Selection of a set of specific primers for the identification of Tuber rufum: a truffle species with high genetic variability

Identification and full-length genome characterization of a novel mitovirus hosted by the truffle species Tuber rufum

Studying the diversity of viruses found in uncultivated fungi, including those forming mycorrhizal relationships, is essential. It's equally important to explore viral communities in fungi that cause plant diseases or are economically significant. This dual approach helps us grasp the full scope of mycovirus diversity and evolution. Mycorrhizal fungi, in particular, host a wide range of viruses, shedding light on viral diversity and evolution. In this study, we present the discovery and complete genome characterization of a novel mitovirus infecting the hypogeous mycorrhizal fungus Tuber rufum. This virus, denominated "Tuber rufum mitovirus 1" (TrMV1) has a genome size of 2864 nucleotides with a G + C content of 37.53%. It contains a single open reading frame (ORF) responsible for encoding RNA dependent RNA polymerase (RdRp). Comparative analysis using BLASTp reveals that the protein encoded by TrMV1 shares significant sequence similarities with those found in the Triamitovirus genus. Specifically, TrMV1 shows the closest resemblance (43.35% identity) to Sopawar virus, a mitovirus previously detected in soil environments through metatranscriptomic analyses. Phylogenetic examination categorizes TrMV1 as a member of the Triamitovirus genus within the Mitoviridae family. This finding marks the first identification of a mitovirus within the hypogeous mycorrhizal fungus Tuber rufum. The discovery of TrMV1 expands our knowledge of Mitoviridae family diversity and evolution, contributing to the growing repository of mycovirus sequences.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-024-00887-6.

European Tuber melanosporum plantations: adaptation status in Hungary, mycorrhizal level, and first ascocarp detection in two truffle orchards

Tuber melanosporum is one of the most economically important truffle species. Besides harvesting from its natural habitats, this truffle can also be extensively grown through artificial cultivation. However, the natural habitat of T. melanosporum has drastically declined, and the demand for the truffle in society is rapidly increasing. Therefore, enhancing production in truffle orchards by seeking new places for the establishment and regularly monitoring its adaptability might be an effective method for ensuring the sustainable productivity of the species. As a truffle science, recent information is important to further success in the growth of this truffle species. This study reports mycorrhization level and ascocarp production in two truffle plantations in Hungary. The estimated mycorrhization levels of the host plants were 43.36% in Biatorbágy and 42.93% in Jászszentandrás plantations. In March 2020, the 6-year-old and 18-year-old T. melanosporum plantations yielded around 100 g and 980 g of ascocarps, respectively. In general, adaptation of mycorrhizal seedlings in Hungary may become more effective as present management practices improve.

Ectomycorrhizal Fungal Community and Ascoma Production in a Declining Tuber borchii Plantation

Tuber borchii is an edible ectomycorrhizal mushroom of considerable economic value. Its cultivation has become popular in recent years, but there are few studies on the factors affecting its productivity. In this work, the ascoma production and the ectomycorrhizal (ECM) community of a T. borchii plantation, established in an intensive farming area where this truffle is not naturally present, were studied. Tuber borchii production drastically declined from 2016 to 2021, and ascomata of other Tuber species (T. maculatum and T. rufum) were found from 2017. Molecular characterization of ectomycorrhizae carried out in 2016 identified 21 ECM fungal species, of which T. maculatum (22%) and Tomentella coerulea (19%) were the most abundant. Tuber borchii ectomycorrizae (16%) were almost entirely confined to the fruiting points. The diversity and structure of the ECM community on Pinus pinea were significantly different from those observed on hardwood trees. The obtained results suggest that T. maculatum (a native of the study site) tends to replace T. borchii through a mechanism of competitive exclusion. Although T. borchii cultivation is possible in suboptimal environments, particular care should be taken to limit competition with ECM fungi more suitable for local conditions.

Tuber wenchuanense, a holarctic truffle with a wide range of host plants and description of its ectomycorrhiza with spruce

Tuber wenchuanense ascomata (Ascomycota, Pezizales), a species originally described from Sichuan (China), were found in the Tatra Mountains in southern Poland. The purpose of this work was to (i) report and assess the first case of the holarctic natural distribution of a Tuber species, (ii) amend the original description of the species, (iii) summarize data on its host plants and (iv) describe its ectomycorrhiza. Specimens of Tuber wenchuanense from the Tatra Mountains were studied morphologically and molecularly. The ectomycorrhiza of this truffle with Picea abies was described for the first time. The distribution of T. wenchuanense, which is reconstructed based on sequences deposited in the publicly available nucleotide sequence databases, makes it the first holarctic Tuber species and the one with the northernmost habitat. In fact, its habitat is confined mainly to mountain coniferous forests and alpine and arctic tundra; although, according to known observations, the fruiting bodies of T. wenchuanense can be produced only under conifers. Based on the sequences of the internal transcribed spacer, this species appears to have low genetic variability over the entire distribution range. The phylogenetic tree showed that some of the unidentified phylotypes from the Rufum clade found by other researchers belong to T. wenchuanense. The ecological implications of these findings are discussed.

Co-occurrence of true truffle mycelia in Tuber magnatum fruiting sites

Tuber magnatum (the white truffle) is the most precious species of the genus Tuber which comprises the hypogeous ectomycorrhizal species called "true truffle." Despite its high economic value, the knowledge on its ecology is scant, principally due to the difficulty to find its mycorrhizas in the soil. The possibility to detect its mycelium by DNA extracted from soil has given a new chance for studying this truffle species. In this work, the co-occurrence of other Tuber species with T. magnatum mycelium was investigated by using species-specific primers in several productive areas located in central and northern Italy. Most (82%) of the examined soil samples showed at least one other Tuber species in addition to T. magnatum. The most common was T. maculatum (72% of soil samples) followed by T. borchii, T. rufum, T. brumale, T. dryophilum, T. macrosporum, and T. melanosporum (40%, 37%, 22%, 19%, 12%, and 1% of soil samples, respectively). Tuber aestivum was never detected in T. magnatum productive patches. Analysis of species co-occurrence showed that the pairwise associations between T. dryophilum-T. brumale, T. brumale-T. borchii, and T. borchii-T. dryophilum was significant. The results suggest that Tuber mycelial network in white truffle grounds is much more extensive than the distribution of their ectomycorrhizas and competitive exclusion between different Tuber species seems to take place only for root colonization.

Soil Metabarcoding Offers a New Tool for the Investigation and Hunting of Truffles in Northern Thailand

Truffles (Tuber spp.) are well-known as edible ectomycorrhizal mushrooms, and some species are one of the most expensive foods in the world. During the fruiting process, truffles produce hypogeous ascocarps; a trained pig or dog is needed to locate the ascocarps under the ground. Truffles in northern Thailand have been recorded in association with Betulaalnoides and Carpinus poilanei. In this study, we investigated the soil mycobiota diversity of soil samples from both of these truffle host plants in native forests using environmental DNA metabarcoding to target the internal transcribed spacer 1 (ITS1) region of the rDNA gene for the purposes of investigation of truffle diversity and locating truffles during the non-fruiting phase. In this study, a total of 38 soil samples were collected from different locations. Of these, truffles had been found at three of these locations. Subsequently, a total of 1341 putative taxonomic units (OTUs) were obtained. The overall fungal community was dominated by phylum-level sequences assigned to Ascomycota (57.63%), Basidiomycota (37.26%), Blastocladiomycota (0.007%), Chytridiomycota (0.21%), Glomeromycota (0.01%), Kickxellomycota (0.01%), Mortierellomycota (2.08%), Mucoromycota (0.24%), Rozellomycota (0.01%), Zoopagomycota (0.003%), and unidentified (2.54%). The results revealed that six OTUs were determined to be representative and belonged to the genus Tuber. OTU162, OTU187, OTU447, and OTU530 belonged to T. thailandicum, T. lannaense, T. bomiense, and T. magnatum, whereas OTU105 and OTU720 were acknowledged as unrecognized Tuber species. From 38 locations, OTUs of truffles were found in 33 locations (including three previously known truffle locations). Thus, 30 collection sites were considered new locations for T. thailandicum, T. bomiense, and other unrecognized Tuber species. Interestingly, at 16 new locations, mature ascocarps of truffles that were undergoing the fruiting phase were located underground. All 16 truffle samples were identified as T. thailandicum based on morphological characteristics and molecular phylogenetic analysis. However, ascocarps of other truffle species were not found at the new OTUs representative locations. The knowledge gained from this study can be used to lead researchers to a better understanding of the occurrence of truffles using soil mycobiota diversity investigation. The outcomes of this study will be particularly beneficial with respect to the search and hunt for truffles without the need for trained animals. In addition, the findings of this study will be useful for the management and conservation of truffle habitats in northern Thailand.

Two new species of Tuber previously reported as Tuber malacodermum

Recent collections of Tuber malacodermum from Spain, Corsica, and Mexico were compared in an integrative morphological and molecular phylogenetic framework, including study of type material. Phylogenetic analyses of nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) and nuc 28S rDNA (28S) regions showed that specimens from Spain and Corsica form a monophyletic group closely related to T. melosporum and T. rufum, whereas Mexican specimens form a clade within the T. lyonii species complex. Peridium and ascospore morphology contribute clear morphological distinctions among specimens from Spain and Corsica, Mexico, and the type specimen of T. malacodermum. Based on results of the morphological and molecular phylogenetic analyses, we assigned the specimens from Spain and Corsica to Tuber pustulatum, sp. nov., and the Mexican specimens to Tuber theleascum, sp. nov. We restrict T. malacodermum to the sole type material. Formal descriptions and illustrations of these taxa are provided.

Tuberpulchrosporum sp. nov., a black truffle of the Aestivum clade (Tuberaceae, Pezizales) from the Balkan peninsula

Knowledge on the diversity of hypogeous sequestrate ascomycetes is still limited in the Balkan Peninsula. A new species of truffle, Tuberpulchrosporum, is described from Greece and Bulgaria. Specimens were collected from habitats dominated by various oak species (i.e. Quercusilex, Q.coccifera, Q.robur) and other angiosperms. They are morphologically characterised by subglobose, ovoid to irregularly lobed, yellowish-brown to dark brown ascomata, usually with a shallow basal cavity and surface with fissures and small, dense, almost flat, trihedral to polyhedral warts. Ascospores are ellipsoid to subfusiform, uniquely ornamented, crested to incompletely reticulate and are produced in (1-)2-8-spored asci. Hair-like, hyaline to light yellow hyphae protrude from the peridium surface. According to the outcome of ITS rDNA sequence analysis, this species forms a distinct well-supported group in the Aestivum clade, with T.panniferum being the closest phylogenetic taxon.

Truffle biogeography-A case study revealing ecological niche separation of different Tuber species

Ecology of hypogeic mycorrhizal fungi, such as truffles, remains largely unknown, both in terms of their geographical distribution and their environmental niches. Occurrence of true truffles (Tuber spp.) was therefore screened using specific polymerase chain reaction (PCR) assays and subsequent PCR amplicon sequencing in tree roots collected at 322 field sites across the Czech Republic. These sites spanned a wide range of climatic and soil conditions. The sampling was a priori restricted to areas thought to be suitable for Tuber spp. inasmuch as they were characterized by weakly acidic to alkaline soils, warmer climate, and with tree species previously known to host true truffles. Eight operational taxonomic units (OTUs) corresponding to Tuber aestivum, T. borchii, T. foetidum, T. rufum, T. indicum, T. huidongense, T. dryophilum, and T. oligospermum were detected. Among these, T. borchii was the OTU encountered most frequently. It was detected at nearly 19% of the sites. Soil pH was the most important predictor of Tuber spp. distribution. Tuber borchii preferred weakly acidic soils, T. foetidum and T. rufum were most abundant in neutral soils, and T. huidongense was restricted to alkaline soils. Distribution of T. aestivum was mainly dictated by climate, with its range restricted to the warmest sites. Host preferences of the individual Tuber spp. were weak compared to soil and climatic predictors, with the notable exception that T. foetidum appeared to avoid oak trees. Our results open the way to better understanding truffle ecology and, through this new knowledge, also to better-informed trufficulture.

First evidence for truffle production from plants inoculated with mycelial pure cultures

Truffle (Tuber spp.) cultivation is based on raising mycorrhizal trees in greenhouses that have been inoculated with suspensions of ascospores. The problem with this is that pests, pathogens, and other mycorrhizal fungi can contaminate the trees. Furthermore, because ascospores are produced sexually, each plant potentially has a different genetic mycorrhizal makeup from each other so tailoring the mycorrhizal component of plants to suit a particular set of soil and climatic conditions is out of the question. Here, we report on the production of Tuber borchii-mycorrhized plants using pure cultures, establishing a truffière with these and subsequent production of its fruiting bodies. This study opens up the possibility of producing commercial numbers of Tuber-mycorrhized trees for truffle cultivation using mycelial inoculation techniques. It also poses questions about the mechanism of fertilization between the different strains which were located in different parts of the experimental truffière.

Species-specific ITS primers for the identification of Picoa juniperi and Picoa lefebvrei and using nested-PCR for detection of P. juniperi in planta

Desert truffles, hypogeous Pezizales (Ascomycota), are difficult to identify due to evolutionary convergence of morphological characters among taxa that share a similar habitat and mode of spore dispersal. Also, during their symbiotic phase, these are barely distinguishable morphologically, and molecular probes are needed for their identification. We have developed a PCR-based method for the identification of Picoa juniperi and Picoa lefebvrei based on internal transcribed spacers of rDNA. Two PCR primers specific for P. lefebvrei (FLE/RLE) and two specific for P. juniperi (FJU/RJU) were designed. A collection of samples from different geographical areas representing diversity of these species were examined for unique regions of internal transcribed spacers 1, 2 and 5.8S gene of rDNA (ITS) compared to other closely related species. Annealing temperatures and extension times were optimized for each set of primers for maximum specificity and efficiency. They proved to be efficient to specifically detect the presence of P. juniperi and P. lefebvrei by PCR and neither set amplified purified DNA from other truffle species as well as some ascomycetous fungi. The partial small subunit of ribosomal DNA genes of P. juniperi were amplified with the genomic DNA extracted from Helianthemum ledifolium var. ledifolium roots by nested polymerase chain reaction (PCR) using the universal fungal primer pair ITS1/ITS4 and specific primer pair FTC/RTC, which was designed based on internal transcribed spacer 1, 2 and 5.8S gene of rDNA sequences of P juniperi. The nested-PCR was sensitive enough to re-amplify the direct-PCR product, resulting in a DNA fragment of 426 bp. The efficacy of nested-PCR showed that it could re-amplify the direct-PCR product and detect 200 fg genomic DNA.

Assessment of ectomycorrhizal fungal communities in the natural habitats of Tuber magnatum (Ascomycota, Pezizales)

The ectomycorrhizal (ECM) fungal communities of four natural Tuber magnatum truffle grounds, located in different Italian regions (Abruzzo, Emilia-Romagna, Molise, and Tuscany), were studied. The main objective of this study was to characterize and compare the ECM fungal communities in the different regions and in productive (where T. magnatum ascomata were found) and nonproductive points. More than 8,000 (8,100) colonized root tips were counted in 73 soil cores, and 129 operational taxonomic units were identified using morphological and molecular methods. Although the composition of the ECM fungal communities studied varied, we were able to highlight some common characteristics. The most plentiful ECM fungal taxa belong to the Thelephoraceae and Sebacinaceae families followed by Inocybaceae and Russulaceae. Although several ectomycorrhizas belonging to Tuber genus were identified, no T. magnatum ectomycorrhizas were found. The putative ecological significance of some species is discussed.

Development and validation of a real-time PCR assay for detection and quantification of Tuber magnatum in soil

BACKGROUND

Tuber magnatum, the Italian white truffle, is the most sought-after edible ectomycorrhizal mushroom. Previous studies report the difficulties of detecting its mycorrhizas and the widespread presence of its mycelium in natural production areas, suggesting that the soil mycelium could be a good indicator to evaluate its presence in the soil. In this study a specific real-time PCR assay using TaqMan chemistry was developed to detect and quantify T. magnatum in soil. This technique was then applied to four natural T. magnatum truffières located in different regions of Italy to validate the method under different environmental conditions.

RESULTS

The primer/probe sets for the detection and quantification of T. magnatum were selected from the ITS rDNA regions. Their specificity was tested in silico and using qualitative PCR on DNA extracted from 25 different fungal species. The T. magnatum DNA concentration was different in the four experimental truffières and higher in the productive plots. T. magnatum mycelium was however also detected in most of the non-productive plots. Ascoma production during the three years of the study was correlated with the concentration of T. magnatum DNA.

CONCLUSIONS

Taken together, these results suggest that the specific real-time PCR assay perfected in this study could be an useful tool to evaluate the presence and dynamics of this precious truffle in natural and cultivated truffières.

Traceability of marketable Japanese shoro in New Zealand: using multiplex PCR to exploit phylogeographic variation among taxa in the Rhizopogon subgenus Roseoli

Rhizopogon roseolus Corda (synonym Rhizopogon rubescens Tul.), an economically important edible mushroom associated with the Pinaceae (mostly Pinus sp.), has a global distribution resulting from the introduction of exotic trees into the Southern Hemisphere for plantation forestry. However, the marketability of R. roseolus varies with the place of origin. R. roseolus strains cultivated in New Zealand from local carpophores for the Japanese market are morphologically and biologically distinct from those produced in Japan and are consequently considered less valuable. In this study, the ITS1-5.8S-ITS2 rRNA (internal transcribed spacer [ITS]) region was used to examine the phylogenetic relationships of R. roseolus and other closely related fungi belonging to Rhizopogon subgenus Roseoli to determine the genetic basis for phenotypic differences among R. roseolus isolates from different geographic regions. Phylogenetic comparison revealed phylogeographic variation within Rhizopogon subgenus Roseoli. Collections from the United States and Europe grouped into four distinct clades. Rhizopogon roseolus isolates found in New Zealand were closely related to those from the United States, likely due to introduction of Pinus radiata from its native California in the United States. In contrast, Japanese R. roseolus isolates clustered closely with European collections. Phylogenetic differences between Japanese and New Zealand R. roseolus isolates may explain the morphological and biological properties attributed to these geographical variants. The ITS region was subsequently used to design a multiplex PCR for the simultaneous identification of Japanese and New Zealand R. roseolus isolates to track the establishment of ectomycorrhiza on P. radiata seedlings inoculated with commercially valuable R. roseolus. This diagnostic demonstrated the first fruiting of Japanese shoro cultivated on P. radiata in the Southern Hemisphere.