Host species effects on bacterial communities associated with the fruiting bodies of Tuber species from the Sichuan Province in Southwest China

Fungal and Bacterial Diversity in the Tuber magnatum Ecosystem and Microbiome

Fungi belonging to the genus Tuber produce edible ascocarps known as truffles. Tuber magnatum Picco may be the most appreciated truffle species given its peculiar aroma. While its life cycle is not yet fully elucidated, some studies demonstrated an active role of microorganisms. The main goal of this study was to determine how the T. magnatum microbiome varies across space and time. To address this, we characterized microbial communities associated with T. magnatum through high-throughput amplicon sequencing of internal transcribed spacer (ITS) and 16S rDNAs in three productive natural sites in Italy across 2 years. At each site, four truffles were sampled as well as the soil underneath and at 40, 100, and 200 cm from the harvesting points, to assess for microbial variation between substrates, years, and sites. A statistically significant site-related effect on microbial communities was identified, whereas only the prokaryotic community was significantly affected by the distance of soil from the truffle. Significant differences between sampling years were also found, demonstrating a possible relation among rainfall precipitation and Firmicutes and Actinobacteria. Thirty-six bacterial OTUs in truffles and 11 bacterial OTUs in soils beneath truffles were identified as indicator taxa. As shown for other truffle species, the dominance of Bradyrhizobium, Rhizobium, and Ensifer spp. within the truffle fruiting body suggests an evolutionary adaptation of this microorganism to the genus Tuber. The present work offers novel and relevant insights into the microbial ecology of T. magnatum ecosystems and fruiting bodies. The function and role of these bacteria in the truffle microbiome and life cycle are in need of further investigation.

Bacterial Communities in the Fruiting Bodies and Background Soils of the White Truffle Tuber magnatum

Tuber magnatum Picco is a greatly appreciated truffle species mainly distributed in Italy. Its price and characteristics mostly depend on its geographical origin. Truffles represent a fundamental step of the life cycle of Tuber species promoting spore dissemination. They consist of two main parts, gleba, the inner part, and peridium, which is in direct contact with ground soil. Within the truffle and around in the growing soil, both the occurrence and abundance of different microbial species seem to play an essential role in truffle production. The development of the next-generation sequencing (NGS) based technology has greatly improved to deepen the role of the composition of microbial communities, thus improving the knowledge of the existing relationships between microbial taxa in a specific condition. Here, we applied a metabarcoding approach to assess the differences in T. magnatum samples collected from three areas in Tuscany (Italy). Peridium and gleba were analyzed separately with the aim to distinguish them based on their microbial composition. Also, soil samples were collected and analyzed to compare productive and unproductive truffle grounds to confirm the presence of specific patterns linked to truffle production. Results indicate that differences occurred between truffle compartments (gleba and peridium) as well as between analyzed soils (productive and unproductive), with distinctive taxa associated. Furthermore, findings also demonstrated specific characteristics associated with truffle collection areas, thus indicating a degree of microbial selection related to different environments.

Global diversity and distribution of mushroom-inhabiting bacteria

Mushroom-forming fungi are important sources of food and medicine in many regions of the world, and their development and health are known to depend on various microbes. Recent studies have examined the structure of mushroom-inhabiting bacterial (MIB) communities and their association with local environmental variables, but global-scale diversity and determinants of these communities remain poorly understood. Here we examined the MIB global diversity and community composition in relation to climate, soil and host factors. We found a core global mushroom microbiome, accounting for 30% of sequence reads, while comprising a few bacterial genera such as Halomonas, Serratia, Bacillus, Cutibacterium, Bradyrhizobium and Burkholderia. Our analysis further revealed an important role of host phylogeny in shaping the communities of MIB, whereas the effects of climate and soil factors remained negligible. The results suggest that the communities of MIB and free-living bacteria are structured by contrasting community assembly processes and that fungal-bacterial interactions are an important determinant of MIB community structure.

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.

Heterogeneity of the white truffle Tuber magnatum in a limited geographic area of Central-Southern Italy

Molise region (Central-Southern Italy) is one of the Italian richest areas of truffles and contributes significantly to the national production of the precious Tuber magnatum. Nevertheless, Molise truffle has received little scientific attention. Accordingly, in the present study, two T. magnatum populations collected in two different sites of Molise region were characterised from a morphological, genetic and microbiological point of view. A considerable variability between and within the two analysed groups emerged, suggesting an interesting heterogeneity of Molise white truffle populations. Ascocarps of the two groups significantly differed in size and maturation degree, although no linear correlation between weight and maturity was found. Genetic investigations focused on the Sequence-Characterised Amplified Region SCAR A21-inf. Three haplotypes, randomly distributed within the two truffle groups regardless of their collection sites, were detected. The 16S rRNA gene amplicon high-throughput sequencing provided an overview of the composition of the ascocarp-associated bacterial communities. A predominance of α-Proteobacteria was observed, with Bradyrhizobium among the main genera. However, some truffles showed unusual microbial profiles, with Pedobacter, Polaromonas and other bacterial genera as dominant taxa.

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

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

Bacterial community dynamics across developmental stages of fungal fruiting bodies

Increasing evidence suggest that bacteria form diverse communities in various eukaryotic hosts, including fungi. However, little is known about their succession and the functional potential at different host development stages. Here we examined the effect of fruiting body parts and developmental stages on the structure and potential function of fungus-associated bacterial communities. Using high-throughput sequencing, we characterized bacterial communities and their associated potential functions in fruiting bodies from ten genera belonging to four major mushroom-forming orders and three different developmental stages of a model host species Cantharellus cibarius. Our results demonstrate that bacterial community structure differs between internal and external parts of the fruiting body but not between inner tissues. The structure of the bacterial communities showed significant variation across fruiting body developmental stages. We provide evidence that certain functional groups, such as those related to nitrogen fixation, persist in fruiting bodies during the maturation, but are replaced by putative parasites/pathogens afterwards. These data suggest that bacterial communities inhabiting fungal fruiting bodies may play important roles in their growth and development.

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.

Tuber melanosporum shapes nirS-type denitrifying and ammonia-oxidizing bacterial communities in Carya illinoinensis ectomycorrhizosphere soils

Background

NirS-type denitrifying bacteria and ammonia-oxidizing bacteria (AOB) play a key role in the soil nitrogen cycle, which may affect the growth and development of underground truffles. We aimed to investigate nirS-type denitrifying bacterial and AOB community structures in the rhizosphere soils of Carya illinoinensis seedlings inoculated with the black truffle (Tuber melanosporum) during the early symbiotic stage.

Methods

The C. illinoinensis seedlings inoculated with or without T. melanosporum were cultivated in a greenhouse for six months. Next-generation sequencing (NGS) technology was used to analyze nirS-type denitrifying bacterial and AOB community structures in the rhizosphere soils of these seedlings. Additionally, the soil properties were determined.

Results

The results indicated that the abundance and diversity of AOB were significantly reduced due to the inoculation of T. melanosporum, while these of nirS-type denitrifying bacteria increased significantly. Proteobacteria were the dominant bacterial groups, and Rhodanobacter, Pseudomonas, Nitrosospira and Nitrosomonas were the dominant classified bacterial genera in all the soil samples. Pseudomonas was the most abundant classified nirS-type denitrifying bacterial genus in ectomycorrhizosphere soils whose relative abundance could significantly increase after T. melanosporum inoculation. A large number of unclassified nirS-type denitrifying bacteria and AOB were observed. Moreover, T. melanosporum inoculation had little effect on the pH, total nitrogen (TN), nitrate-nitrogen (NO\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${}_{3}^{-}$\end{document}3−-N) and ammonium-nitrogen (NH\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}${}_{4}^{+}$\end{document}4+-N) contents in ectomycorrhizosphere soils. Overall, our results showed that nirS-type denitrifying bacterial and AOB communities in C. illinoinensis rhizosphere soils were significantly affected by T. melanosporum on the initial stage of ectomycorrhizal symbiosis, without obvious variation of soil N contents.

Chinese Black Truffle-Associated Bacterial Communities of Tuber indicum From Different Geographical Regions With Nitrogen Fixing Bioactivity

It is well known that the microbes associated with truffle fruiting bodies play a very important role during the truffle lifecycle. Tuber indicum, commonly called Chinese black truffle, is a species endemic to Eastern Asia and in the genus of Tuber. Here, we reported the bacterial communities of T. indicum from different geographical regions and described the bacterial diversity from three compartments (soil, ectomycorrhizae and ascocarps) of T. indicum using high-throughput sequencing combined tissue culture. The results revealed that Bradyrhizobium was the dominant genus in fruiting bodies of T. indicum from nine geographical sites in China, and the microbes in T. indicum ascocarps were influenced by geological locations and soil characteristics. More specific bacterial taxa were enriched in the fruiting bodies than in the ectomycorrhizae and soil. In addition, 60 cultural bacteria were isolated from T. indicum fruiting bodies (4 families, 24 genera), and Pseudomonas, Alcaligenes faecalis, Microbacterium, and Arthrobacter were dominant. One of 13 strains that have potential nitrogen-fixation activities was further verified by an acetylene reduction assay (ARA). Together, this research provides new and important data for better understanding of the interaction between truffle and associated microbe and the biology of truffle itself.

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.

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.

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.