Isolation and characterization of MAT genes in the symbiotic ascomycete Tuber melanosporum

Hidden fairy rings and males-Genetic patterns of natural Burgundy truffle (Tuber aestivum Vittad.) populations reveal new insights into its life cycle

Burgundy truffles are heterothallic ascomycetes that grow in symbiosis with trees. Despite their esteemed belowground fruitbodies, the species' complex lifecycle is still not fully understood. Here, we present the genetic patterns in three natural Burgundy truffle populations based on genotyped fruitbodies, ascospore extracts and ectomycorrhizal root tips using microsatellites and the mating-type locus. Distinct genetic structures with high relatedness in close vicinity were found for females (forming the fruitbodies) and males (fertilizing partner as inferred from ascospore extracts), with high genotypic diversity and annual turnover of males, suggesting that ephemeral male mating partners are germinating ascospores from decaying fruitbodies. The presence of hermaphrodites and the interannual persistence of a few males suggest that persistent mycelia may sporadically also act as males. Only female or hermaphroditic individuals were detected on root tips. At one site, fruitbodies grew in a fairy ring formed by a large female individual that showed an outward growth rate of 30 cm per year, with the mycelium decaying within the ring and being fertilized by over 50 male individuals. While fairy ring structures have never been shown for truffles, the genetics of Burgundy truffle populations support a similar reproductive biology as those of other highly prized truffles.

Diversity Analysis of the Rice False Smut Pathogen Ustilaginoidea virens in Southwest China

Rice false smut caused by Ustilaginoidea virens is a destructive disease in rice cropping areas of the world. The present study is focused on the morphology, pathogenicity, mating-type loci distribution, and genetic characterization of different isolates of U. virens. A total of 221 strains of U. virens were collected from 13 rice-growing regions in southwest China. The morphological features of these strains exhibited high diversity, and the pathogenicity of the smut fungus showed significant differentiation. There was no correlation between pathogenicity and sporulation. Mating-type locus (MAT) analysis revealed that all 221 isolates comprised heterothallic and homothallic forms, wherein 204 (92.31%) and 17 (7.69%) isolates belonged to heterothallic and homothallic mating types, respectively. Among 204 strains of heterothallic mating types, 62 (28.05%) contained MAT1-1-1 idiomorphs, and 142 isolates (64.25%) had the MAT1-2-1 idiomorph. Interestingly, strains isolated from the same fungus ball had different mating types. The genetic structure of the isolates was analyzed using simple sequence repeats (SSRs) and single-nucleotide polymorphisms (SNPs). All isolates were clustered into five genetic groups. The values of Nei's gene diversity (H) and Shannon's information index (I) indicated that all strains as a group had higher genetic diversity than strains from a single geographical population. The pairwise population fixation index (FST) values also indicated significant genetic differentiation among all compared geographical populations. The analysis of molecular variation (AMOVA) indicated greater genetic variation within individual populations and less genetic variation among populations. The results showed that most of the strains were not clustered according to their geographical origin, showing the rich genetic diversity and the complex and diverse genetic background of U. virens in southwest China. These results should help to better understand the biological and genetic diversity of U. virens in southwest China and provide a theoretical basis for building effective management strategies.

Efficiency of the traditional practice of traps to stimulate black truffle production, and its ecological mechanisms

The black truffle Tuber melanosporum was disseminated all over the world, propelled by the development of a wide variety of empirical practices. A widespread practice, called ‘truffle trap’, consists of placing pieces of truffles into excavations dug under host trees, and of collecting truffle in these traps in the next years. This research aims at (1) evaluating the effect of this practice on fruitbody production based on the analysis of 9924 truffle traps installed in 11 orchards across T. melanosporum native area in France and (2) exploring the mechanisms involved in fruitbody emergence using traps where the genotypes of introduced truffles were compared with those of fruitbodies collected in the same traps. We confirmed that truffle traps provide a major and highly variable part of truffle ground production, representing up to 89% of the collected fruitbodies. We evidenced a genetic link between introduced spores and collected fruitbodies, and then demonstrated that truffle growers provide paternal partners for mating with local maternal mycelia. We also highlighted that soil disturbance stimulate the vegetative development of established maternal mycelia. This research supports that a widely used traditional practice enhances fruitbody production by shaping favorable conditions and providing sexual partners required for fruiting.

Intraspecific Competition Results in Reduced Evenness of Tuber melanosporum Mating-Type Abundance from the Nursery Stage

The highly prized black truffle is a fungus mostly harvested in orchards planted with mycorrhizal seedlings. It is an obligatory outcrossing fungus with a single MAT locus containing two alternative mating-type idiomorphs. In the orchards, at the mycorrhizal level, these mating types are frequently spatially segregated. Some studies found that this segregation was pronounced from the nursery stage, whereas others did not find such a marked segregation. Besides, information on the host tree species and nursery conditions used in Spain, one of the main truffle-producing countries, are very scarce. In this study, we investigated the temporal dynamics of mating types in nursery seedlings of Quercus ilex and Quercus faginea, as well as the influence of cultural conditions in the nursery. Our results indicated that at the plant level, there was a trend for one of the mating types to dominate over the other from the first to the second year in the nursery, in both host species and both nursery conditions tested. However, this segregation process was not so sharp as previously reported. Our results support the hypothesis that intraspecific competition results in reduced evenness of mating-type abundance from the nursery stage, although almost all seedlings maintained both mating types and, at the seedling batch scale, the occurrence of both mating types was roughly balanced.

Mitospore formation on pure cultures of Tuber japonicum (Tuberaceae, Pezizales) in vitro

The members of the genus Tuber are Ascomycota that form ectomycorrhizal associations with various coniferous and broadleaf tree species. In the teleomorphic stage, the species of the genus produce fruit bodies known as true truffles. Recent studies have discovered mitosporic structures, including spore mats, of several Tuber species on forest soils, indicating the presence of a cryptic anamorphic stage or an unknown reproductive strategy. Here, we report in vitro mitospore formation on the mycelium of T. japonicum, which belongs to the Japonicum clade, collected in several regions in Japan. Twenty of the 25 strains formed mitospores on modified Melin-Norkrans agar medium, indicating that mitospore formation is likely a common trait among strains of T. japonicum. The fungus forms repeatedly branched conidiophores on aerial hyphae on colonies and generates holoblastic mitospores sympodially on the terminal and near apical parts and/or occasionally on the middle and basal parts of the conidiogenous cells. Mitospores are hyaline and elliptical, obovate, oblong, or occasionally bacilliform, with a vacuole and often distinct hilar appendices. Formation of mitospores by T. japonicum in vitro is useful in understanding the functions of mitospores in the genus Tuber under controlled environmental conditions.

De novo genome assembly and functional annotation for Fusarium langsethiae

Background

Fusarium langsethiae is a T-2 and HT-2 mycotoxins producing species firstly characterised in 2004. It is commonly isolated from oats in Northern Europe. T-2 and HT-2 mycotoxins exhibit immunological and haemotological effects in animal health mainly through inhibition of protein, RNA and DNA synthesis. The development of a high-quality and comprehensively annotated assembly for this species is therefore essential in providing the molecular understanding and the mechanism of T-2 and HT-2 biosynthesis in F. langsethiae to help develop effective control strategies.

Results

The F. langsethiae assembly was produced using PacBio long reads, which were then assembled independently using Canu, SMARTdenovo and Flye. A total of 19,336 coding genes were identified using RNA-Seq informed ab-initio gene prediction. Finally, predicting genes were annotated using the basic local alignment search tool (BLAST) against the NCBI non-redundant (NR) genome database and protein hits were annotated using InterProScan. Genes with blast hits were functionally annotated with Gene Ontology.

Conclusions

We developed a high-quality genome assembly of a total length of 59 Mb and N50 of 3.51 Mb. Raw sequence reads and assembled genome is publicly available and can be downloaded from: GenBank under the accession JAFFKB000000000.

All commands used to generate this assembly are accessible via GitHub: https://github.com/FadyMohareb/fusarium_langsethiae.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08368-0.

Life Cycle and Phylogeography of True Truffles

True truffle (Tuber spp.) is one group of ascomycetes with great economic importance. During the last 30 years, numerous fine-scale population genetics studies were conducted on different truffle species, aiming to answer several key questions regarding their life cycles; these questions are important for their cultivation. It is now evident that truffles are heterothallic, but with a prevalent haploid lifestyle. Strains forming ectomycorrhizas and germinating ascospores act as maternal and paternal partners respectively. At the same time, a number of large-scale studies were carried out, highlighting the influences of the last glaciation and river isolations on the genetic structure of truffles. A retreat to southern refugia during glaciation, and a northward expansion post glaciation, were revealed in all studied European truffles. The Mediterranean Sea, acting as a barrier, has led to the existence of several refugia in different peninsulas for a single species. Similarly, large rivers in southwestern China act as physical barriers to gene flow for truffles in this region. Further studies can pay special attention to population genetics of species with a wide distribution range, such as T. himalayense, and the correlation between truffle genetic structure and the community composition of truffle-associated bacteria.

Effect of slug mycophagy on Tuber aestivum spores

Truffles in the genus Tuber produce subterranean fruiting bodies that are not able to actively discharge their spores in the environment. For this reason, truffles depend on mycophagous animals for reproduction. Fungus consumption (mycophagy) is a behaviour typical of both vertebrates and invertebrates. Mammals, especially rodents, are the most studied group of mycophagists and have been found to consume a great variety of fungi. Among invertebrates, mycophagy is documented in arthropods, but rarely in molluscs. In our study we assessed the effect on the morphology and mycorrhizal colonization of Tuber aestivum spores after passage through the gut of slugs (Deroceras invadens) and, for comparison, of a house mouse (Mus musculus). Light, scanning electron and atomic force microscopy revealed that the digestion, especially by slugs, freed spores from the asci and modified their morphology. These are believed to be the reasons why we observed an improvement in oak mycorrhization with the slug and rodent ingested spores in comparison to a fresh spore inoculation. We also demonstrated by molecular barcoding that slugs' guts sampled on a Tuber melanosporum truffle ground contain spores from this species and Tuber brumale, further suggesting that some invertebrates are efficient Tuber spore dispersers.

Frequency of the two mating types in the soil under productive and non-productive trees in five French orchards of the Périgord black truffle (Tuber melanosporum Vittad.)

The Périgord black truffle (Tuber melanosporum Vittad.) is an ectomycorrhizal fungus forming edible fructifications. The production of T. melanosporum relies mainly on man-made plantations. T. melanosporum is a heterothallic species requiring the meeting of two partners of opposite mating types to fruit. It is common to have productive and non-productive trees in the same orchard. The aim of our study was to assess the distribution of T. melanosporum mating types in soil under productive and non-productive trees to test whether the presence or absence of one or two mating types could be an indicator of productivity. To achieve this aim, five orchards were selected in various French regions. Soils were harvested under productive and non-productive Quercus pubescens; soil characteristics and the distribution of the mating types in the soil were investigated. No significant differences between productive and non-productive soils according to soil parameters were detected. The total content of T. melanosporum DNA in the soil was significantly higher under productive trees compared with non-productive trees, and it was positively correlated only with soil available phosphorous. Under productive trees, it was more frequent to find both mating types than under non-productive trees. Soils with only one mating type were more frequent under non-productive trees than under productive ones. Moreover, no mating type was detected in the soil of 22% of the non-productive trees. These results suggest that the detection of T. melanosporum mating types in soil could be a tool to optimise the management of truffle orchards (e.g. by spore inoculation).

Effects of truffle inoculation on a nursery culture substrate environment and seedling of Carya illinoinensis

We inoculated Tuber aestivum and Tuber sinoaestivum on Carya illinoinensis to explore the effects of inoculation on host plant growth, enzyme activities, the physicochemical properties of rhizosphere soil, the denitrifying bacterial community in the rhizosphere, and the distribution of mating type genes in the rhizosphere. We found that the Tuber spp. inoculation increased the height of the host plant and that the stem circumference of the host was greater two months after inoculation. Six months after inoculation, the peroxidase activity of the seedlings inoculated with T. sinoaestivum was higher than that of the control. At four and six months after inoculation, the superoxidase dismutase activities of the seedlings inoculated with T. aestivum were higher than those of the seedlings inoculated with T. sinoaestivum. Six months after inoculation, nitrate nitrogen content was lowest in the control and highest in the T. sinoaestivum treatment. Among the nirS-type denitrifying bacteria community, the relative abundances of Proteobacteria were high. T. aestivum and T. sinoaestivum inoculation did not affect the diversity of denitrifying bacteria. The mating type genes MAT1-1-1 and MAT1-2-1 were detected in the rhizosphere of C. illinoinensis inoculated with T. sinoaestivum and T. aestivum, and MAT1-1-1 dominated over MAT1-2-1.

Desert truffle genomes reveal their reproductive modes and new insights into plant-fungal interaction and ectendomycorrhizal lifestyle

Desert truffles are edible hypogeous fungi forming ectendomycorrhizal symbiosis with plants of Cistaceae family. Knowledge about the reproductive modes of these fungi and the molecular mechanisms driving the ectendomycorrhizal interaction is lacking. Genomes of the highly appreciated edible desert truffles Terfezia claveryi Chatin and Tirmania nivea Trappe have been sequenced and compared with other Pezizomycetes. Transcriptomes of T. claveryi × Helianthemum almeriense mycorrhiza from well-watered and drought-stressed plants, when intracellular colonizations is promoted, were investigated. We have identified the fungal genes related to sexual reproduction in desert truffles and desert-truffles-specific genomic and secretomic features with respect to other Pezizomycetes, such as the expansion of a large set of gene families with unknown Pfam domains and a number of species or desert-truffle-specific small secreted proteins differentially regulated in symbiosis. A core set of plant genes, including carbohydrate, lipid-metabolism, and defence-related genes, differentially expressed in mycorrhiza under both conditions was found. Our results highlight the singularities of desert truffles with respect to other mycorrhizal fungi while providing a first glimpse on plant and fungal determinants involved in ecto to endo symbiotic switch that occurs in desert truffle under dry conditions.

Genome-Wide Analyses of Repeat-Induced Point Mutations in the Ascomycota

The Repeat-Induced Point (RIP) mutation pathway is a fungus-specific genome defense mechanism that mitigates the deleterious consequences of repeated genomic regions and transposable elements (TEs). RIP mutates targeted sequences by introducing cytosine to thymine transitions. We investigated the genome-wide occurrence and extent of RIP with a sliding-window approach. Using genome-wide RIP data and two sets of control groups, the association between RIP, TEs, and GC content were contrasted in organisms capable and incapable of RIP. Based on these data, we then set out to determine the extent and occurrence of RIP in 58 representatives of the Ascomycota. The findings were summarized by placing each of the fungi investigated in one of six categories based on the extent of genome-wide RIP. In silico RIP analyses, using a sliding-window approach with stringent RIP parameters, implemented simultaneously within the same genetic context, on high quality genome assemblies, yielded superior results in determining the genome-wide RIP among the Ascomycota. Most Ascomycota had RIP and these mutations were particularly widespread among classes of the Pezizomycotina, including the early diverging Orbiliomycetes and the Pezizomycetes. The most extreme cases of RIP were limited to representatives of the Dothideomycetes and Sordariomycetes. By contrast, the genomes of the Taphrinomycotina and Saccharomycotina contained no detectable evidence of RIP. Also, recent losses in RIP combined with controlled TE proliferation in the Pezizomycotina subphyla may promote substantial genome enlargement as well as the formation of sub-genomic compartments. These findings have broadened our understanding of the taxonomic range and extent of RIP in Ascomycota and how this pathway affects the genomes of fungi harboring it.

Successes and challenges in the sustainable cultivation of edible mycorrhizal fungi – furthering the dream

The cultivation of edible mycorrhizal fungi (EMF) has made great progress since the first cultivation of Tuber melanosporum in 1977 but remains in its infancy. Five cultivation steps are required: (1) mycorrhizal synthesis, (2) mycorrhiza development and acclimation, (3) out-planting of mycorrhizal seedlings, (4) onset of fructification, and (5) performing tree orchards. We provide examples of successes and challenges associated with each step, including fruiting of the prestigious chanterelles in Japan recently. We highlight the challenges in establishing performing tree orchards. We report on the monitoring of two orchards established between Lactarius deliciosus (saffron milk cap) and pines in New Zealand. Saffron milk caps yields reached 0.4 and 1100 kg/ha under Pinus radiata and P. sylvestris 6 and 9 y after planting, respectively. Canopy closure began under P. radiata 7 y after planting, followed by a drastic reduction of yields, while P. sylvestris yields still hovered at 690 to 780 kg/ha after 11 y, without canopy closure. The establishment of full-scale field trials to predict yields is crucial to making the cultivation of EMF a reality in tomorrow's cropping landscape. Sustainable EMF cultivation utilizing trees in non-forested land could contribute to carbon storage, while providing revenue and other ecosystem services.

The 287,403 bp Mitochondrial Genome of Ectomycorrhizal Fungus Tuber calosporum Reveals Intron Expansion, tRNA Loss, and Gene Rearrangement

In the present study, the mitogenome of Tuber calosporum was assembled and analyzed. The mitogenome of T. calosporum comprises 15 conserved protein-coding genes, two rRNA genes, and 14 tRNAs, with a total size of 287,403 bp. Fifty-eight introns with 170 intronic open reading frames were detected in the T. calosporum mitogenome. The intronic region occupied 69.41% of the T. calosporum mitogenome, which contributed to the T. calosporum mitogenome significantly expand relative to most fungal species. Comparative mitogenomic analysis revealed large-scale gene rearrangements occurred in the mitogenome of T. calosporum, involving gene relocations and position exchanges. The mitogenome of T. calosporum was found to have lost several tRNA genes encoding for cysteine, aspartate, histidine, etc. In addition, a pair of fragments with a total length of 32.91 kb in both the nuclear and mitochondrial genomes of T. calosporum was detected, indicating possible gene transfer events. A total of 12.83% intragenomic duplications were detected in the T. calosporum mitogenome. Phylogenetic analysis based on mitochondrial gene datasets obtained well-supported tree topologies, indicating that mitochondrial genes could be reliable molecular markers for phylogenetic analyses of Ascomycota. This study served as the first report on mitogenome in the family Tuberaceae, thereby laying the groundwork for our understanding of the evolution, phylogeny, and population genetics of these important ectomycorrhizal fungi.

Persistence of Tuber melanosporum in truffle orchards in North Carolina, USA

A survey was conducted to determine the persistence of mycorrhization by Tuber melanosporum in truffle orchards established with European and American species of oak and common hazel trees in North Carolina. The trees had reportedly been inoculated and colonized by T. melanosporum prior to planting. Root samples were collected from 95 trees among seven orchards in 2015 and roots were analyzed by morphology and quantitative PCR. Samples that tested negative for T. melanosporum or where ectomycorrhizal morphology was not observed were analyzed by sequencing to identify the mycorrhizal fungal symbiont present. The presence of T. melanosporum was detected in all seven orchards. In six orchards, T. melanosporum was detected on all trees, but in only two of fifteen trees in one orchard. Other species of Tuber including T. brennemanii, T. canaliculatum, and T. lyonii, species of Scleroderma, and members of the Pezizales were also detected by sequence analysis. Sporocarps of T. aestivum and T. brumale were found in 2017 and 2018 in separate orchards in North Carolina after the survey was conducted. Overall, results indicate that T. melanosporum has persisted in truffle orchards sampled in North Carolina. Indigenous and contaminating fungal species, including Tuber species, were also detected and present a challenge to the truffle industry in North Carolina.

Colonization by Tuber melanosporum and Tuber indicum affects the growth of Pinus armandii and phoD alkaline phosphatase encoding bacterial community in the rhizosphere

The synthesis of truffle ectomycorrhizae and the ecology of truffle-colonized seedlings in the early symbiotic stage are important for the successful truffle cultivation. In this study, two black truffle species, Tuber melanosporum and Tuber indicum, were selected to colonize Pinus armandii seedlings. 2, 4, 6 and 8 months after inoculation, the growth performance of the host and the rhizosphere soil properties were detected. The dynamic changes of two mating type genes in substrate were also monitored to assess the sexual distribution of truffles. Additionally, the variation of soil bacterial communities encoded by phoD alkaline phosphatase genes was investigated through next-generation sequencing. The results indicated that both T. melanosporum and T. indicum colonization promoted the growth of P. armandii seedlings to some extent, including improving their biomass, total root surface area, root superoxide dismutases and peroxidase activity. The organic matter and available phosphorus in rhizosphere soil were also significantly enhanced by two truffles' colonization. The phoD-harboring bacterial community structure was altered by both truffles, and T. melanosporum decreased their diversity or richness on the 6th and 8th month after inoculation. Pseudomonas, Xanthomonas, and Sinorhizobium, a N₂-fixer with phoD genes, were found more abundant in truffle-colonized treatments. The mating type distribution of the two truffles was uneven, with MAT1-1-1 gene occupying the majority. Overall, T. melanosporum and T. indicum colonization affected the micro-ecology of truffle symbionts during the early symbiotic stage. These results could give us a better understanding on the truffle-plant-soil-microbe interactions, which would be beneficial to the subsequent truffle cultivation.

Two ectomycorrhizal truffles, Tuber melanosporum and T. aestivum, endophytically colonise roots of non-ectomycorrhizal plants in natural environments

Serendipitous findings and studies on Tuber species suggest that some ectomycorrhizal fungi, beyond their complex interaction with ectomycorrhizal hosts, also colonise roots of nonectomycorrhizal plants in a loose way called endophytism. Here, we investigate endophytism of T. melanosporum and T. aestivum. We visualised endophytic T. melanosporum hyphae by fluorescent in situ hybridisation on nonectomycorrhizal plants. For the two Tuber species, microsatellite genotyping investigated the endophytic presence of the individuals whose mating produced nearby ascocarps. We quantified the expression of four T. aestivum genes in roots of endophyted, non-ectomycorrhizal plants. Tuber melanosporum hyphae colonised the apoplast of healthy roots, confirming endophytism. Endophytic Tuber melanosporum and T. aestivum contributed to nearby ascocarps, but only as maternal parents (forming the flesh). Paternal individuals (giving only genes found in meiotic spores of ascocarps) were not detected. Gene expression of T. aestivum in non-ectomycorrhizal plants confirmed a living status. Tuber species, and likely other ectomycorrhizal fungi found in nonectomycorrhizal plant roots in this study, can be root endophytes. This is relevant for the ecology (brûlé formation) and commercial production of truffles. Evolutionarily speaking, endophytism may be an ancestral trait in some ectomycorrhizal fungi that evolved from root endophytes.

Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes

Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes.

Ascoma genotyping and mating type analyses of mycorrhizas and soil mycelia of Tuber borchii in a truffle orchard established by mycelial inoculated plants

Tuber borchii (the Bianchetto truffle) is a heterothallic Ascomycete living in symbiotic association with trees and shrubs. Maternal and paternal genotype dynamics have already been studied for the black truffles Tuber melanosporum and Tuber aestivum but not yet for T. borchii. In this study, we analysed maternal and paternal genotypes in the first truffle orchard realized with plants inoculated with five different T. borchii mycelia. Our aims were to test the persistence of the inoculated mycelia, if maternal and/or paternal genotypes correspond to inoculated mycelia and to assess the hermaphroditism of T. borchii. The mating type of each isolate as well as those of mycorrhizas, ascomata and extraradical soil mycelia was determined. Moreover, simple sequence repeat (SSR) profiles of maternal and paternal genotypes were assessed in 18 fruiting bodies to investigate the sexual behaviour of this truffle. The maternal genotypes of the fruiting bodies corresponded to those of the inoculated mycelia with only two exceptions. This confirmed that the inoculated mycelia persisted 9 years after plantation. As regards paternal partner, only two had the same genotype as those of the inoculated mycelia, suggesting hermaphroditism. Most of the new paternal genotypes originated from a recombination of those of inoculated mycelia.

Orchard Conditions and Fruiting Body Characteristics Drive the Microbiome of the Black Truffle Tuber aestivum

Truffle fungi are well known for their enticing aromas partially emitted by microbes colonizing truffle fruiting bodies. The identity and diversity of these microbes remain poorly investigated, because few studies have determined truffle-associated bacterial communities while considering only a small number of fruiting bodies. Hence, the factors driving the assembly of truffle microbiomes are yet to be elucidated. Here we investigated the bacterial community structure of more than 50 fruiting bodies of the black truffle Tuber aestivum in one French and one Swiss orchard using 16S rRNA gene amplicon high-throughput sequencing. Bacterial communities from truffles collected in both orchards shared their main dominant taxa: while 60% of fruiting bodies were dominated by α-Proteobacteria, in some cases the β-Proteobacteria or the Sphingobacteriia classes were the most abundant, suggesting that specific factors (i.e., truffle maturation and soil properties) shape differently truffle-associated microbiomes. We further attempted to assess the influence in truffle microbiome variation of factors related to collection season, truffle mating type, degree of maturation, and location within the truffle orchards. These factors had differential effects between the two truffle orchards, with season being the strongest predictor of community variation in the French orchard, and spatial location in the Swiss one. Surprisingly, genotype and fruiting body maturation did not have a significant effect on microbial community composition. In summary, our results show, regardless of the geographical location considered, the existence of heterogeneous bacterial communities within T. aestivum fruiting bodies that are dominated by three bacterial classes. They also indicate that factors shaping microbial communities within truffle fruiting bodies differ across local conditions.

Ribosomal DNA polymorphisms reveal genetic structure and a phylogeographic pattern in the Burgundy truffle Tuber aestivum Vittad

Ectomycorrhizal ascomycetes belonging to the genus Tuber produce edible fruiting bodies known as truffles. Tuber aestivum, in particular, is a fungus appreciated worldwide and has a natural distribution throughout Europe. Most of the molecular studies conducted on this species have been focused on the question as to whether or not T. aestivum and the morphologically similar T. uncinatum are conspecific. Conversely, only a handful of studies have assessed the level and distribution of genetic diversity and occurrence of phylogeographic patterns in this species. Here, we analyzed the genetic diversity of T. aestivum over a wide geographic range, performing an extensive sampling of specimens from Turkey, which is novel, to the best of our knowledge. We compared the internal transcribed spacer (ITS) profiles of 45 samples collected in different Turkish areas with those of 144 samples from all over Europe. We identified 63 haplotypes, 32 of which were exclusively present in Turkey. The majority of these haplotyes were also population specific. Haplotype network analysis and statistical tests highlighted the presence of a genetic structure and phylogeographic pattern, with three spatially distinct genetic clusters (northeastern Europe, southern Europe, and Turkey), with Turkey representing a diversity hotspot. Based on these results, we hypothesize the presence of glacial refugia for T. aestivum in Turkey, whereas European populations likely experienced a population bottleneck. The possible occurrence of cryptic species among Turkish T. aestivum samples also emerged. Our results are of practical relevance for the marketing of T. aestivum truffles and mycorrhizal seedlings and the preservation of the biodiversity of this species.

Mycelium of Terfezia claveryi as inoculum source to produce desert truffle mycorrhizal plants

Terfezia claveryi Chatin was the first desert truffle species to be cultivated, the mycorrhizal plants being successfully produced by using both desert truffle spores and mycelia. However, it is more advisable to use mycelium than spores whenever possible and profitable. Given the low yields of mycelia obtained using traditional culture methods of this truffle, the medium composition was modified in an attempt to determine its nutritional requirements. For this, an assay involving response surface methodology was performed using Box-Behnken design to find the optimal parameters for the high production of mycelial biomass. The best results were obtained with glucose as carbon source, buffering the pH at 5 during culture, adding a pool of vitamins, and adjusting the optimal concentrations of carbon and nitrogen sources of the MMN medium. Biomass production increased from 0.3 to 3 g L^-1 dry weight and productivity increased from 10.7 to 95.8 mg L^-1 day^-1 dry weight. The produced mycelium was able to colonize Helianthemum roots efficiently, providing more than 50% ectomycorrhizal colonization.

The Uneven Distribution of Mating Type Genes in Natural and Cultivated Truffle Orchards Contributes to the Fructification of Tuber indicum

The aim of this study was to investigate the pattern of distribution of mating type (MAT) genes of Tuber indicum in ectomycorhizosphere soils from natural T. indicum-producing areas and cultivated truffle orchards and ascocarp samples from different regions. Quantitative real-time PCR and multiplex PCR were used to weight the copy numbers of MAT1-1-1 and MAT1-2-1 in natural truffle soils and cultivated orchard soils. The effect of limestone on the pattern of truffle MAT genes and the correlation between soil properties and the proportion of MAT genes were also assessed. These results indicated that an uneven and nonrandom distribution of MAT genes was common in truffle-producing areas, cultivated truffle orchards, and ascocarps gleba. The competition between the two mating type genes and the expansion of unbalanced distribution was found to be closely related to truffle fructification. Limestone treatments failed to alter the proportion of the two mating type genes in the soil. The content of available phosphorus in soil was significantly correlated with the value of MAT1-1-1/MAT1-2-1 in cultivated and natural ectomycorhizosphere soils. The application of real-time quantitative PCR can provide reference for monitoring the dynamic changes of mating type genes in soil. This study investigates the distributional pattern of T. indicum MAT genes in the ectomycorhizosphere soil and ascocarp gleba from different regions, which may provide a foundation for the cultivation of T. indicum.

Using mating-type loci to improve taxonomy of the Tuber indicum complex, and discovery of a new species, T. longispinosum

Black truffles that morphologically resemble Tuber indicum have been known to occur in Japan since 1979. Our previous studies showed that there are two phylotypes of these truffles, both of which fell into the T. indicum complex (hereinafter "Tuber sp. 6" and "Tuber sp. 7"). However, their taxonomic treatment is still unclear. In this study, we conducted morphological and phylogenetic analyses for a total of 52 specimens from Japan (16 Tuber sp. 6 and 13 Tuber sp. 7), China (10 T. himalayense and 8 T. indicum), and Taiwan (5 T. formosanum). We compared ascospore ornamentation, size, distribution of asci with average number of spores per ascus, spine size and shape of the Japanese specimens with their allied taxa. For phylogenetic analysis, we sequenced two mating loci (MAT1-1-1 and MAT1-2-1) and three commonly used loci (ITS, β-tubulin, and TEF1-α). Three distinct lineages were recognized by phylogenetic analyses based on the sequences of the two mating-related loci and three independent loci. The Tuber sp. 6 sequences clustered with those of T. himalayense and T. formosanum, and there was no clear difference in morphology among them. Tuber sp. 7 formed a distinct lineage in each phylogram. The specimens tended to have five-spored asci more frequently than other allied species and could be characterized as having ascospore ornamentation with longer spines and narrower spine bases. We therefore described Tuber sp. 7 as a new species (T. longispinosum), and treat Tuber sp. 6 and T. formosanum as synonyms of T. himalayense.

Recent Insights on Biological and Ecological Aspects of Ectomycorrhizal Fungi and Their Interactions

The roots of most terrestrial plants are colonized by mycorrhizal fungi. They play a key role in terrestrial environments influencing soil structure and ecosystem functionality. Around them a peculiar region, the mycorrhizosphere, develops. This is a very dynamic environment where plants, soil and microorganisms interact. Interest in this fascinating environment has increased over the years. For a long period the knowledge of the microbial populations in the rhizosphere has been limited, because they have always been studied by traditional culture-based techniques. These methods, which only allow the study of cultured microorganisms, do not allow the characterization of most organisms existing in nature. The introduction in the last few years of methodologies that are independent of culture techniques has bypassed this limitation. This together with the development of high-throughput molecular tools has given new insights into the biology, evolution, and biodiversity of mycorrhizal associations, as well as, the molecular dialog between plants and fungi. The genomes of many mycorrhizal fungal species have been sequenced so far allowing to better understanding the lifestyle of these fungi, their sexual reproduction modalities and metabolic functions. The possibility to detect the mycelium and the mycorrhizae of heterothallic fungi has also allowed to follow the spatial and temporal distributional patterns of strains of different mating types. On the other hand, the availability of the genome sequencing from several mycorrhizal fungi with a different lifestyle, or belonging to different groups, allowed to verify the common feature of the mycorrhizal symbiosis as well as the differences on how different mycorrhizal species interact and dialog with the plant. Here, we will consider the aspects described before, mainly focusing on ectomycorrhizal fungi and their interactions with plants and other soil microorganisms.

Seasonal dynamics of extraradical mycelium and mycorrhizas in a black truffle (Tuber melanosporum) plantation

Seasonal dynamics of black truffle (Tuber melanosporum) extraradical mycelium as well as the associated mycorrhizal community have been evaluated in a 16-year-old plantation with productive and non-productive trees. Mycelium biomass was seasonally quantified by real-time PCR over two consecutive years and the correlation with environmental variables explored. Extraradical mycelium biomass varied seasonally and between the two consecutive years, being correlated with the precipitation that occurred 1 month before sampling. In addition, productive trees had more mycelium in the brûlé area than non-productive trees did. The ectomycorrhizal community composition inside the burnt areas was seasonally evaluated during a year. Ten mycorrhizal morphotypes were detected; T. melanosporum was the most abundant in productive and non-productive trees. Black truffle mycorrhizas were more abundant (mycorrhizal tips per unit of soil volume) in productive trees, and no seasonal variation was observed. The occurrence of black truffle mycorrhizas was significantly and positively correlated with the biomass of extraradical mycelium. The mycorrhizal community within the brûlé areas was significantly different between productive and non-productive trees, and no variation was detected between seasons. The assessment of the fungal vegetative structures in a mature plantation is of paramount importance to develop trufficulture methods based on the knowledge of the biological cycle of the fungus and its relationships with the associated ectomycorrhizal communities.

Black Truffle, a Hermaphrodite with Forced Unisexual Behaviour

The life cycle of the black truffle (Tuber melanosporum) includes a mating before sporulation: although the species is hermaphroditic, mating turns out to involve parents with very different features, that mostly behave as male or female only, suggesting that this species undergoes forced dioecism.

Fungi as a Source of Food

In this article, we review some of the best-studied fungi used as food sources, in particular, the cheese fungi, the truffles, and the fungi used for drink fermentation such as beer, wine, and sake. We discuss their history of consumption by humans and the genomic mechanisms of adaptation during artificial selection.

Mycorrhization of pecan (Carya illinoinensis) with black truffles: Tuber melanosporum and Tuber brumale

Pecan, Carya illinoinensis, is an economically important nut producing tree that can establish ectomycorrhizal symbiosis with a high diversity of fungi. In the southern USA, truffles (Tuber spp.) sometimes fruit prolifically in cultivated pecan orchards and regularly associate with pecan roots as ectomycorrhizae (ECMs). It has been demonstrated that some valuable European truffle species (e.g., Tuber borchii and Tuber aestivum) can form ECMs with pecan seedlings in nursery conditions. Thus, pecan may represent an attractive alternative host to forest trees for truffle growers given the potential for co-cropping truffles and pecans. To further explore the capacity of pecan to host truffle symbionts, pecan seedlings were inoculated with species of black truffles that are economically important in Europe, T. melanosporum and T. brumale. Ectomycorrhizae were characterized molecularly and their morphology was described in detail. Mycorrhization rates on pecan roots were assessed over a 2-year period. Tuber melanosporum and T. brumale produced well-formed ECMs with a level of root colonization in the first year of 37.3 and 34.5%, respectively. After 24 months, the level of mycorrhization increased for T. brumale (49.4%) and decreased for T. melanosporum (10.5%) inversely to that of non-target ECM greenhouse contaminants (e.g., Sphaerosporella brunnea, Trichophaea woolhopeia, Pulvinula constellatio). To assess whether mating types segregated in T. melanosporum as been reported for other host species, we amplified the mating-type locus from single T. melanosporum ECM belonging to different seedlings over a 2-year period. The two mating idiomorphs were nearly equally represented along the 2-year time span: MAT 1-1-1 decreased from 59.4% in the first year to 48.5% in the second year after inoculation. Data reported in this study add to knowledge on the mycorrhization of pecan trees with commercial truffles and has application to truffle and nut co-cropping systems.

New Insights into the Complex Relationship between Weight and Maturity of Burgundy Truffles (Tuber aestivum)

Despite an increasing demand for Burgundy truffles (Tuber aestivum), gaps remain in our understanding of the fungus’ overall lifecycle and ecology. Here, we compile evidence from three independent surveys in Hungary and Switzerland. First, we measured the weight and maturity of 2,656 T. aestivum fruit bodies from a three-day harvest in August 2014 in a highly productive orchard in Hungary. All specimens ranging between 2 and 755 g were almost evenly distributed through five maturation classes. Then, we measured the weight and maturity of another 4,795 T. aestivum fruit bodies harvested on four occasions between June and October 2015 in the same truffière. Again, different maturation stages occurred at varying fruit body size and during the entire fruiting season. Finally, the predominantly unrelated weight and maturity of 81 T. aestivum fruit bodies from four fruiting seasons between 2010 and 2013 in Switzerland confirmed the Hungarian results. The spatiotemporal coexistence of 7,532 small-ripe and large-unripe T. aestivum, which accumulate to ~182 kg, differs from species-specific associations between the size and ripeness that have been reported for other mushrooms. Although size-independent truffle maturation stages may possibly relate to the perpetual belowground environment, the role of mycelial connectivity, soil property, microclimatology, as well as other abiotic factors and a combination thereof, is still unclear. Despite its massive sample size and proof of concept, this study, together with existing literature, suggests consideration of a wider ecological and biogeographical range, as well as the complex symbiotic fungus-host interaction, to further illuminate the hidden development of belowground truffle fruit bodies.

Fine-scale genetic structure of natural Tuber aestivum sites in southern Germany

Although the Burgundy truffle (Tuber aestivum) is an ectomycorrhizal fungus of important economic value, its subterranean life cycle and population biology are still poorly understood. Here, we determine mating type and simple sequence repeat (SSR) maternal genotypes of mapped fruiting bodies to assess their genetic structure within two naturally colonized forest sites in southern Germany. Forty-one genotypes were identified from 112 fruiting bodies. According to their mating types, the maternal genotypes were aggregated only in one population. Genotypic diversity of individuals that mostly were small and occurred in 1 out of 2 years of sampling was high. Although these results suggested a ruderal colonization strategy, some genets spread several hundred meters. This result indicates that, besides sexual spore dispersal, vegetative growth or spreading by mycelial propagules contributes to dissemination. In one site, fewer individuals with a tendency to expand genets belonging to only one genetic group were observed. In the second site, numerous small individuals were found and were grouped into two clearly differentiated genetic groups that were spatially intermingled. Forest characteristics and disturbances are possible reasons for the observed genetic patterns. Our findings contribute to a better understanding of the biology of one of the most widespread and commercially important truffle species. This knowledge is critical for establishing and maintaining sustainable long-term truffle cultivations.

Soil microbial communities of three major Chinese truffles in southwest China

Tuber pseudoexcavatum, Tuber sinoaestivum, and Tuber indicum are the 3 most important truffles growing in southeast China; however, their cultivation is still inefficient owing to the lack of understanding regarding the composition and function of the bacterial and fungal communities from the soils around the fruit bodies and the ectomycorrhiza of these truffles. The aim of this study was to disclose the microbial communities in truffle-producing soils in Huidong County, Sichuan, China, by using barcoded pyrosequencing. Approximately 350 000 quality-controlled sequences were obtained and grouped into 14 025 bacterial operational taxonomic units (OTUs) and 4385 fungal OTUs, which included 29 bacterial and 7 fungal phyla, respectively. The bacterial genus Acidobacterium and fungal genera Modicella, Pseudogymnoascus, and Mortierella were significantly more abundant in the control soils than in the truffle-producing soils (P < 0.05), while the bacterial genus Sphingomonas (Alphaproteobacteria) and arbuscular mycorrhizal fungal genus Glomus were significantly enriched in truffle-producing soil than in the control (P < 0.05), indicating their different roles within truffle grounds. Notably, some nonfungal organisms detected by 18S rDNA pyrosequencing were of high abundance, among which Cercozoa and Ochrophyta were significantly (P < 0.05) more abundant in truffle soils than in control soils, indicating their interactions with truffles.

Characterization of the reproductive mode and life cycle of the whitish truffle T. borchii

Truffles are the fruiting structures of ascomycetes in the genus Tuber. Because of their economic importance, truffles have been cultivated for many years using artificially inoculated host plants. Nevertheless, the life cycle and reproductive mode of Tuber spp. are still poorly understood. In filamentous ascomycetes, sexual reproduction is genetically controlled by the mating-type (MAT) locus. Among Tuber spp., the MAT locus has been recently characterized in the black truffles Tuber melanosporum and Tuber indicum. Here, by using sequence information derived from these species and from a Tuber borchii expressed sequence tag (EST) showing similarity to the mat1 gene of Alternaria brassicicola, we embarked on a chromosome-walking procedure to sequence the complete MAT region of T. borchii. This fungus produces highly commercialized whitish truffles and represents a model species for addressing basic questions concerning the life cycle of Tuber spp. We show that T. borchii is heterothallic, as its MAT locus is organized into two idiomorphs, each harbored by different mycelial strains. The alignment of the MAT locus from black truffles and T. borchii reveals that extensive sequence rearrangements and inversions occurred between these species. Moreover, by coupling mating-type analyses to karyological observation, we show that mycelia isolated from ascocarps and mycorrhizae are formed by homokaryotic hyphae.

Bacteria of the genus Rhodopseudomonas (Bradyrhizobiaceae): obligate symbionts in mycelial cultures of the black truffles Tuber melanosporum and Tuber brumale

BACKGROUND

This work aimed at characterizing 12 isolates of the genus Tuber including Tuber melanosporum (11 isolates) and Tuber brumale (one isolate). This was done using internal transcribed spacer (ITS) sequences, confirming their origin.

RESULTS

Analysis of their mating type revealed that both MAT1-1 and MAT1-2 exist within these isolates (with 3 and 8 of each, respectively). We observed that each of these cultures was consistently associated with one bacterium that was intimately linked to fungal growth. These bacterial associates failed to grow in the absence of fungus. We extracted DNA from bacterial colonies in the margin of mycelium and sequenced a nearly complete 16S rDNA gene and a partial ITS fragment. We found they all belonged to the genus Rhodopseudomonas, fitting within different phylogenetic clusters. No relationships were evidenced between bacterial and fungal strains or mating types. Rhodopseudomonas being a sister genus to Bradyrhizobium, we tested the nodulation ability of these bacteria on a promiscuously nodulating legume (Acacia mangium), without success. We failed to identify any nifH genes among these isolates, using two different sets of primers.

CONCLUSIONS

While the mechanisms of interaction between Tuber and Rhodopseudomonas remain to be elucidated, their interdependency for in vitro growth seems a novel feature of this fungus.

SSR-based identification of genetic groups within European populations of Tuber aestivum Vittad

Tuber species are ectomycorrhizal ascomycetes establishing relationships with different host trees and forming hypogeous fruiting bodies known as truffles. Among Tuber species, Tuber aestivum Vittad. has a wide distributional range being found naturally all over Europe. Here, we performed large-scale population genetic analyses in T. aestivum to (i) investigate its genetic diversity at the European scale, (ii) characterize its genetic structure and test for the presence of ecotypes and (iii) shed light into its demographic history. To reach these goals, 230 ascocarps from different populations were genotyped using 15 polymorphic simple sequence repeat markers. We identified 181 multilocus genotypes and four genetic groups which did not show a clear geographical separation; although, one of them was present exclusively in Southeast France, Italy and Spain. Fixation index values between pairs of genetic groups were generally high and ranged from 0.29 to 0.45. A significant deficit of heterozygosity indicated a population expansion instead of a recent population bottleneck, suggesting that T. aestivum is not endangered in Europe, not even in Mediterranean regions. Our study based on a large-scale population genetic analysis suggests that genetically distinct populations and likely ecotypes within T. aestivum are present. In turn, this study paves the way to future investigations aimed at addressing the biological and/or ecological factors that have concurred in shaping the population genetic structure of this species. Present results should also have implications for the truffle market since defining genetic markers are now possible at least for some specific T. aestivum genetic groups.

Identification and In Situ Distribution of a Fungal Gene Marker: The Mating Type Genes of the Black Truffle

Truffles are ectomycorrhizal fungi harvested mainly in human managed agroforestry ecosystems. Truffle production in truffle orchards faces two important bottlenecks or challenges: the initiation of the sexual reproduction and the growth of the ascocarps during several months. The black Périgord truffle, Tuber melanosporum, is a heterothallic species and the mating type genes (MAT1-1 and M1T1-2) have been characterized. In this context, the unraveling of the T. melanosporum mating type strains distribution in truffle orchards is a critical starting point to provide new insights into its sexual reproduction. The aim of this chapter is to present the protocol used to characterize the T. melanosporum mating type present in a truffle orchard from ascocarps, hazel mycorrhizal root tips, and/or soil samples, by polymerase chain reactions using specific primers for those genes, but it can be adapted for other fungal species.

Diversity, population genetics, and evolution of macrofungi associated with animals

Macrofungi refers to all fungi that produce visible fruiting bodies. These fungi are evolutionarily and ecologically very divergent. Evolutionarily, they belong to two main phyla, Ascomycota and Basidiomycota, and many of them have relatives that cannot form visible fruiting bodies. Ecologically, macrofungi can be associated with dead organic matter, plants, and animals. Here we review our current understanding of population structure and biogeography of macrofungi associated with animals. Their interactions, functions, and patterns of coevolution are described and discussed. Our focus is on studies using molecular markers. Our analyses suggest that the types of fungi-animal associations play an important role in the structure of these animal-associated fungal populations.