Morphological and molecular characterisation of Pulvinula constellatio ectomycorrhizae

Warming and rainfall reduction alter soil microbial diversity and co-occurrence networks and enhance pathogenic fungi in dryland soils

In this 9-year manipulative field experiment, we examined the impacts of experimental warming (2 °C, W), rainfall reduction (30 % decrease in annual rainfall, RR), and their combination (W + RR) on soil microbial communities and native vegetation in a semi-arid shrubland in south-eastern Spain. Warming had strong negative effects on plant performance across five coexisting native shrub species, consistently reducing their aboveground biomass growth and long-term survival. The impacts of rainfall reduction on plant growth and survival were species-specific and more variable. Warming strongly altered the soil microbial community alpha-diversity and changed the co-occurrence network structure. The relative abundance of symbiotic arbuscular mycorrhizal fungi (AMF) increased under W and W + RR, which could help buffer the direct negative impacts of climate change on their host plants nutrition and enhance their resistance to heat and drought stress. Indicator microbial taxa analyses evidenced that the marked sequence abundance of many plant pathogenic fungi, such as Phaeoacremonium, Cyberlindnera, Acremonium, Occultifur, Neodevriesia and Stagonosporopsis, increased significantly in the W and W + RR treatments. Moreover, the relative abundance of fungal animal pathogens and mycoparasites in soil also increased significantly under climate warming. Our findings indicate that warmer and drier conditions sustained over several years can alter the soil microbial community structure, composition, and network topology. The projected warmer and drier climate favours pathogenic fungi, which could offset the benefits of increased AMF abundance under warming and further aggravate the severe detrimental impacts of increased abiotic stress on native vegetation performance and ecosystem services in drylands.

Systemic effects of Tuber melanosporum inoculation in two Corylus avellana genotypes

Roots of the European hazelnut (Corylus avellana L.), i.e., one of the most economically important nut species, form symbiosis with ectomycorrhizal (ECM) fungi, including truffles. Although physical interactions only occur in roots, the presence of mycorrhizal fungi can lead to metabolic changes at a systemic level, i.e., in leaves. However, how root colonization by ECM fungi modifies these processes in the host plant has so far not been widely studied. This work aimed to investigate the response in two C. avellana genotypes, focusing on leaves from plants inoculated with the black truffle Tuber melanosporum Vittad. Transcriptomic profiles of leaves of colonized plants were compared with those of non-colonized plants, as well as sugar and polyphenolic content. Results suggested that T. melanosporum has the potential to support plants in stressed conditions, leading to the systemic regulation of several genes involved in signaling and defense responses. Although further confirmation is needed, our results open new perspectives for future research aimed to highlight novel aspects in ECM symbiosis.

An overview of the genus Coprotus (Pezizales, Ascomycota) with notes on the type species and description of C. epithecioides sp. nov

In a mycological research performed in the Sjeverni Velebit National Park, Croatia, a new species of Coprotus was discovered, described here as C.epithecioides. Along with the microscopic examination, phylogenetic analysis of the type material, based on ITS and LSU sequences, was performed in order to evaluate its relationship with the type species, C.sexdecimsporus. The type species was sequenced in this study for the first time, providing ITS and LSU sequences from two separate collections which displayed differences in macroscopic characters and content of paraphyses. An extended description of C.sexdecimsporus based on Croatian material is also provided. A worldwide identification key to the species assigned to the genus Coprotus is presented, along with a species overview, containing a data matrix. The phylogenetic position of Coprotus in the Boubovia-Coprotus clade within Pyronemataceae s.l. is discussed. Coprotussexdecimsporus is also reported here as new to the Croatian mycobiota.

A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits

Pyronemataceae is the largest and most heterogeneous family of Pezizomycetes. It is morphologically and ecologically highly diverse, comprising saprobic, ectomycorrhizal, bryosymbiotic and parasitic species, occurring in a broad range of habitats (on soil, burnt ground, debris, wood, dung and inside living bryophytes, plants and lichens). To assess the monophyly of Pyronemataceae and provide a phylogenetic hypothesis of the group, we compiled a four-gene dataset including one nuclear ribosomal and three protein-coding genes for 132 distinct Pezizomycetes species (4437 nucleotides with all markers available for 80% of the total 142 included taxa). This is the most comprehensive molecular phylogeny of Pyronemataceae, and Pezizomycetes, to date. Three hundred ninety-four new sequences were generated during this project, with the following numbers for each gene: RPB1 (124), RPB2 (99), EF-1α (120) and LSU rDNA (51). The dataset includes 93 unique species from 40 genera of Pyronemataceae, and 34 species from 25 genera representing an additional 12 families of the class. Parsimony, maximum likelihood and Bayesian analyses suggest that Pyronemataceae is paraphyletic due to the nesting of both Ascodesmidaceae and Glaziellaceae within the family. Four lineages with taxa currently classified in the family, the Boubovia, Geopyxis, Pseudombrophila and Pulvinula lineages, form a monophyletic group with Ascodesmidaceae and Glaziellaceae. We advocate the exclusion of these four lineages in order to recognize a monophyletic Pyronemataceae. The genus Coprotus (Thelebolales, Leotiomycetes) is shown to belong to Pezizomycetes, forming a strongly supported monophyletic group with Boubovia. Ten strongly supported lineages are identified within Pyronemataceae s. str. Of these, the Pyropyxis and Otidea lineages are identified as successive sister lineages to the rest of Pyronemataceae s. str. The highly reduced (gymnohymenial) Monascella is shown to belong to Pezizomycetes and is for the first time suggested to be closely related to the cleistothecial Warcupia, as a sister group to the primarily apothecial Otidea. None of the lineages of pyronemataceous taxa identified here correspond to previous families or subfamily classifications. Ancestral character state reconstructions (ASR) using a Bayesian approach support that the ancestors of Pezizomycetes and Pyronemataceae were soil inhabiting and saprobic. Ectomycorrhizae have arisen within both lineages A, B and C of Pezizomycetes and are suggested to have evolved independently seven to eight times within Pyronemataceae s. l., whereas an obligate bryosymbiotic lifestyle has arisen only twice. No reversals to a free-living, saprobic lifestyle have happened from symbiotic or parasitic Pyronemataceae. Specializations to various substrates (e.g. burnt ground and dung) are suggested to have occurred several times in mainly saprobic lineages. Although carotenoids in the apothecia are shown to have arisen at least four times in Pezizomycetes, the ancestor of Pyronemataceae s. str., excluding the Pyropyxis and Otidea lineages, most likely produced carotenoids, which were then subsequently lost in some clades (- and possibly gained again). Excipular hairs were found with a high probability to be absent from apothecia in the deepest nodes of Pezizomycetes and in the ancestor of Pyronemataceae s. str. True hairs are restricted to the core group of Pyronemataceae s. str., but are also found in Lasiobolus (Ascodesmidaceae), the Pseudombrophila lineage and the clade of Chorioactidaceae, Sarcoscyphaceae and Sarcosomataceae. The number of gains and losses of true hairs within Pyronemataceae s. str., however, remains uncertain. The ASR of ascospore guttulation under binary coding (present or absent) indicates that this character is fast evolving and prone to shifts.

Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages

The ectomycorrhizal (EcM) symbiosis involves a large number of plant and fungal taxa worldwide. During studies on EcM diversity, numerous misidentifications, and contradictory reports on EcM status have been published. This review aims to: (1) critically assess the current knowledge of the fungi involved in the EcM by integrating data from axenic synthesis trials, anatomical, molecular, and isotope studies; (2) group these taxa into monophyletic lineages based on molecular sequence data and published phylogenies; (3) investigate the trophic status of sister taxa to EcM lineages; (4) highlight other potentially EcM taxa that lack both information on EcM status and DNA sequence data; (5) recover the main distribution patterns of the EcM fungal lineages in the world. Based on critically examining original reports, EcM lifestyle is proven in 162 fungal genera that are supplemented by two genera based on isotopic evidence and 52 genera based on phylogenetic data. Additionally, 33 genera are highlighted as potentially EcM based on habitat, although their EcM records and DNA sequence data are lacking. Molecular phylogenetic and identification studies suggest that EcM symbiosis has arisen independently and persisted at least 66 times in fungi, in the Basidiomycota, Ascomycota, and Zygomycota. The orders Pezizales, Agaricales, Helotiales, Boletales, and Cantharellales include the largest number of EcM fungal lineages. Regular updates of the EcM lineages and genera therein can be found at the UNITE homepage http://unite.ut.ee/EcM_lineages . The vast majority of EcM fungi evolved from humus and wood saprotrophic ancestors without any obvious reversals. Herbarium records from 11 major biogeographic regions revealed three main patterns in distribution of EcM lineages: (1) Austral; (2) Panglobal; (3) Holarctic (with or without some reports from the Austral or tropical realms). The holarctic regions host the largest number of EcM lineages; none are restricted to a tropical distribution with Dipterocarpaceae and Caesalpiniaceae hosts. We caution that EcM-dominated habitats and hosts in South America, Southeast Asia, Africa, and Australia remain undersampled relative to the north temperate regions. In conclusion, EcM fungi are phylogenetically highly diverse, and molecular surveys particularly in tropical and south temperate habitats are likely to supplement to the present figures. Due to great risk of contamination, future reports on EcM status of previously unstudied taxa should integrate molecular identification tools with axenic synthesis experiments, detailed morphological descriptions, and/or stable isotope investigations. We believe that the introduced lineage concept facilitates design of biogeographical studies and improves our understanding about phylogenetic structure of EcM fungal communities.

Tuber melanosporum, when dominant, affects fungal dynamics in truffle grounds

The fruiting bodies of the ectomycorrhizal (ECM) fungus Tuber melanosporum are usually collected in an area devoid of vegetation which is defined as a 'burnt area' (brulé in French). Here, the soil fungal populations of inside and outside brulé were compared in order to understand whether the scanty plant cover was related to a change in fungal biodiversity. Both denaturing gradient gel electrophoresis (DGGE) and molecular cloning of the internal transcribed spacer (ITS) marker were employed on soil DNA to obtain profiles from nine truffle grounds and fungal sequences from one selected truffle ground sampled in two years. Denaturant gradient gel electrophoresis profiles from the two areas formed two distinct clusters while molecular cloning allowed 417 fungal sequences to be identified. T. melanosporum was the dominant fungus within the brulé. There were nine new haplotypes, which had never been detected in fruiting bodies. The Basidiomycota ECM fungi decreased within the brulé, indicating a competitive effect of T. melanosporum on the other ECM fungi. Among other factors, the dynamics of fungal populations seems to be correlated to brulé formation.

Otidea subterranea sp. nov.: Otidea goes below ground

Evidence suggests that truffle-like sporocarp forms have evolved many times in the Pezizales, but primarily from epigeous ancestors within ectomycorrhizal clades. There are several ectomycorrhizal clades, however, that contain no known hypogeous species. We collected specimens of an unusual unidentified truffle from mixed oak woodlands in Iowa. Although clearly a member of the Pezizales (Ascomycota), this hypogeous species did not belong to any of the described truffle genera. Based on a combination of ecological, phylogenetic, and morphological evidence we determined that this new truffle is a hypogeous member of the genus Otidea (Pyronemataceae), a lineage with no described truffle species. We describe it here as a new species, Otidea subterranea.

A phylogenetic overview of the family Pyronemataceae (Ascomycota, Pezizales)

Partial sequences of nuLSU rDNA were obtained to investigate the phylogenetic relationships of Pyronemataceae, the largest and least studied family of Pezizales. The dataset includes sequences for 162 species from 51 genera of Pyronemataceae, and 39 species from an additional 13 families of Pezizales. Parsimony, ML, and Bayesian analyses suggest that Pyronemataceae is not monophyletic as it is currently circumscribed. Ascodesmidaceae is nested within Pyronemataceae, and several pyronemataceous taxa are resolved outside the family. Glaziellaceae forms the sister group to Pyronemataceae in ML analyses, but this relationship, as well as those of Pyronemataceae to the other members of the lineage, are not resolved with support. Fourteen clades of pyronemataceous taxa are well supported and/or present in all recovered trees. Several pyronemataceous genera are suggested to be non-monophyletic, including Anthracobia, Cheilymenia, Geopyxis, Humaria, Lasiobolidium, Neottiella, Octospora, Pulvinula, Stephensia, Tricharina, and Trichophaea. Cleistothecial and truffle or truffle-like ascomata forms appear to have evolved independently multiple times within Pyronemataceae. Results of these analyses do not support previous classifications of Pyronemataceae, and suggest that morphological characters traditionally used to segregate the family into subfamilial groups are not phylogenetically informative above the genus level.

Genetic diversity of naturally established ectomycorrhizal fungi on Norway spruce seedlings under nursery conditions

We have assessed ectomycorrhizal fungi colonizing Norway spruce (Picea abies L.) seedlings in nine forest nurseries using restriction fragment length polymorphism (RFLP) and sequencing analyses of the internal transcribed spacers (ITS1-5.8S-ITS2) amplicons. Restriction analysis of the amplified DNA fragments with HinfI, MboI, and TaqI enzymes allowed the definition of 17 RFLP genotypes; five of them could be unambiguously assigned to Thelephora terrestris, Hebeloma longicaudum, H. crustuliniforme, Tricharina ochroleuca, and Cenococcum geophilum species by comparison with the sporocarp RFLP-pattern database. The remaining genotypes have been sequenced and compared with sequences deposited in the GenBank database. The phylogenetic analysis of resulting sequences and their identified matches indicated that isolated genotypes have formed seven clades. The ascomycetes were predominant: we have determined eight species--Wilcoxina mikolae, Phialophora finlandia, Tuber sp., Cenococcum geophilum, Tricharina ochroleuca, Pulvinula constellatio, and two unidentified ascomycetes--whereas the basidiomycetes were less common (four species denoted: Amphinema byssoides, Hebeloma crustuliniforme, H. longicaudum, and Thelephora terrestris). Wilcoxina mikolae and Phialophora finlandia were the most frequent fungi. Analysis of variance revealed that ascomycetes abundance was higher in nurseries that used organic fertilizer.

Molecular and morphological diversity of pezizalean ectomycorrhiza

A growing body of molecular research is discovering a high diversity of pezizalean ectomycorrhiza (EcM), yet most remain unidentified at the genus or species level. This study describes EcM-forming taxa within the Pezizales. EcM-forming Pezizales were revealed by morphotyping and sequencing of EcM root tips from forests in Estonia and Denmark. The taxa on EcM root tips were identified using phylogenetic analyses of large-subunit rDNA sequences derived from sporocarps of 301 pezizalean species, and comparisons with internal transcribed spacer rDNA sequences. Thirty-three species are suggested as EcM symbionts, representing all three major clades of Pezizales, the genera Genea, Geopora, Humaria, Tarzetta, Trichophaea, Wilcoxina, Helvella, Hydnotrya, Tuber, Pachyphloeus, Peziza and Sarcosphaera, and two Pezizaceae anamorphs. EcM of Pezizales species are easily distinguished by their anatomy, particularly thick cell walls and stout hyphae. This study demonstrates that Pezizales species constitute a considerable proportion of the mycobionts in EcM fungal communities in mature boreal deciduous and coniferous forests, in several soil types. Fruit-body sequences and EcM descriptions will facilitate identification of pezizalean EcM in future studies.

A quick and precise technique for identifying ectomycorrhizas by PCR

A rapid procedure was developed to amplify ITS fragments directly from Tuber ectomycorrhizas either synthesized in a greenhouse or collected from the field. The addition of Bovine Serum Albumin (BSA) to the reaction mixtures overcame the presence of reaction inhibitors present in fungal and root cells, and enabled the amplification of the ITS regions directly from ectomycorrhizal tissues. This method is cheaper and less time-consuming than conventional procedures, and reduces the time required from 1-4 h to a few minutes. It is also much more sensitive, allowing the identification of just a small fragment of a mycorrhizal root tip. Because of this it is possible to select only the target fungal tissue and hence minimise the risk of contamination by saprobic or other mycorrhizal species. The method also avoids the use of toxic or hazardous substances. This method could have a wider application in other areas of applied mycology.

A revision of the descriptions of ectomycorrhizas published since 1961

All available publications providing descriptions of ectomycorrhizas (ECM) were reviewed in order to build a database containing details on fungus forming the ECM, host tree, country where the material for description was collected, and habitat of the ECM. Other secondary data were also recorded. In all 1244 descriptions of ECM published since 1961 in 479 papers were reviewed. The number of different ECM morphotypes described was 814. Most ECM described were collected in Europe and North America. Gymnosperms were the most common tree associates, and boreal and temperate forests the most studied ecosystems. Fungal symbionts were mostly Basidiomycota, epigeous, and with mushroom-like morphology. The paper also addresses the gaps in ECM knowledge that mycorrhizologists should address in future studies.

Molecular identification of Tuber magnatum ectomycorrhizae in the field

Tuber ectomycorrhizae in a Tuber magnatum "truffière", located in Central Italy, were studied using molecular methods. Specifically, RFLP-ITS analyses, ITS sequencing and specific probes hybridization were used to identify 335 Tuber-like ectomycorrhizal morphotypes. Molecular identification was possible even when distinct morphological characteristics were lacking. For the first time, T. magnatum ectomycorrhizae and other coexisting Tuber species collected in the field were analysed using molecular tools for unambiguous identification. Although the "truffière" under investigation yields good harvests of T. magnatum fruiting bodies, the percentage of T. magnatum ectomycorrhizae found was very low (less than 4.4% of the 335 root tips analysed), whereas the percentages of Tuber maculatum and Tuber rufum were considerably higher (48.9% and 19.0%, respectively).

Morphological and molecular characterization of mycelia of some Tuber species in pure culture

•  Pure cultures of Tuber maculatum , Tuber melanosporum , Tuber aestivum , Tuber macrosporum , Tuber rufum and Tuber brumale were isolated and characterized by morphological and molecular methods. •  The Tuber mycelia were isolated from fruit bodies and molecular identification was performed using specific primers, restriction fragment length polymorphism and/or sequence analyses of the ITS region. •  The species grew between 1.1 mm wk ^-1 and 14 mm wk ^-1 on the selected medium. The mycelium of different Tuber species showed several common morphological features such as hyphal anastomoses, vesicle formation and hyphal aggregation. Differences were found in the frequency of these morphological features and in the hyphal pattern. The isolated mycelia also showed differences in the hyphal branch angle, septal distance, hyphal diameter and rate of growth of the hyphae. •  This result opens the possibility of using pure mycelial cultures of Tuber spp. for experimental purposes and for the commercial production of infected truffle plants.