidiomycota and Mortierellomycota, and by decreasing Ascomycota and Rozellomycota. Pyrenochaeta, Mortierella, Saitozyma, and Cladophialophora were identified as keystone taxa. Soil fungal communities were significantly related to the pH, NH4-N, AP, C3, and the C4 fractions of SOC. Random forest modeling identified soil C3 and Mortierella as the most important predictors of the CMI. Our results suggest that reducing human interference would be beneficial for fungal community improvement and C sequestration in Moso bamboo plantations.
Cover crops can promote the subsequent plant growth and improve soil potassium (K) fertility. However, whether and how wheat cover crop benefits cucumber growth and yield under different K regimes and their functional roles are still unclear. In this study, a two-year greenhouse experiment from spring 2017 to autumn 2018 was conducted to evaluate the effects of wheat cover crop on cucumber plant growth, nutrition and yield. Moreover, a litterbag experiment was carried out in the greenhouse in spring 2018 to investigate the nutrient dynamics during decomposition of wheat shoot and root residues under the two K regimes. Soil bacterial and fungal communities during residues decomposition were analyzed by high-throughput amplicon sequencing, and the abundances of total bacterial, fungal, Bacillus and Pseudomonas spp. communities were also estimated by quantitative PCR. The responses of cucumber growth to changes in the soil microbial communities induced by wheat cover crop were assessed by plant-soil feedback experiment. Wheat cover crop increased cucumber yield except for in spring 2017 and plant growth and K concentration at 70 d in spring 2018, and reduced K application did not weaken the beneficial effects of wheat on cucumber growth and yield. Decomposition rate and nutrient release of wheat shoot residue differed from root residue, but no differences in shoot or root residue decomposition rate and nutrient release between the two K regimes. Wheat shoot and root residues differently changed the abundances, compositions and diversities of soil bacterial and fungal communities. Wheat shoot residue increased total bacteria, Bacillus and Pseudomonas spp. community abundances compared with root residue irrespective of K regimes, and Bacillus spp. community abundance was higher in shoot residue with reduced K application than that with normal K application from 220 to 240 d. Wheat shoot residue decreased the Shannon and inverse Simpson diversities of soil bacterial and fungal communities compared with root residue from 200 to 240 d. Moreover, there was significant difference in these diversities of soil fungal community of root residue between the two K regimes except for 240 d. In addition, wheat cover crop caused more stable co-occurrence network with more positive and negative total links and wheat shoot residue had higher these links than root residue, while reduced K application decreased these links of both shoot and root residues. Feedback effects of changes in soil microbial communities induced by wheat cover crop on cucumber growth were positive, and such effect was stronger in shoot residue than in root residue irrespective of K regimes. Overall, wheat cover crop can alter soil microbial communities and enhance cucumber productivity through positive plant-soil feedbacks mediated by soil biota, and reduced K application did not weaken such beneficial effects.
Elucidating the diversity patterns and drivers of soil microbes at high altitudes contributes to understanding the role microbes play in ecosystem services, but little is known about the soil microbial diversity, richness and abundance patterns across elevations on the Tibetan Plateau. This study was conducted to explore the shifts of forest soil bacterial and fungal community diversities and the regulating factors along an elevation gradient (2980–4050 m a.s.l.) in the Southern Himalayas of China. Illumina sequencing of 16S rRNA and ITS1, and quantitative real-time PCR were used to determine soil bacterial and fungal communities, coupled with plant diversity survey and edaphic properties analysis. The results revealed that plant alpha-diversity reached the highest level at an elevation of 3255 m and subsequently decreased with higher elevations; while soil bacterial alpha-diversity and fungal richness reached the lowest at 3590 m and 3772 m respectively, then increased with higher elevations; soil microbial abundance decreased with increasing elevation. The soil pH was the main driver of the elevation-related soil bacterial richness, diversity, and abundance. Soil nutrients contributed most to the fungal richness, diversity, and abundance. The total phosphorus content was the optimal predictor of fungal richness and abundance, while nitrate levels determined the fungal diversity. The community structures of bacteria and fungi differed significantly among elevations (Pbacteria = 0.001, Pfungi = 0.001). The elevation and edaphic properties (including the contents of soil organic matter and pH) controlled the elevation patterns of soil bacterial community structures and explained 56.1 % of the total variation. In contrast, edaphic properties (including SOC, TP and pH) primarily shaped the elevation patterns of soil fungal community structures and explained 38.7 % of the total variation. This study provides comprehensive insights into soil microbial geography associated with the biogeochemical cycling on the Tibetan Plateau.
Fungi have unique ecosystem functions, such as organic matter decomposition, parasitism, and symbiosis with other organisms in terrestrial and aquatic ecosystems. Their taxonomic and functional diversities are essential factors for predicting ecosystem functions and their responses to environmental changes. With the widespread use of high‐throughput sequencing (HTS) in recent years, the detection of fungal DNA sequences in various regions and on different environmental substrates has advanced. HTS‐obtained DNA sequences can be compared with those in databases to identify the taxa of organisms from which they are derived. Therefore, a global DNA database containing taxonomic information has been developed. However, functional data on the distribution and function of individual taxa remain scarce. In this study, the ecological information of each fungal family was compiled from review papers and published books. Specifically, the following information was collected: reported distribution (11 categories including information on the presence of fungi in Japan) and function (38 categories related to ecological functional data, such as guilds and habitats) of 553 families included in the literature. These data will provide information on the ecology of specific fungi detected in the field and help estimate the functional group composition and diversity of fungi from their DNA assemblage data. The detailed Metadata for this abstract published in the Data Article section of the journal is available in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2022-02.1/jalter-en. Although, global DNA database of fungi containing taxonomic information is being developed, functional data on the distribution and function of individual taxa remain scarce. Here, we compiled information on the reported distribution (11 categories including information on presence in Japan extracted from Japanese literature) and function (38 categories related to ecological functional data, such as guilds and habitats) of a total of 553 families included in published literature. These data will not only provide information on the ecology of specific fungi detected in the field, but also help estimate the functional group composition and diversity of the fungi from their DNA assemblage data.
Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
Fungal taxonomists pursue a seemingly impossible quest: to discover and give names to all of the world's mushrooms, moulds and yeasts. Taxonomists have a reputation for being traditionalists, but as we outline here, the community has recently embraced the modernization of its nomenclatural rules by discarding the requirement for Latin descriptions, endorsing electronic publication and ending the dual system of nomenclature, which used different names for the sexual and asexual phases of pleomorphic species. The next, and more difficult, step will be to develop community standards for sequence-based classification.
Fungi from the Ceratobasidiaceae family have important ecological roles as pathogens, saprotrophs, non-mycorrhizal endophytes, orchid mycorrhizal and ectomycorrhizal symbionts, but little is known about the distribution and evolution of these nutritional modes. All public ITS sequences of Ceratobasidiaceae were downloaded from databases, annotated with ecological and taxonomic metadata, and tested for the non-random phylogenetic distribution of nutritional modes. Phylogenetic analysis revealed six main clades within Ceratobasidiaceae and a poor correlation between molecular phylogeny and morphological–cytological characters traditionally used for taxonomy. Sequences derived from soil (representing putative saprotrophs) and orchid mycorrhiza clustered together, but remained distinct from pathogens. All nutritional modes were phylogenetically conserved in the Ceratobasidiaceae based on at least one index. Our analyses suggest that in general, autotrophic orchids form root symbiosis with available Ceratobasidiaceae isolates in soil. Ectomycorrhiza-forming capability has evolved twice within the Ceratobasidiaceae and it had a strong influence on the evolution of mycoheterotrophy and host specificity in certain orchid taxa.
This report summarizes a meeting held in Boulder, CO USA (19-20 October 2012) on fungal community analyses using ultra-high-throughput sequencing of the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA (rRNA) genes. The meeting was organized as a two-day workshop, with the primary goal of supporting collaboration among researchers for improving fungal ITS sequence resources and developing recommendations for standard ITS primers for the research community.
Phylogenetic relationships of the edible shiitake mushroom (Lentinula, Tricholomataceae) were studied using DNA sequences from the internal transcribed spacers (ITS) of nuclear ribosomal DNA. The ingroup consisted of seven isolates of L. edodes from Japan and Thailand, nine isolates of L. lateritia from Borneo, Papua New Guinea, and Tasmania, and five isolates of L. novaezelandieae from New Zealand. These species designations are based on morphological species concepts in Lentinula. However, because Lentinula isolates from throughout Asia-Australasia are mating compatible, some authors treat all of these as belonging to L. edodes. The outgroup included two isolates of L. boryana from Mexico. Parsimony, distance, and maximum likelihood analyses were performed, with various combinations of taxa, characters, and character codings, and bootstrap and decay index measures of robustness. Alternate topologies were evaluated in terms of tree lengths, maximum likelihood ratios, and Templeton's nonparametric test of parsimony. Results suggest that there are four independent lineages of shiitake in Asia-Australasia, which provides partial support for the morphologically based species concepts. Lentinula novaezelandieae and L. edodes sensu stricto were supported as monophyletic, but L. lateritia appears to be paraphyletic. A corollary of this is that the morphology of L. lateritia should be plesiomorphic for shiitake, which seems plausible based on outgroup comparison. In general, there is a strong correlation between the geographic origins of the isolates and the lineages supported. Biogeographic interpretation of ITS trees suggests that the ancestral area for shiitake in Asia-Australasia is in the South Pacific, which was the most phylogenetically diverse area examined. Phylogenetic analyses including previously published ITS2 sequences of three shiitake isolates of unknown origin placed the unknown isolates in a group of L. edodes sensu stricto isolates from Japan and Thailand, which suggests that the unknown isolates are from northeast or continental Asia. ITS-based cladograms have points of agreement as well as disagreement with previously published mitochondrial DNA-based dendrograms from a subset of the isolates used in this study. Discrepancies between the ITS and mtDNA trees could mean that the nuclear ITS and the mtDNA have different evolutionary histories. However, comparison of mtDNA and ITS data are complicated by the fact that the mtDNA data are based on pairwise distances, whereas the ITS data are discrete. Practical implications of the results for shiitake breeding and conservation are discussed.
Fungal taxonomy seeks to discover, describe, and classify all species of Fungi and provide tools for their identification. About 100,000 fungal species have been described so far, but it has been estimated that there may be from 1.5 to 5.1million extant fungal species. Over the last decade, about 1200 new species of Fungi have been described in each year. At that rate, it may take up to 4000y to describe all species of Fungi using current specimen-based approaches. At the same time, the number of molecular operational taxonomic units (MOTUs) discovered in ecological surveys has been increasing dramatically. We analyzed ribosomal RNA internal transcribed spacer (ITS) sequences in the GenBank nucleotide database and classified them as “environmental” or “specimen-based”. We obtained 91,225 sequences, of which 30,217 (33%) were of environmental origin. Clustering at an average 93% identity in extracted ITS1 and ITS2 sequences yielded 16,969 clusters, including 6230 (37%) clusters with only environmental sequences, and 2223 (13%) clusters with both environmental and specimen-based sequences. In 2008 and 2009, the number of purely environmental clusters deposited in GenBank exceeded the number of species described based on specimens, and this does not include the huge number of unnamed MOTUs discovered in pyrosequencing studies. To enable communication about fungal diversity, there is a pressing need to develop classification systems based on environmental sequences. Assigning Latin binomials to MOTUs would promote their integration with specimen-based taxonomic databases, whereas the use of numerical codes for MOTUs would perpetuate a disconnect with the taxonomic literature. MOTUs could be formally named under the existing International Code of Botanical Nomenclature if the concept of a nomenclatural type was expanded to include environmental samples or illustrations of sequence chromatograms (or alignments). Alternatively, a “candidate species” category could be created for Fungi, based on the candidatus taxon status employed by microbiologists.