Truffle brûlé: an efficient fungal life strategy

Both a Growth-Defence Trade-Off and a Leaf N: P Stoichiometric Imbalance Can Account For Ectomycorrhizal Hyphae Inhibited Non-Host Plant Growth

Previous studies indicated that ectomycorrhizal (EM) hyphae can access non-host plant roots and inhibit their growth, with the underlying mechanisms remaining largely unexplored. This study established a tripartite co-culture system consisting of EM fungi supported Quercus Mongolica and non-host plants Arabidopsis thaliana or Setaria italica. Plant growth, nutrient concentrations, transcriptome, microbial communities and fatty acids were determined to comprehensively understand the effects of EM on non-host plants. The results showed that roots of non-host plants were colonised by EM hyphae of Scleroderma, which significantly inhibited non-host growth and decreased their leaf [N], but increased leaf [P] and leaf free fatty acid concentrations. A small amount of 15N was transferred from non-host to Q. mongolica leaves. Foliar N application alleviated EM hyphae inhibited non-host plant growth. Genes associated with plant-pathogen interaction and defence hormone responses were activated, but those involved in photosynthesis and growth hormone responses were suppressed in A. thaliana leaves. Our findings suggest that a growth-defence trade-off, in conjunction with a leaf N: P stoichiometric imbalance, may explain the observed inhibition of non-host plant growth by EM hyphae. This study provides insights into ectomycorrhiza mediated host and non-host plants interaction, which is important for plant community establishment.

Tuber cumberlandense and T. canirevelatum, two new edible Tuber species from eastern North America discovered by truffle-hunting dogs

Ectomycorrhizal fungi in the genus Tuber form hypogeous fruiting bodies called truffles. Many Tuber species are highly prized due to their edible and aromatic ascomata. Historically, there has been attention on cultivating and selling European truffle species, but there is growing interest in cultivating, wild-harvesting, and selling species of truffles endemic to North America. North America has many endemic Tuber species that remain undescribed, including some that have favorable culinary qualities. Here, we describe two such Tuber species from eastern North America. Maximum likelihood and Bayesian phylogenetic analyses of ITS (internal transcribed spacer), tef1 (translation elongation factor 1-alpha), and rpb2 (second largest subunit of RNA polymerase II) sequences were used to place these species within a phylogenetic context. We coupled these data with morphological analyses and volatile analyses based on gas chromatography-mass spectrometry. Tuber cumberlandense, sp. nov. (previously referred to as Tuber sp. 66), is a member of the Rufum clade that has been opportunistically harvested for commercial sale from T. melanosporum orchards across eastern North America. Tuber canirevelatum, sp. nov. belongs in the Macrosporum clade and thus far is only known from eastern Tennessee, USA. Both new species were discovered with the assistance of trained truffle dogs. The volatile profiles of T. canirevelatum and T. cumberlandense were measured in order to characterize aromas based on the chemical compounds produced by these fungi. Ascomata from both species were enriched in acetone, dimethyl sulfide, 1-(methylthio)-1-propene, and 1-(methylthio)propane. In this work, we celebrate and encourage the use of trained truffle-hunting dogs for fungal biodiversity discovery and research.

Changes in Black Truffle (Tuber melanosporum) Aroma during Storage under Different Conditions

The enticing aroma of truffles is a key factor for their culinary value. Although all truffle species tend to be pricy, the most intensely aromatic species are the most sought after. Research into the aroma of truffles encompasses various disciplines including chemistry, biology, and sensory science. This study focusses on the chemical composition of the aroma of black truffles (Tuber melanosporum) and the changes occurring under different storage conditions. For this, truffle samples were stored under different treatments, at different temperatures, and measured over a total storage time of 12 days. Measurements of the truffle aroma profiles were taken with SPME/GC-MS at regular intervals. To handle the ample data collected, a systematic approach utilizing multivariate data analysis techniques was taken. This approach led to a vast amount of data which we made publicly available for future exploration. Results reveal the complexity of aroma changes, with 695 compounds identified, highlighting the need for a comprehensive understanding. Principal component analyses offer initial insights into truffle composition, while individual compounds may serve as markers for age (formic acid, 1-methylpropyl ester), freshness (2-Methyl-1-propanal; 1-(methylthio)-propane), freezing (tetrahydrofuran), salt treatment (1-chloropentane), or heat exposure (4-hydroxy-3-methyl-2-butanone). This research suggests that heat treatment or salt contact significantly affects truffle aroma, while freezing and cutting have less pronounced effects in comparison. The enrichment of compounds showing significant changes during storage was investigated with a metabolomic pathway analysis. The involvement of some of the enriched compounds on the pyruvate/glycolysis and sulfur pathways was shown.

Diversity and Network Relationship Construction of Soil Fungal Communities in Lactarius hatsudake Tanaka Orchard during Harvest

Lactarius hatsudake Tanaka is a mycorrhizal edible mushroom with rich economic and nutritional value. Although it is artificially planted, its yield is unstable. Soil fungi, including L. hatsudake, coexist with many other microorganisms and plants. Therefore, complex microbial communities have an influence on the fruiting body formation of L. hatsudake. L. hatsudake and its interactions with the rest of the fungal community over time are not completely understood. In this study, we performed high-throughput sequencing of microorganisms in the basal soil of the fruiting body (JT), mycorrhizosphere soil (JG), and non-mushroom-producing soil (CK) in a 6-year-old L. hatsudake plantation at harvest. The results showed that the soil of the L. hatsudake plantation was rich in fungal communities and a total of 10 phyla, 19 classes, 53 orders, 90 families, 139 genera, and 149 species of fungi were detected. At the phylum level, the major groups were Basidiomycota and Ascomycota. At the genus level, the dominant groups were Lactarius, Trichoderma, Suillus, and Penicillium. Among them, L. hatsudake had an absolute dominant position in the soil fungal community of the plantation, and was the only group of Lactarius in the plantation soil. Penicillium cryptum and Penicillium adametzii were unique to the JT soil sample. Chaetopsphaeria, Myxocephala, Devriesia, and Psathyrella were positively correlated with L. hatsudake. In the constructed fungal network, the total number of nodes were ranked in descending order as JG (441) > CK (405) > JT (399), while the total number of edges were ranked in descending order as CK (1360) > JG (647) > JT (586). Analysis of the fungal assembly process revealed that groups CK and JG have determinative processes that dominated community building, while the JT group exhibited a dominant random process with a 0.60 probability. The results indicated that L. hatsudake was successfully colonized in the plantation soil. During harvest, the CK group exhibited the largest network size and the most complex fungal interactions, while the fungal community structure in the mushroom cultivation zone (JT and JG) was stable and less susceptible to external environmental interference. L. hatsudake affects the fungal community in the soil surrounding its fruiting body.

Aromatic Plants and Their Associated Arbuscular Mycorrhizal Fungi Outcompete Tuber melanosporum in Compatibility Assays with Truffle-Oaks

The high value of black truffle recompenses the slow growth of the fungus when established in the field. Adding a secondary crop, such as medicinal and aromatic plants (MAPs), could further enhance the sustainability of truffle production agro-forest systems. The dual cultures of ectomycorrhizal truffle-oak seedlings and MAPs (lavender, thyme, and sage) previously inoculated and non-inoculated with native arbuscular mycorrhizal fungi (AMF), were established to evaluate plant-fungi relationships. After 12 months in a shadehouse, plants' growth, mycorrhizal colonization, and extraradical soil mycelium (both of Tuber melanosporum and AMF) were measured. Overall, truffle-oaks' growth was negatively affected by the presence of MAPs, especially when inoculated with AMF. In turn, the presence of truffle-oaks barely affected the co-cultured MAPs, and only lavenders showed a significant growth reduction. All AMF-inoculated MAPs showed higher shoot and root biomass than non-inoculated ones. Compared to truffle-oaks growing alone, the presence of co-cultured MAPs, especially when they were AMF-inoculated, significantly decreased both the ectomycorrhizas and soil mycelium of T. melanosporum. These results reveal the strong competition between AMF and T. melanosporum and warn about the need for the protection of intercropping plants and their associated symbiotic fungi to avoid reciprocal counterproductive effects in mixed truffle-oak-AMF-MAP plantations.

The fall of the summer truffle: Recurring hot, dry summers result in declining fruitbody production of Tuber aestivum in Central Europe

Global warming is pushing populations outside their range of physiological tolerance. According to the environmental envelope framework, the most vulnerable populations occur near the climatic edge of their species' distributions. In contrast, populations from the climatic center of the species range should be relatively buffered against climate warming. We tested this latter prediction using a combination of linear mixed effects and machine learning algorithms on an extensive, citizen-scientist generated dataset on the fruitbody productivity of the Burgundy (aka summer) truffle (Tuber aestivum Vittad.), a keystone, ectomycorrhizal tree-symbiont occurring on a wide range of temperate climates. T. aestivum's fruitbody productivity was monitored at 3-week resolution over up to 8 continuous years at 20 sites distributed in the climatic center of its European distribution in southwest Germany and Switzerland. We found that T. aestivum fruitbody production is more sensitive to summer drought than would be expected from the breadth of its species' climatic niche. The monitored populations occurring nearly 5°C colder than the edge of their species' climatic distribution. However, interannual fruitbody productivity (truffle mass year^-1 ) fell by a median loss of 22% for every 1°C increase in summer temperature over a site's 30-year mean. Among the most productive monitored populations, the temperature sensitivity was even higher, with single summer temperature anomalies of 3°C sufficient to stop fruitbody production altogether. Interannual truffle productivity was also related to the phenology of host trees, with ~22 g less truffle mass for each 1-day reduction in the length of the tree growing season. Increasing summer drought extremes are therefore likely to reduce fruiting among summer truffle populations throughout Central Europe. Our results suggest that European T. aestivum may be a mosaic of vulnerable populations, sensitive to climate-driven declines at lower thresholds than implied by its species distribution model.

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.

Non-host plants: Are they mycorrhizal networks players?

Common mycorrhizal networks (CMNs) that connect individual plants of the same or different species together play important roles in nutrient and signal transportation, and plant community organization. However, about 10% of land plants are non-mycorrhizal species with roots that do not form any well-recognized types of mycorrhizas; and each mycorrhizal fungus can only colonize a limited number of plant species, resulting in numerous non-host plants that could not establish typical mycorrhizal symbiosis with a specific mycorrhizal fungus. If and how non-mycorrhizal or non-host plants are able to involve in CMNs remains unclear. Here we summarize studies focusing on mycorrhizal-mediated host and non-host plant interaction. Evidence has showed that some host-supported both arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) hyphae can access to non-host plant roots without forming typical mycorrhizal structures, while such non-typical mycorrhizal colonization often inhibits the growth but enhances the induced system resistance of non-host plants. Meanwhile, the host growth is also differentially affected, depending on plant and fungi species. Molecular analyses suggested that the AMF colonization to non-hosts is different from pathogenic and endophytic fungi colonization, and the hyphae in non-host roots may be alive and have some unknown functions. Thus we propose that non-host plants are also important CMNs players. Using non-mycorrhizal model species Arabidopsis, tripartite culture system and new technologies such as nanoscale secondary ion mass spectrometry and multi-omics, to study nutrient and signal transportation between host and non-host plants via CMNs may provide new insights into the mechanisms underlying benefits of intercropping and agro-forestry systems, as well as plant community establishment and stability.

Truffle species strongly shape their surrounding soil mycobiota in a Pinus armandii forest

Truffles contribute to crucial soil systems dynamics, being involved in plentiful ecological functions important for ecosystems. Despite this, the interactions between truffles and their surrounding mycobiome remain unknown. Here, we investigate soil mycobiome differences between two truffle species, Tuber indicum (Ti) and Tuber pseudohimalayense (Tp), and their relative influence on surrounding soil mycobiota. Using traditional chemical analysis and ITS Illumina sequencing, we compared soil nutrients and the mycobiota, respectively, in soil, gleba, and peridium of the two truffle species inhabiting the same Pinus armandii forest in southwestern China. Tp soil was more acidic (pH 6.42) and had a higher nutrient content (total C, N content) than Ti soil (pH 6.62). Fungal richness and diversity of fruiting bodies (ascomata) and surrounding soils were significantly higher in Tp than in Ti. Truffle species recruited unique soil mycobiota around their ascomata: in Ti soil, fungal taxa, including Suillus, Alternaria, Phacidium, Mycosphaerella, Halokirschsteiniothelia, and Pseudogymnoascus, were abundant, while in Tp soil species of Melanophyllum, Inocybe, Rhizopogon, Rhacidium, and Lecanicillium showed higher abundances. Three dissimilarity tests, including adonis, anosim, and MRPP, showed that differences in fungal community structure between the two truffle species and their surrounding soils were stronger in Tp than in Ti, and these differences extended to truffle tissues (peridium and gleba). Redundancy analysis (RDA) further demonstrated that correlations between soil fungal taxa and soil properties changed from negative (Tp) to positive (Ti) and shifted from a moisture-driven (Tp) to a total N-driven (Ti) relationship. Overall, our results shed light on the influence that truffles have on their surrounding soil mycobiome. However, further studies are required on a broader range of truffle species in different soil conditions in order to determine causal relationships between truffles and their soil mycobiome.

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.

Virtual Truffle Hunting—A New Method of Burgundy Truffle (Tuber aestivum Vittad.) Site Typing

The aim of this study was to enable searches for truffles (Tuber spp.), particularly the Burgundy truffle (T. aestivum Vittad.), to be carried out in forests based on a method that has been constantly developed since 2007 by the Forest Research Institute. The method is termed “Virtual Truffle Hunting” and it takes 12 parameters into account: bedrock, soil pH, Ca+ and CaCO3 content in soil, C/N ratio, soil structure, altitude of terrain, type of forest site, forest structure, the Burgundy truffle host trees, and the presence of particular species including orchids and insects. A simple “Virtual Truffle Hunting” software has also been developed, which makes the use of the method easy, fast, and effective. This method is to ascertain the truffle potential for all areas in which digital maps are not available. In 2015, the method was tested in 20 sites, representing forests in 5 Polish macroregions. Hunting for hypogeous fungi was conducted from June to October with the help of trained dogs. Thanks to this method, 14 new truffle sites were found. The knowledge of environmental conditions conducive to the Burgundy truffle growth enabled us to form an effective tool in order to identify new sites of truffle presence.

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.

Roles of Fungal Volatiles from Perspective of Distinct Lifestyles in Filamentous Fungi

Volatile compounds (VOCs) are not only media for communication within a species but also effective tools for sender to manipulate behavior and physiology of receiver species. Although the influence of VOCs on the interactions among organisms is evident, types of VOCs and specific mechanisms through which VOCs work during such interactions are only beginning to become clear. Here, we review the fungal volatile compounds (FVOCs) and their impacts on different recipient organisms from perspective of distinct lifestyles of the filamentous fungi. Particularly, we discuss the possibility that different lifestyles are intimately associated with an ability to produce a repertoire of FVOCs in fungi. The FVOCs discussed here have been identified and analyzed as relevant signals under a range of experimental settings. However, mechanistic insight into how specific interactions are mediated by such FVOCs at the molecular levels, amidst complex community of microbes and plants, requires further testing. Experimental designs and advanced technologies that attempt to address this question will facilitate our understanding and applications of FVOCs to agriculture and ecosystem management.

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.

Exogenous Nitric Oxide and Phosphorus Stress Affect the Mycorrhization, Plant Growth, and Associated Microbes of Carya illinoinensis Seedlings Colonized by Tuber indicum

In the artificial cultivation of truffles, ectomycorrhizal colonization level, host plant quality, and the associated microbes in the rhizosphere soil are vitally important. To explore the effects of nitric oxide (NO) and phosphorus (P) stress on the early symbiosis of truffles and host plants, different concentrations of exogenous NO donor sodium nitroprusside (SNP) and P were applied to Carya illinoinensis seedlings inoculated with the Chinese black truffle (Tuber indicum). The growth of T. indicum-mycorrhized seedlings and their mycorrhizal colonization rate were investigated. Additionally, the denitrifying bacterial community harboring NO reductase (norB) genes and the fungal community in the rhizosphere of the host were analyzed by high-throughput sequencing. The results showed that the colonization rate of T. indicum was significantly influenced by SNP treatments and P stress, with the highest level being obtained when the SNP was 100 μmol/L under low P stress (5 μmol/L). Treatment with 100 μmol/L SNP alone also increased the colonization rate of T. indicum and had positive effects on the plant height, stem circumference, biomass, root-shoot ratio and root POD activity of the seedlings at different times after inoculation. Under low P stress, the 100 μmol/L SNP increased the richness of the norB-type denitrifying bacterial community. Interestingly, the diversity and richness of norB-type denitrifying bacteria were significantly positively correlated with the colonization rate of T. indicum. SNP treatments under low P stress altered the abundance of some dominant taxa such as Alphaproteobacteria, Gammaproteobacteria, Pseudomonas, Ensifer, and Sulfitobacter. Evaluation of the fungal community in the rhizosphere revealed that 100 μmol/L SNP treatment alone had no noticeable effect on their richness and diversity, but it did shape the abundance of some fungi. Buellia, Podospora, Phaeoisaria, Ascotaiwania, and Lophiostoma were more abundant following exogenous NO application, while the abundance of Acremonium, Monographella, and Penicillium were decreased. Network analysis indicated that T. indicum was positively and negatively correlated with some fungal genera when treated with 100 μmol/L SNP. Overall, these results revealed how exogenous NO and P stress influence the symbiosis of truffles and host plants, and indicate that application of SNP treatments has the potential for ectomycorrhizal synthesis and truffle cultivation.

Soil spore bank in Tuber melanosporum: up to 42% of fruitbodies remain unremoved in managed truffle grounds

Fungi fruiting hypogeously are believed to form spore banks in soil especially because some fruitbodies are not removed by animals. However, little is known on the proportion of fruitbodies that are not removed by animals. We took advantage of the brûlé phenomenon, which allows delineation of the mycelium distribution, to assess the proportion of unremoved black truffle (Tuber melanosporum) fruitbodies in the context of plantations where fruitbodies are actively sought and harvested by truffle growers. We inspected portions of the brûlés after the harvest season to find unremoved fruitbodies. On average, from six truffle grounds in which a total of 38 brûlés were investigated, unremoved fruitbodies represented 33% of the whole fruitbody production (42% when averaging all the brûlés). We discuss this value and its high variability among truffle grounds. Beyond the local and variable accidental reasons that may lead to this high proportion, we speculate that the formation of some undetectable fruitbodies may be under selection pressure, given the reproductive biology of T. melanosporum.

LC-MS-Based Metabolomic Approach Revealed the Significantly Different Metabolic Profiles of Five Commercial Truffle Species

Truffles are ascomycetous ectomycorrhizal fungi that have elevated status in the culinary field due to their unique aroma and taste as well as their nutritional value and potential biological activities. Tuber melanosporum, T. indicum, T. panzhihuanense, T. sinoaestivum, and T. pseudoexcavatum are five commercial truffle species mainly distributed in Europe or China. In this study, an untargeted metabolomics technology based on an ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method was applied to analyze the metabolic profiles and variations among these five truffle species. In our results, a total of 2376 metabolites were identified under positive ion mode, of which 1282 had significantly differential amounts and covered 110 pathways or metabolisms. Principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) revealed a clear separation from each of these five truffles, indicating a significantly different metabolic profile among them, with the biggest difference between T. melanosporum and the other four truffles. The differential metabolites covered various chemical categories, and a detailed analysis was performed for nine metabolic categories, including amino acids, saccharides and nucleosides, organic acids, alkaloids, flavonoids, carnitines, phenols and alcohols, esters, and sulfur compounds. For each of the nine categories, most of metabolites predominantly accumulated in T. melanosporum compared with the other four truffles. Meanwhile, there were significant differences of the average ion intensity in each category among the five truffles, e.g., higher amounts of amino acids was detected in T. panzhihuanense and T. pseudoexcavatum; T. indicum contained significantly more carnitines, while there were more alkaloids in T. melanosporum. Additionally, some metabolites with biological activities were discussed for each category, such as acetyl-L-carnitine, adenine, neobavaisoflavone, and anandamide. Generally, this study may provide the valuable information regarding the variation of the metabolic composition of these five commercial truffle species, and the biological significance of these metabolites was uncovered to explore the metabolic mechanisms of truffles, which would be helpful for further research on the compounds and potential biological functions in truffles that have not yet been investigated.

Mycorrhization of Quercus acutissima with Chinese black truffle significantly altered the host physiology and root-associated microbiomes

Background

Our aim was to explore how the ectomycorrhizae of an indigenous tree,Quercus acutissima, with a commercial truffle, Chinese black truffle (Tuber indicum), affects the host plant physiology and shapes the associated microbial communities in the surrounding environment during the early stage of symbiosis.

Methods

To achieve this, changes in root morphology and microscopic characteristics, plant physiology indices, and the rhizosphere soil properties were investigated when six-month-old ectomycorrhizae were synthesized. Meanwhile, next-generation sequencing technology was used to analyze the bacterial and fungal communities in the root endosphere and rhizosphere soil inoculated with T. indicum or not.

Results

The results showed that colonization by T. indicum significantly improved the activity of superoxide dismutase in roots but significantly decreased the root activity. The biomass, leaf chlorophyll content and root peroxidase activity did not obviously differ. Ectomycorrhization of Q. acutissima with T. indicum affected the characteristics of the rhizosphere soil, improving the content of organic matter, total nitrogen, total phosphorus and available nitrogen. The bacterial and fungal community composition in the root endosphere and rhizosphere soil was altered by T. indicum colonization, as was the community richness and diversity. The dominant bacteria in all the samples were Proteobacteria and Actinobacteria, and the dominant fungi were Eukaryota_norank, Ascomycota, and Mucoromycota. Some bacterial communities, such as Streptomyces, SM1A02, and Rhizomicrobium were more abundant in the ectomycorrhizae or ectomycorrhizosphere soil. Tuber was the second-most abundant fungal genus, and Fusarium was present at lower amounts in the inoculated samples.

Discussion

Overall, the symbiotic relationship between Q. acutissima and T. indicum had an obvious effect on host plant physiology, soil properties, and microbial community composition in the root endosphere and rhizosphere soil, which could improve our understanding of the symbiotic relationship between Q. acutissima and T. indicum, and may contribute to the cultivation of truffle.

Tuber borchii Shapes the Ectomycorrhizosphere Microbial Communities of Corylus avellana

In this study, eight-month-old ectomycorrhizae of Tuber borchii with Corylus avellana were synthesized to explore the influence of T. borchii colonization on the soil properties and the microbial communities associated with C. avellana during the early symbiotic stage. The results showed that the bacterial richness and diversity in the ectomycorrhizae were significantly higher than those in the control roots, whereas the fungal diversity was not changed in response to T. borchii colonization. Tuber was the dominant taxon (82.97%) in ectomycorrhizae. Some pathogenic fungi, including Ilyonectria and Podospora, and other competitive mycorrhizal fungi, such as Hymenochaete, had significantly lower abundance in the T. borchii inoculation treatment. It was found that the ectomycorrhizae of C. avellana contained some more abundant bacterial genera (e.g., Rhizobium, Pedomicrobium, Ilumatobacter, Streptomyces, and Geobacillus) and fungal genera (e.g., Trechispora and Humicola) than the control roots. The properties of rhizosphere soils were also changed by T. borchii colonization, like available nitrogen, available phosphorus and exchangeable magnesium, which indicated a feedback effect of mycorrhizal synthesis on soil properties. Overall, this work highlighted the interactions between the symbionts and the microbes present in the host, which shed light on our understanding of the ecological functions of T. borchii and facilitate its commercial cultivation.

Fungal Planet description sheets: 716-784

Novel species of fungi described in this study include those from various countries as follows: Australia, Chaetopsina eucalypti on Eucalyptus leaf litter, Colletotrichum cobbittiense from Cordyline stricta × C. australis hybrid, Cyanodermella banksiae on Banksia ericifolia subsp. macrantha, Discosia macrozamiae on Macrozamia miquelii, Elsinoë banksiigena on Banksia marginata, Elsinoë elaeocarpi on Elaeocarpus sp., Elsinoë leucopogonis on Leucopogon sp., Helminthosporium livistonae on Livistona australis, Idriellomyces eucalypti (incl. Idriellomyces gen. nov.) on Eucalyptus obliqua, Lareunionomyces eucalypti on Eucalyptus sp., Myrotheciomyces corymbiae (incl. Myrotheciomyces gen. nov., Myrotheciomycetaceae fam. nov.), Neolauriomyces eucalypti (incl. Neolauriomyces gen. nov., Neolauriomycetaceae fam. nov.) on Eucalyptus sp., Nullicamyces eucalypti (incl. Nullicamyces gen. nov.) on Eucalyptus leaf litter, Oidiodendron eucalypti on Eucalyptus maidenii, Paracladophialophora cyperacearum (incl. Paracladophialophoraceae fam. nov.) and Periconia cyperacearum on leaves of Cyperaceae, Porodiplodia livistonae (incl. Porodiplodia gen. nov., Porodiplodiaceae fam. nov.) on Livistona australis, Sporidesmium melaleucae (incl. Sporidesmiales ord. nov.) on Melaleuca sp., Teratosphaeria sieberi on Eucalyptus sieberi, Thecaphora australiensis in capsules of a variant of Oxalis exilis. Brazil, Aspergillus serratalhadensis from soil, Diaporthe pseudoinconspicua from Poincianella pyramidalis, Fomitiporella pertenuis on dead wood, Geastrum magnosporum on soil, Marquesius aquaticus (incl. Marquesius gen. nov.) from submerged decaying twig and leaves of unidentified plant, Mastigosporella pigmentata from leaves of Qualea parviflorae, Mucor souzae from soil, Mycocalia aquaphila on decaying wood from tidal detritus, Preussia citrullina as endophyte from leaves of Citrullus lanatus, Queiroziella brasiliensis (incl. Queiroziella gen. nov.) as epiphytic yeast on leaves of Portea leptantha, Quixadomyces cearensis (incl. Quixadomyces gen. nov.) on decaying bark, Xylophallus clavatus on rotten wood. Canada, Didymella cari on Carum carvi and Coriandrum sativum. Chile, Araucasphaeria foliorum (incl. Araucasphaeria gen. nov.) on Araucaria araucana, Aspergillus tumidus from soil, Lomentospora valparaisensis from soil. Colombia, Corynespora pseudocassiicola on Byrsonima sp., Eucalyptostroma eucalyptorum on Eucalyptus pellita, Neometulocladosporiella eucalypti (incl. Neometulocladosporiella gen. nov.) on Eucalyptus grandis × urophylla, Tracylla eucalypti (incl. Tracyllaceae fam. nov., Tracyllalales ord. nov.) on Eucalyptus urophylla. Cyprus, Gyromitra anthracobia (incl. Gyromitra subg. Pseudoverpa) on burned soil. Czech Republic, Lecanicillium restrictum from the surface of the wooden barrel, Lecanicillium testudineum from scales of Trachemys scripta elegans. Ecuador, Entoloma yanacolor and Saproamanita quitensis on soil. France, Lentithecium carbonneanum from submerged decorticated Populus branch. Hungary, Pleuromyces hungaricus (incl. Pleuromyces gen. nov.) from a large Fagus sylvatica log. Iran, Zymoseptoria crescenta on Aegilops triuncialis. Malaysia, Ochroconis musicola on Musa sp. Mexico, Cladosporium michoacanense from soil. New Zealand , Acrodontium metrosideri on Metrosideros excelsa, Polynema podocarpi on Podocarpus totara, Pseudoarthrographis phlogis (incl. Pseudoarthrographis gen. nov.) on Phlox subulata. Nigeria, Coprinopsis afrocinerea on soil. Pakistan, Russula mansehraensis on soil under Pinus roxburghii. Russia, Baorangia alexandri on soil in deciduous forests with Quercus mongolica. South Africa, Didymocyrtis brachylaenae on Brachylaena discolor. Spain, Alfaria dactylis from fruit of Phoenix dactylifera, Dothiora infuscans from a blackened wall, Exophiala nidicola from the nest of an unidentified bird, Matsushimaea monilioides from soil, Terfezia morenoi on soil. United Arab Emirates, Tirmania honrubiae on soil. USA, Arxotrichum wyomingense (incl. Arxotrichum gen. nov.) from soil, Hongkongmyces snookiorum from submerged detritus from a fresh water fen, Leratiomyces tesquorum from soil, Talaromyces tabacinus on leaves of Nicotiana tabacum. Vietnam, Afroboletus vietnamensis on soil in an evergreen tropical forest, Colletotrichum condaoense from Ipomoea pes-caprae. Morphological and culture characteristics along with DNA barcodes are provided.

Chinese Black Truffle (Tuber indicum) Alters the Ectomycorrhizosphere and Endoectomycosphere Microbiome and Metabolic Profiles of the Host Tree Quercus aliena

Truffles are one group of the most famous ectomycorrhizal fungi in the world. There is little information on the ecological mechanisms of truffle ectomycorrhizal synthesis in vitro. In this study, we investigated the ecological effects of Tuber indicum – Quercus aliena ectomycorrhizal synthesis on microbial communities in the host plant roots and the surrounding soil using high-throughput sequencing and on the metabolic profiles of host plant roots using metabolomics approaches. We observed an increase in the diversity and richness of prokaryotic communities and a decrease in richness of fungal communities in the presence of T. indicum. The microbial community structures in the host roots and the surrounding soil were altered by ectomycorrhizal synthesis in the greenhouse. Bacterial genera Pedomicrobium, Variibacter, and Woodsholea and fungal genera Aspergillus, Phaeoacremonium, and Pochonia were significantly more abundant in ectomycorhizae and the ectomycorrhizosphere soil compared with the corresponding T. indicum-free controls (P < 0.05). Truffle-colonization reduced the abundance of some fungal genera surrounding the host tree, such as Acremonium, Aspergillus, and Penicillium. Putative prokaryotic metabolic functions and fungal functional groups (guilds) were also differentiated by ectomycorrhizal synthesis. The ectomycorrhizal synthesis had great impact on the measured soil physicochemical properties. Metabolic profiling analysis uncovered 55 named differentially abundant metabolites between the ectomycorhizae and the control roots, including 44 upregulated and 11 downregulated metabolites. Organic acids and carbohydrates were two major upregulated metabolites in ectomycorhizae, which were found formed dense interactions with other metabolites, suggesting their crucial roles in sustaining the metabolic functions in the truffle ectomycorrhization system. This study revealed the effects of truffle-colonization on the metabolites of ectomycorrhiza and illustrates an interactive network between truffles, the host plant, soil and associated microbial communities, shedding light on understanding the ecological effects of truffles.

Does soil fauna like truffles just as humans do? One-year study of biodiversity in natural brûlés of Tuber aestivum Vittad

There are numerous aspects related to Tuber species, which have not been explored to date. Tuber aestivum Vitt. is an ectomycorrhizal fungus, that produces an area (called brûlé) around the host plant trunk, where the germination of other plants is inhibited. What happens inside this particular environment is still not sufficiently understood, especially in terms of soil fauna. A previous work showed that there were higher microarthropod abundances outside during the period of maximum activity of the mycelium. The genus Folsomia (Isotomidae Family; Order Collembola) showed higher abundance inside. The aim of this paper is to investigate the effects of brûlé, on soil parameters and soil fauna, during the annual biological cycle of T. aestivum. This study was carried out in nine spontaneous brûlés situated in Northern Italy (Emilia Romagna Region - Piacenza Province). Soil cores were collected in order to perform soil chemical and biological analysis. Moisture content, pH, organic matter content, total organic carbon were analyzed. Biodiversity and soil quality indices were applied. We found higher pH, lower carbon and organic matter content within the brûlé. Soil fauna community also showed some differences, seasonal and inside vs outside the brûlé. Some groups seem to be negatively affected by Tuber while Folsomia genus recorded almost always higher values inside. These results suggest that some organisms, such as some Collembola, might find a favorable environment inside the brûlé, while others - a negative one. However, these results should be compared by other analysis either on other Tuber species and on other soil organisms, such as nematodes and earthworms.

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii)

The aim of this study was to investigate the effect of an ectomycorrhizal fungus (Tuber indicum) on the diversity of microbial communities associated with an indigenous tree, Pinus armandii, and the microbial communities in the surrounding ectomycorhizosphere soil. High-throughput sequencing was used to analyze the richness of microbial communities in the roots or rhizosphere of treatments with or without ectomycorrhizae. The results indicated that the bacterial diversity of ectomycorhizosphere soil was significantly lower compared with the control soil. Presumably, the dominance of truffle mycelia in ectomycorhizosphere soil (80.91%) and ectomycorrhizae (97.64%) was the main factor that resulted in lower diversity and abundance of endophytic pathogenic fungi, including Fusarium, Monographella, Ustilago and Rhizopus and other competitive mycorrhizal fungi, such as Amanita, Lactarius and Boletus. Bacterial genera Reyranena, Rhizomicrobium, Nordella, Pseudomonas and fungal genera, Cuphophyllus, Leucangium, Histoplasma were significantly more abundant in ectomycorrhizosphere soil and ectomycorrhizae. Hierarchical cluster analysis of the similarities between rhizosphere and ectomycorrhizosphere soil based on the soil properties differed significantly, indicating the mycorrhizal synthesis may have a feedback effect on soil properties. Meanwhile, some soil properties were significantly correlated with bacterial and fungal diversity in the rhizosphere or root tips. Overall, this work illustrates the interactive network that exists among ectomycorrhizal fungi, soil properties and microbial communities associated with the host plant and furthers our understanding of the ecology and cultivation of T. indicum.

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.

Soil metaproteomics reveals an inter-kingdom stress response to the presence of black truffles

For some truffle species of the Tuber genus, the symbiotic phase is often associated with the presence of an area of scant vegetation, commonly known as the brûlé, around the host tree. Previous metagenomics studies have identified the microorganisms present inside and outside the brûlé of a Tuber melanosporum truffle-ground, but the molecular mechanisms that operate in this ecological niche remain to be clarified. To elucidate the metabolic pathways present in the brûlé, we conducted a metaproteomics analysis on the soil of a characterized truffle-ground and cross-referenced the resulting proteins with a database we constructed, incorporating the metagenomics data for the organisms previously identified in this soil. The soil inside the brûlé contained a larger number of proteins and, surprisingly, more proteins from plants, compared with the soil outside the brûlé. In addition, Fisher's Exact Tests detected more biological processes inside the brûlé; these processes were related to responses to multiple types of stress. Thus, although the brûlé has a reduced diversity of plant and microbial species, the organisms in the brûlé show strong metabolic activity. Also, the combination of metagenomics and metaproteomics provides a powerful tool to reveal soil functioning.

Revisiting the 'Gadgil effect': do interguild fungal interactions control carbon cycling in forest soils?

In forest ecosystems, ectomycorrhizal and saprotrophic fungi play a central role in the breakdown of soil organic matter (SOM). Competition between these two fungal guilds has long been hypothesized to lead to suppression of decomposition rates, a phenomenon known as the 'Gadgil effect'. In this review, we examine the documentation, generality, and potential mechanisms involved in the 'Gadgil effect'. We find that the influence of ectomycorrhizal fungi on litter and SOM decomposition is much more variable than previously recognized. To explain the inconsistency in size and direction of the 'Gadgil effect', we argue that a better understanding of underlying mechanisms is required. We discuss the strengths and weaknesses of each of the primary mechanisms proposed to date and how using different experimental methods (trenching, girdling, microcosms), as well as considering different temporal and spatial scales, could influence the conclusions drawn about this phenomenon. Finally, we suggest that combining new research tools such as high-throughput sequencing with experiments utilizing natural environmental gradients will significantly deepen our understanding of the 'Gadgil effect' and its consequences on forest soil carbon and nutrient cycling.

Current progress on truffle submerged fermentation: a promising alternative to its fruiting bodies

Truffle (Tuber spp.), also known as "underground gold," is popular in various cuisines because of its unique and characteristic aroma. Currently, truffle fruiting bodies are mostly obtained from nature and semi-artificial cultivation. However, the former source is scarce, and the latter is time-consuming, usually taking 4 to 12 years before harvest of the fruiting body. The truffle submerged fermentation process was first developed in Tang's lab as an alternative to its fruiting bodies. To the best of our knowledge, most reports of truffle submerged fermentation come from Tang's group. This review examines the current state of the truffle submerged fermentation process. First, the strategy to optimize the truffle submerged fermentation process is summarized; the final conditions yielded not only the highest reported truffle biomass but also the highest production of extracellular and intracellular polysaccharides. Second, the comparison of metabolites produced by truffle fermentation and fruiting bodies is presented, and the former were superior to the latter. Third, metabolites (i.e., volatile organic compounds, equivalent umami concentration, and sterol) derived from truffle fermentation could be regulated by fermentation process optimization. These findings indicated that submerged fermentation of truffles can be used for commercial production of biomass and metabolites as a promising alternative to generating its fruiting bodies in bioreactor.

Tuber aestivum association with non-host roots

Mycorrhizal fungi provide direct and functional interconnection of soil environment with their host plant roots. Colonization of non-host plants have occasionally been described, but its intensity and functional significance in complex plant communities remain generally unknown. Here, the abundance of ectomycorrhizal fungus Tuber aestivum was measured in the roots of host and non-host (non-ectomycorrhizal) plants in a naturally occurring T. aestivum colony using a quantitative PCR approach. The roots of non-host plant species found inside the brûlé area were extensively colonized by T. aestivum mycelium, although the levels were significantly lower than those found in host Carpinus betulus roots. However, fungal biomass concentration in the non-host roots was one to two orders of magnitude higher than that in the surrounding soil. This indicates existence of an important biotic interaction between T. aestivum mycelium and the non-host, mostly herbaceous plants. Roots, either host or non-host, thus probably constitute hot spots of T. aestivum activity in the soil ecosystem with as yet uncovered functional significance.

Persistence and detection of black truffle ectomycorrhizas in plantations: comparison between two field detection methods

Owners of black truffle (Tuber melanosporum) plantations are concerned about the persistence of its mycorrhizas and mycelium in the soil, especially until the appearance of the "truffle burn" areas and the triggering of sporocarp production, at least 5-7 years after planting truffle-inoculated seedlings. During this period, the farmer does not know whether his management is promoting black truffle development. To study the presence and abundance of T. melanosporum ectomycorrhizas in plantations, two sampling methods, direct sampling of root tips and soil core collection, are compared by analyzing 48 evergreen oak trees (Quercus ilex) inoculated with truffle. Those trees are grouped by age (<6, 6-9, >9 years old) and presence or absence of truffle production. T. melanosporum was present in 46 out of the 48 studied trees, and its ectomycorrhizas appeared in 65% of the ectomycorrhizal tips. Its abundance is significantly higher with productive trees and young trees. Direct sampling of root tips and soil core collection were equally effective in detecting this species, although soil core collection proved a better method to also evaluate ectomycorrhizal fungal diversity. To detect the presence of T. melanosporum in a given plantation, three samples suffice, with a single sample per random tree. Although the presence of mycorrhizas is not a sure sign of the future success of a black truffle plantation, its absence influences managers as to whether to continue culturing truffles in a plantation.

Pattern of Tuber melanosporum extramatrical mycelium expansion over a 20-year chronosequence in Quercus ilex-truffle orchards

Successful cultivation of black truffle (Tuber melanosporum) requires a long-term investment and the maintenance of the symbiosis throughout its preproductive and productive years. Monitoring the symbiosis over time is challenging, as it requires methods that can detect the belowground proliferation of the fungus associated with its host tree. In this study, we used a chronosequence design to study the expansion pattern of this fungus as the host tree grows. We hypothesize that this expansion can be estimated by monitoring T. melanosporum DNA from soil beneath host trees of different ages (3, 5, 7, 10, 14, and 20 years old) and at different distances from the trunk of the trees (40, 100, and 200 cm). We also wished to evaluate the presences of Tuber brumale and Tuber indicum, potentially problematic truffle species, in these plantations. To detect the mycelium of T. melanosporum in these soils, we extracted DNA and performed polymerase chain reaction (PCR) with Tuber species-specific primers, and to estimate DNA amount, we measured relative band intensities from the amplicons in agarose gels. Both age and distance were related to T. melanosporum DNA quantity, which was more abundant in the oldest age classes, reaching a plateau in 5-7 years. At 40 cm from the tree, there were no differences in T. melanosporum DNA amounts in orchards of different ages, but at 100 and 200 cm, younger orchards had less T. melanosporum DNA. We did not detect DNA from T. brumale or T. indicum in any of our samples.

Truffle brûlés have an impact on the diversity of soil bacterial communities

BACKGROUND

The development of Tuber melanosporum mycorrhizal symbiosis is associated with the production of an area devoid of vegetation (commonly referred to by the French word 'brûlé') around the symbiotic plants and where the fruiting bodies of T. melanosporum are usually collected. The extent of the ecological impact of such an area is still being discovered. While the relationship between T. melanosporum and the other fungi present in the brûlé has been assessed, no data are available on the relationship between this fungus and the bacteria inhabiting the brûlé.

METHODOLOGY/PRINCIPAL FINDINGS

We used DGGE and DNA microarrays of 16S rRNA gene fragments to compare the bacterial and archaeal communities inside and outside of truffle brûlés. Soil samples were collected in 2008 from four productive T. melanosporum/Quercus pubescens truffle-grounds located in Cahors, France, showing characteristic truffle brûlé. All the samples were analyzed by DGGE and one truffle-ground was analyzed also using phylogenetic microarrays. DGGE profiles showed differences in the bacterial community composition, and the microarrays revealed a few differences in relative richness between the brûlé interior and exterior zones, as well as differences in the relative abundance of several taxa.

CONCLUSIONS/SIGNIFICANCE

The different signal intensities we have measured for members of bacteria and archaea inside versus outside the brûlé are the first demonstration, to our knowledge, that not only fungal communities, but also other microorganisms are affected by T. melanosporum. Firmicutes (e.g., Bacillus), several genera of Actinobacteria, and a few Cyanobacteria had greater representation inside the brûlé compared with outside, whereas Pseudomonas and several genera within the class Flavobacteriaceae had higher relative abundances outside the brûlé. The findings from this study may contribute to future searches for microbial bio-indicators of brûlés.

An improved method compatible with metagenomic analyses to extract genomic DNA from soils in Tuber melanosporum orchards

AIMS

The development of high-throughput methods such as pyrosequencing and microarrays has greatly improved our understanding of the microbial diversity in complex environments such as soils. Nevertheless, albeit advancements in such techniques, the first major step is to obtain high quantity and good quality genomic DNA (gDNA). The work presented here aims to present an inherent problem with 260 : 230 nm ratio of extracted gDNA from calcareous soils of Tuber melanosporum orchards and a protocol to overcome this problem.

METHODS AND RESULTS

Using two commercial gDNA extraction kits on spatially distant truffle orchards, we demonstrated that the 260 : 230 nm ratio was very low, consequentially yielding gDNA incompatible with microarray analyses. In order to solve this problem, optimization steps were tested including several wash steps performed before and/or after lysis. These washes significantly improved the gDNA quality (ratio 260 : 230 nm >1·7) without modification of the structure of the bacterial communities as stated by temporal temperature gradient gel electrophoresis analysis. A final re-extraction with phenol/chloroform was required for one of the soil samples.

CONCLUSIONS

A combination of wash steps included into the extraction protocol followed by phenol: chloroform re-extraction is recommended to obtain high-quality gDNA from calcareous soils of T. melanosporum orchards.

SIGNIFICANCE AND IMPACT OF THE STUDY

The method recommended here significantly improves gDNA quality obtained from T. melanosporum orchards to make it acceptable for highly sensitive methods such as microarray.

Laser microdissection and microarray analysis of Tuber melanosporum ectomycorrhizas reveal functional heterogeneity between mantle and Hartig net compartments

The ectomycorrhizal (ECM) symbiosis, a mutualistic plant-fungus association, plays a fundamental role in forest ecosystems by enhancing plant growth and by providing host protection from root diseases. The cellular complexity of the symbiotic organ, characterized by the differentiation of structurally specialized tissues (i.e. the fungal mantle and the Hartig net), is the major limitation to study fungal gene expression in such specific compartments. We investigated the transcriptional landscape of the ECM fungus Tuber melanosporum during the major stages of its life cycle and we particularly focused on the complex symbiotic stage by combining the use of laser capture microdissection and microarray gene expression analysis. We isolated the fungal/soil (i.e. the mantle) and the fungal/plant (i.e. the Hartig net) interfaces from transverse sections of T. melanosporum/Corylus avellana ectomycorrhizas and identified the distinct genetic programmes associated with each compartment. Particularly, nitrogen and water acquisition from soil, synthesis of secondary metabolites and detoxification mechanisms appear to be important processes in the fungal mantle. In contrast, transport activity is enhanced in the Hartig net and we identified carbohydrate and nitrogen-derived transporters that might play a key role in the reciprocal resources' transfer between the host and the symbiont.

Quantification of extraradical mycelium of Tuber melanosporum in soils from truffle orchards in northern Spain

Quantification of extraradical mycelium of black truffle (Tuber melanosporum) has been carried out in a natural truffle ground and in seven truffle orchards (around 20 years old) established in Tierra Estella and Valdorba sites, within the natural distribution area of the black truffles in Navarre (northern Spain). Specific primers and a Taqman® probe were designed to perform real-time PCR with DNA extracted from soil samples. Amplification of T. melanosporum DNA was obtained from 131 out of the 160 soil samples. The detection limit of the technique was 1.48 μg mycelium/g of soil. The extraradical mycelium biomass detected in the soil from the natural truffle ground was significantly greater (up to ten times higher) than the mycelium biomass detected in any of the orchards. Soil from productive, nonirrigated orchards in the Tierra Estella site contained significantly more extraradical mycelium than the rest of orchards irrigated, productive of T. brumale, or nonproductive. The comparison of soil mycelium biomass in nonirrigated evergreen oak orchards in both sites showed significantly more mycelium biomass in the Tierra Estella site. This study is the first attempt to quantify extraradical mycelium of T. melanosporum in the soil using Taqman® probes. The obtained quantitative results are of special interest to evaluate the fungal response to cultural treatments and to monitor the dynamics of the extraradical mycelium of T. melanosporum in the soil.