New evidence for bacterial diversity in the ascoma of the ectomycorrhizal fungusTuber borchiiVittad

In vitro interactions between Bradyrhizobium spp. and Tuber magnatum mycelium

Tuber magnatum is the most expensive truffle, but its large-scale cultivation is still a challenge compared to other valuable Tuber species. T. magnatum mycelium has never been grown profitably until now, which has led to difficulties to studying it in vitro. This study describes beneficial interactions between T. magnatum mycelium and never before described bradyrhizobia, which allows the in vitro growth of T. magnatum mycelium. Three T. magnatum strains were co-isolated on modified Woody Plant Medium (mWPM) with aerobic bacteria and characterised through microscopic observations. The difficulties of growing alone both partners, bacteria and T. magnatum mycelium, on mWPM demonstrated the reciprocal dependency. Three bacterial isolates for each T. magnatum strain were obtained and molecularly characterised by sequencing the 16S rRNA, glnII, recA and nifH genes. Phylogenetic analyses showed that all nine bacterial strains were distributed among five subclades included in a new monophyletic lineage belonging to the Bradyrhizobium genus within the Bradyrhizobium jicamae supergroup. The nifH genes were detected in all bacterial isolates, suggesting nitrogen-fixing capacities. This is the first report of consistent T. magnatum mycelium growth in vitro conditions. It has important implications for the development of new technologies in white truffle cultivation and for further studies on T. magnatum biology and genetics.

Co-responses of bacterial and fungal communities to fire management treatments in Mediterranean pyrophytic ecosystems

Cistus scrublands are pyrophytic ecosystems and occur widely across Mediterranean regions. Management of these scrublands is critical to prevent major disturbances, such as recurring wildfires. This is because management appears to compromise the synergies necessary for forest health and the provision of ecosystem services. Furthermore, it supports high microbial diversity, opening questions of how forest management practices impact belowground associated diversity as research related to this issue is scarce. This study aims to investigate the effects of different fire prevention treatments and site history on bacterial and fungi co-response and co-occurrence patterns over a fire-risky scrubland ecosystem. Two different site histories were studied by applying three different fire prevention treatments and samples were analyzed by amplification and sequencing of ITS2 and 16S rDNA for fungi and bacteria, respectively. The data revealed that site history, especially regarding fire occurrence, strongly influenced the microbial community. Young burnt areas tended to have a more homogeneous and lower microbial diversity, suggesting environmental filtering to a heat-resistant community. In comparison, young clearing history also showed a significant impact on the fungal community but not on the bacteria. Some bacteria genera were efficient predictors of fungal diversity and richness. For instance, Ktedonobacter and Desertibacter were a predictor of the presence of the edible mycorrhizal bolete Boletus edulis. These results demonstrate fungal and bacterial community co-response to fire prevention treatments and provide new tools for forecasting forest management impacts on microbial communities.

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.

Both abundant and rare fungi colonizing Fagus sylvatica ectomycorrhizal root-tips shape associated bacterial communities

Ectomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.

The Microbiome Structure of the Symbiosis between the Desert Truffle Terfezia boudieri and Its Host Plant Helianthemum sessiliflorum

The desert truffle Terfezia boudieri is an ascomycete fungus that forms ect-endomycorrhiza in the roots of plants belonging to Cistaceae. The fungus forms hypogeous edible fruit bodies, appreciated as gourmet food. Truffles and host plants are colonized by various microbes, which may contribute to their development. However, the diversity and composition of the bacterial community under field conditions in the Negev desert are still unknown. The overall goal of this research was to identify the rhizosphere microbial community supporting the establishment of a symbiotic association between T. boudieri and Helianthemum sessiliflorum. The bacterial community was characterized by fruiting bodies, mycorrhized roots, and rhizosphere soil. Based on next-generation sequencing meta-analyses of the 16S rRNA gene, we discovered diverse bacterial communities of fruit bodies that differed from those found in the roots and rhizosphere. Families of Proteobacteria, Planctomycetes, and Actinobacteria were present in all four samples. Alpha diversity analysis revealed that the rhizosphere and roots contain significantly higher bacterial species numbers compared to the fruit. Additionally, ANOSIM and PCoA provided a comparative analysis of the bacterial taxa associated with fruiting bodies, roots, and rhizosphere. The core microbiome described consists of groups whose biological role triggers important traits supporting plant growth and fruit body development.

Fungal and Bacterial Communities in Tuber melanosporum Plantations from Northern Spain

Tuber melanosporum (Ascomycota, Pezizales) is an ectomycorrhizal fungus that produces highly appreciated hypogeous fruiting bodies called black truffles. The aim of this paper was to research the composition of ectomycorrhiza-associated fungal and bacterial communities in T. melanosporum oak plantations. Results of this paper showed the competitive effect of T. melanosporum on other fungal species, especially other mycorrhizal and pathogenic species. T. melanosporum was shown to be associated mainly with bacteria, some of them important for their properties as mycorrhizal helper bacteria. A dendrogram analysis of co-occurrence showed that T. melanosporum tended to co-occur with the following bacteria species: Singulisphaera limicola, Nannocistis excedens and Sporosarcina globispora. In addition, it was linked to fungal species such as Mortierella elongata, M. minutissima, Cryptococcus uzbekistanensis, C. chernovii and C. aerius. This study provides an exhaustive analysis of the diversity, structure and composition of fungal and bacterial communities associated with T. melanosporum to enhance understanding of the biology, composition and role of these communities in truffle plantations.

Microbial communities of ascocarps and soils in a natural habitat of Tuber indicum

Truffles are the fruiting bodies of hypogeous fungi in the genus Tuber. Some truffle species usually grow in an area devoid of vegetation, called brûlé, but limited knowledge is available on the microbial composition and structure of them. Here, we investigated the bacterial and fungal communities of Tuber indicum ascocarps and soils inside and outside a characteristic brûlé from a poplar plantation with no truffle production history in northeastern China using a high-throughput sequencing approach. A predominance of members of the bacterial phylum Proteobacteria was observed in all samples. Members of Bacillus were the main genera in the ascocarps, while members of Lysobacter and unidentified Acidobacteria were more abundant in the soil. In addition, members of Gibberella, Fusarium, and Absidia were the dominant fungi in the ascocarps, while members of Tuber were enriched in the ascocarps and soils inside the brûlé. Some mycorrhization helper bacteria (Rhizobium) and ectomycorrhiza-associated bacteria (Lysobacter) were detected, indicating their potential roles in the complex development of underground fruiting bodies and brûlé formation. These findings may contribute to the protection and cultivation of truffles.

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.

Bacterial Community Analysis and Potential Functions of Core Taxa in Different Parts of the Fungus Cantharellus cibarius

Cantharellus cibarius is a widely distributed, popular, edible fungus with high nutritional and economic value. However, significant challenges persist in the microbial ecology and artificial cultivation of C. cibarius. Based on the 16S rRNA sequencing data, this study analyzed bacterial community structures and diversity of fruit bodies and rhizomorph parts of C. cibarius and mycosphere samples (collected in the Wudang District, Guiyang, Guizhou Province, China). It explored the composition and function of the core bacterial taxa. The analyzed results showed that the rhizomorph bacterial community structure was similar to mycosphere, but differed from the fruit bodies. Members of the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex had the highest abundance in the fruit bodies. However, they were either absent or low in abundance in the rhizomorphs and mycosphere. At the same time, members of the Burkholderia-Caballeronia-Paraburkholderia complex were abundant in the fruit bodies and rhizomorphs parts of C. cibarius, as well as mycosphere. Through functional annotation of core bacterial taxa, we found that there was an apparent trend of potential functional differentiation of related bacterial communities in the fruit body and rhizomorph: potential functional groups of core bacterial taxa in the fruit bodies centered on nitrogen fixation, nitrogen metabolism, and degradation of aromatic compounds, while those in rhizomorphs focused on aerobic chemoheterotrophy, chemoheterotrophy, defense against soil pathogens, decomposition of complex organic compounds, and uptake of insoluble inorganic compounds. The analysis of functional groups of bacteria with different structures is of great significance to understand that bacteria promote the growth and development of C. cibarius.

Truffle Microbiome Is Driven by Fruit Body Compartmentalization Rather than Soils Conditioned by Different Host Trees

Truffles are among the most expensive edible mushrooms; their value is worth billions of U.S. dollars annually in international markets. They establish ectomycorrhizal symbiotic relationships with diverse host tree roots and produce hypogeous ascomata. Their whole life cycle is closely related to their associated microbiome. However, whether truffle-associated compartments or host tree rhizospheres are the vital driver for truffle ascomata microbiome is unclear. To identify and compare fungal and bacterial communities in four truffle-associated compartments (Tuber indicum: bulk soil, adhering soil to peridium, peridium, and gleba) from three host trees, we sequenced their ITS (fungal) and 16S (bacterial) ribosomal DNA using the Illumina MiSeq high-throughput platform. We further applied the amplicon data to analyze the core microbiome and microbial ecological networks. Tuber indicum microbiome composition was strongly driven by its associated compartments rather than by their symbiotic host trees. Truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex interacting network compared to that of the fungal community. The core fungal community changed from Basidiomycota dominated (bulk soil) to Rozellomycota dominated (interphase soil); the core bacterial community shifted from Bacteroidetes to Proteobacteria dominance from truffle peridium to gleba tissue. Especially, at the truffle and soil interphase, the niche-based selection of truffle microbiome was verified by (i) a clear exclusion of four bacterial phyla (Rokubacteria, Nitrospirae, Chloroflexi, and Planctomycetes) in gleba; (ii) a significant decrease in alpha-diversity (as revealed by Chao 1, Shannon, and Simpson indices); and (iii) the complexity of the network substantially decreased from bulk soil to soil-truffle interphase and further to the peridium and gleba. The network analysis of microbiome showed that the microbial positive interactions were higher in truffle tissues than in both bulk soil and peridium-adhering soil and that Cupriavidus, Bradyrhizobium, Aminobacter, and Mesorhizobium spp. were the keystone network hubs in the truffle gleba. This study provides insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components. IMPORTANCE Currently, the factors that drive the microbiome associated with truffles, the most highly prized fungi in the world, are largely unknown. We demonstrate for the first time here that truffle microbiome composition is strongly driven by associated compartments rather than by symbiotic host trees. The truffle microbiome was bacteria dominated, and its bacterial community formed a substantially more complex (with the higher numbers of nodes, links, and modules) interacting network compared to that of the fungal community. Network analysis showed a higher number of positive microbial interactions with each other in truffle tissues than in both bulk soil and peridium-adhering soil. For the first time, the fungal community structure associated with truffles using high-throughput sequencing, microbial networks, and keystone species analyses is presented. This study provides novel insights into the factors that drive the truffle microbiome dynamics and the recruitment and function of the microbiome components, showing that they are more complex than previously thought.

Volatile organic compounds: from figurants to leading actors in fungal symbiosis

Symbiosis involving two (or more) prokaryotic and/or eukaryotic partners is extremely widespread in nature, and it has performed, and is still performing, a key role in the evolution of several biological systems. The interaction between symbiotic partners is based on the emission and perception of a plethora of molecules, including volatile organic compounds (VOCs), synthesized by both prokaryotic and eukaryotic (micro)organisms. VOCs acquire increasing importance since they spread above and below ground and act as infochemicals regulating a very complex network. In this work we review what is known about the VOCs synthesized by fungi prior to and during the interaction(s) with their partners (either prokaryotic or eukaryotic) and their possible role(s) in establishing and maintaining the symbiosis. Lastly, we also describe the potential applications of fungal VOCs from different biotechnological perspectives, including medicinal, pharmaceutical and agronomical.

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.

Metabolic Potential, Ecology and Presence of Associated Bacteria Is Reflected in Genomic Diversity of Mucoromycotina

Mucoromycotina are often considered mainly in pathogenic context but their biology remains understudied. We describe the genomes of six Mucoromycotina fungi representing distant saprotrophic lineages within the subphylum (i.e., Umbelopsidales and Mucorales). We selected two Umbelopsis isolates from soil (i.e., U. isabellina, U. vinacea), two soil-derived Mucor isolates (i.e., M. circinatus, M. plumbeus), and two Mucorales representatives with extended proteolytic activity (i.e., Thamnidium elegans and Mucor saturninus). We complement computational genome annotation with experimental characteristics of their digestive capabilities, cell wall carbohydrate composition, and extensive total lipid profiles. These traits inferred from genome composition, e.g., in terms of identified encoded enzymes, are in accordance with experimental results. Finally, we link the presence of associated bacteria with observed characteristics. Thamnidium elegans genome harbors an additional, complete genome of an associated bacterium classified to Paenibacillus sp. This fungus displays multiple altered traits compared to the remaining isolates, regardless of their evolutionary distance. For instance, it has expanded carbon assimilation capabilities, e.g., efficiently degrades carboxylic acids, and has a higher diacylglycerol:triacylglycerol ratio and skewed phospholipid composition which suggests a more rigid cellular membrane. The bacterium can complement the host enzymatic capabilities, alter the fungal metabolism, cell membrane composition but does not change the composition of the cell wall of the fungus. Comparison of early-diverging Umbelopsidales with evolutionary younger Mucorales points at several subtle differences particularly in their carbon source preferences and encoded carbohydrate repertoire. Nevertheless, all tested Mucoromycotina share features including the ability to produce 18:3 gamma-linoleic acid, use TAG as the storage lipid and have fucose as a cell wall component.

Identification of bacteria and fungi inhabiting fruiting bodies of Burgundy truffle (Tuber aestivum Vittad.)

Tuber species may be regarded as complex microhabitats hosting diverse microorganisms inside their fruiting bodies. Here, we investigated the structure of microbial communities inhabiting the gleba of wild growing (in stands) T. aestivum, using Illumina sequencing and culture-based methods. The two methods used in combination allowed to extract more information on complex microbiota of Tuber aestivum gleba. Analysis of the V3-V4 region of 16S rDNA identified nine phyla of bacteria present in the gleba of T. aestivum ascomata, mostly Proteobacteria from the family Bradyrhizobiaceae. Our results ideally match the earlier data for other Tuber species where the family Bradyrhizobiaceae was the most represented. The ITS1 region of fungal rDNA represented six alien fungal species belonging to three phyla. To complement the metagenomic analysis, cultivable fungi and bacteria were obtained from the gleba of the same T. aestivum fruiting bodies. The identified fungi mostly belong to the phylum Basidiomycota and same to Ascomycota. Analysis of cultivable bacteria revealed that all the specimens were colonized by different strains of Bacillus. Fungal community inhabiting T. aestivum fruiting bodies was never shown before.

Phylum-level diversity of the microbiome of the extremophilic basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert: An island of biodiversity in a thermal soil desert

We used high‐throughput DNA sequencing methods combined with bio‐geochemical profiles to characterize the internal environment and community structure of the microbiome of the basidiomycete fungus Pisolithus arhizus (Scop.) Rauschert from soils within a geothermal feature of Yellowstone National Park. Pisolithus arhizus is unique in that it forms closed fruiting bodies that sequester visible sulfur within. Fourier transform infrared spectroscopy (FTIR) analysis demonstrates that the P. arhizus fruiting body also concentrates copper, manganese, nickel, and zinc and contains pure granular silica. Gas chromatography‐mass spectrometry (GC‐MS) analysis indicates an environment rich in hydrocarbons. Oxygen probe analysis reveals that zones of up to 4× atmospheric oxygen exist within nanometers of zones of near anoxia. Analysis of microbial community structure using high‐throughput DNA sequencing methods shows that the fruiting body supports a microbiome that reflects the physiochemical environment of the fruiting body. Diversity and richness measures indicate a microbiome that is significantly richer and more diverse than that of the soils in which P. arhizus grows. Further, P. arhizus sporocarps are enriched significantly in Proteobacteria (primarily Burkholderia) Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Nitrospirae, Elusimicrobia, and Latescibacteria (WS3) while soils are enriched in Actinobacteria (primarily Mycobacterium), Dormibacteraeota (AD3), and Eremiobacteraeota (WPS‐2). Finally, pairwise % similarity comparisons indicate that P. arhizus harbors two lineages that may represent new groups in the candidate phylum radiation (CPR). Together, these results demonstrate that P. arhizus provides a novel environment for microbiome studies and provides for interesting hypotheses regarding the evolution, origins, and functions of symbioses and novel microbes.

Root-tip cutting and uniconazole treatment improve the colonization rate of Tuber indicum on Pinus armandii seedlings in the greenhouse

The Chinese black truffle Tuber indicum is commercially valuable. The main factors influencing the success or failure of a truffle crop include the mycorrhizal colonization rate and host plant quality. The effects of a plant growth regulator (uniconazole) and plant growth management technique (root‐tip cutting) on T. indicum colonization rate and Pinus armandii seedling growth were assessed under greenhouse conditions. The results indicated that 10 mg l⁻¹ uniconazole or the combination of 5 mg l⁻¹ uniconazole and root‐tip cutting constitutes an effective method for ectomycorrhizal synthesis based on an overall evaluation of colonization rate, plant biomass, plant height, root weight, stem circumference and antioxidant enzyme activities (SOD and POD) of P. armandii. The abundance of Proteobacteria in the rhizosphere of colonized seedlings might serve as an indicator of stable mycorrhizal colonization. This research inspires the potential application of uniconazole and root‐tip cutting treatments for mycorrhizal synthesis and truffle cultivation.

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.

Effect of forest fire prevention treatments on bacterial communities associated with productive Boletus edulis sites

Cistus ladanifer scrublands, traditionally considered as unproductive, have nonetheless been observed to produce large quantities of king bolete (Boletus edulis) fruitbodies. These pyrophytic scrublands are prone to wildfires, which severely affect fungi, hence the need for fire prevention in producing C. ladanifer scrublands. In addition, B. edulis productions have severely decreased in the last years. A deeper understanding of the B. edulis life cycle and of biotic and abiotic factors influencing sporocarp formation is needed to implement management practices that facilitate B. edulis production. For example, some bacteria likely are involved in sporocarp production, representing a key part in the triple symbiosis (plant-fungus-bacteria). In this study, we used soil DNA metabarcoding in C. ladanifer scrublands to (i) assess the effect of site history and fire prevention treatment on bacterial richness and community composition; (ii) test if there was any correlation between various taxonomic groups of bacteria and mycelial biomass and sporocarp production of B. edulis; and to (iii) identify indicator bacteria associated with the most productive B. edulis sites. Our results show that site history drives bacterial richness and community composition, while fire prevention treatments have a weaker, but still detectable effect, particularly in the senescent plots. Sporocarp production correlated positively with genera in Verrucomicrobia. Several genera, e.g. Azospirillum and Gemmatimonas, were identified as indicators of the most productive sites, suggesting a potential biological role in B. edulis fructification. This study provides a better understanding of the triple symbiosis (plant-fungus-bacteria) involved in C. ladanifer-B. edulis systems.

Microbial communities associated with the black morel Morchella sextelata cultivated in greenhouses

Morels (Morchella spp.) are iconic edible mushrooms with a long history of human consumption. Some microbial taxa are hypothesized to be important in triggering the formation of morel primordia and development of fruiting bodies, thus, there is interest in the microbial ecology of these fungi. To identify and compare fungal and prokaryotic communities in soils where Morchella sextelata is cultivated in outdoor greenhouses, ITS and 16S rDNA high throughput amplicon sequencing and microbiome analyses were performed. Pedobacter, Pseudomonas, Stenotrophomonas, and Flavobacterium were found to comprise the core microbiome of M. sextelata ascocarps. These bacterial taxa were also abundant in the soil beneath growing fruiting bodies. A total of 29 bacterial taxa were found to be statistically associated to Morchella fruiting bodies. Bacterial community network analysis revealed high modularity with some 16S rDNA operational taxonomic unit clusters living in specialized fungal niches (e.g., pileus, stipe). Other fungi dominating the soil mycobiome beneath morels included Morchella, Phialophora, and Mortierella. This research informs understanding of microbial indicators and potential facilitators of Morchella ecology and fruiting body production.

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.

The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics

Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.

Bacterial Communities in Boreal Forest Mushrooms Are Shaped Both by Soil Parameters and Host Identity

Despite recent advances in understanding the microbiome of eukaryotes, little is known about microbial communities in fungi. Here we investigate the structure of bacterial communities in mushrooms, including common edible ones, with respect to biotic and abiotic factors in the boreal forest. Using a combination of culture-based and Illumina high-throughput sequencing, we characterized the bacterial communities in fruitbodies of fungi from eight genera spanning four orders of the class Agaricomycetes (Basidiomycota). Our results revealed that soil pH followed by fungal identity are the main determinants of the structure of bacterial communities in mushrooms. While almost half of fruitbody bacteria were also detected from soil, the abundance of several bacterial taxa differed considerably between the two environments. The effect of host identity was significant at the fungal genus and order level and could to some extent be ascribed to the distinct bacterial community of the chanterelle, representing Cantharellales-the earliest diverged group of mushroom-forming basidiomycetes. These data suggest that besides the substantial contribution of soil as a major taxa source of bacterial communities in mushrooms, the structure of these communities is also affected by the identity of the host. Thus, bacteria inhabiting fungal fruitbodies may be non-randomly selected from environment based on their symbiotic functions and/or habitat requirements.

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.

Beneficial native bacteria improve survival and mycorrhization of desert truffle mycorrhizal plants in nursery conditions

Sixty-four native bacterial colonies were isolated from mycorrhizal roots of Helianthemum almeriense colonized by Terfezia claveryi, mycorrhizosphere soil, and peridium of T. claveryi to evaluate their effect on mycorrhizal plant production. Based on the phylogenetic analysis of the 16S rDNA partial sequence, 45 different strains from 17 genera were gathered. The largest genera were Pseudomonas (40.8 % of the isolated strains), Bacillus (12.2 % of isolated strains), and Varivorax (8.2 % of isolated strains). All the bacteria were characterized phenotypically and by their plant growth-promoting rhizobacteria (PGPR) traits (auxin and siderophore production, phosphate solubilization, and ACC deaminase activity). Only bacterial combinations with several PGPR traits or Pseudomonas sp. strain 5, which presents three different PGPR traits, had a positive effect on plant survival and growth. Particularly relevant were the bacterial treatments involving auxin release, which significantly increased the root-shoot ratio and mycorrhizal colonization. Moreover, Pseudomonas mandelii strain 29 was able to considerably increase mycorrhizal colonization but not plant growth, and could be considered as mycorrhiza-helper bacteria. Therefore, the mycorrhizal roots, mycorrhizosphere soil, and peridium of desert truffles are environments enriched in bacteria which may be used to increase the survival and mycorrhization in the desert truffle plant production system at a semi-industrial scale.

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.

The Truffle Microbiome: Species and Geography Effects on Bacteria Associated with Fruiting Bodies of Hypogeous Pezizales

Fungi that produce their fruiting bodies underground within the soil profile are known commonly as truffles. Truffle fruiting bodies harbor a diverse but poorly understood microbial community of bacteria, yeasts, and filamentous fungi. In this study, we used next-generation 454 amplicon pyrosequencing of the V1 and V4 region of the bacterial 16S ribosomal DNA (rDNA) in order to characterize and compare effects of truffle species and geographic origin on the truffle microbiome. We compared truffle microbiomes of the glebal tissue for eight truffle species belonging to four distinct genera within the Pezizales: Tuber, Terfezia, Leucangium, and Kalapuya. The bacterial community within truffles was dominated by Proteobacteria, Bacterioides, Actinobacteria, and Firmicutes. Bacterial richness within truffles was quite low overall, with between 2-23 operational taxonomic units (OTUs). Notably, we found a single Bradyrhizobium OTU to be dominant within truffle species belonging to the genus Tuber, irrespective of geographic origin, but not in other truffle genera sampled. This study offers relevant insights into the truffle microbiome and raises questions concerning the recruitment and function of these fungal-associated bacteria consortia.

Temporal changes of bacterial communities in the Tuber melanosporum ectomycorrhizosphere during ascocarp development

Ectomycorrhizae create a multitrophic ecosystem formed by the association between tree roots, mycelium of the ectomycorrhizal fungus, and a complex microbiome. Despite their importance in the host tree's physiology and in the functioning of the ectomycorrhizal symbiosis, detailed studies on ectomycorrhiza-associated bacterial community composition and their temporal dynamics are rare. Our objective was to investigate the composition and dynamics of Tuber melanosporum ectomycorrhiza-associated bacterial communities from summer to winter seasons in a Corylus avellana tree plantation. We used 16S ribosomal RNA (rRNA)-based pyrosequencing to compare the bacterial community structure and the richness in T. melanosporum's ectomycorrhizae with those of the bulk soil. The T. melanosporum ectomycorrhizae harbored distinct bacterial communities from those of the bulk soil, with an enrichment in Alpha- and Gamma-proteobacteria. In contrast to the bacterial communities of truffle ascocarps that vastly varies in composition and richness during the maturation of the fruiting body and to those from the bulk soil, T. melanosporum ectomycorrhiza-associated bacterial community composition stayed rather stable from September to January. Our results fit with a recent finding from the same experimental site at the same period that a continuous supply of carbohydrates and nitrogen occurs from ectomycorrhizae to the fruiting bodies during the maturation of the ascocarps. We propose that this creates a stable niche in the ectomycorrhizosphere although the phenology of the tree changes.

The Role of the Microbiome of Truffles in Aroma Formation: a Meta-Analysis Approach

Truffles (Tuber spp.) are ascomycete subterraneous fungi that form ectomycorrhizas in a symbiotic relationship with plant roots. Their fruiting bodies are appreciated for their distinctive aroma, which might be partially derived from microbes. Indeed, truffle fruiting bodies are colonized by a diverse microbial community made up of bacteria, yeasts, guest filamentous fungi, and viruses. The aim of this minireview is two-fold. First, the current knowledge on the microbial community composition of truffles has been synthesized to highlight similarities and differences among four truffle (Tuber) species (T. magnatum, T. melanosporum, T. aestivum, and T. borchii) at various stages of their life cycle. Second, the potential role of the microbiome in truffle aroma formation has been addressed for the same four species. Our results suggest that on one hand, odorants, which are common to many truffle species, might be of mixed truffle and microbial origin, while on the other hand, less common odorants might be derived from microbes only. They also highlight that bacteria, the dominant group in the microbiome of the truffle, might also be the most important contributors to truffle aroma not only in T. borchii, as already demonstrated, but also in T. magnatum, T. aestivum, and T. melanosporum.

Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome

Many obligate symbiotic fungi are difficult to maintain in culture, and there is a growing need for alternative approaches to obtaining tissue and subsequent genomic assemblies from such species. In this study, the genome of Elaphomyces granulatus was sequenced from sporocarp tissue. The genome assembly remains on many contigs, but gene space is estimated to be mostly complete. Phylogenetic analyses revealed that the Elaphomyces lineage is most closely related to Talaromyces and Trichocomaceae s.s. The genome of E. granulatus is reduced in carbohydrate-active enzymes, despite a large expansion in genome size, both of which are consistent with what is seen in Tuber melanosporum, the other sequenced ectomycorrhizal ascomycete. A large number of transposable elements are predicted in the E. granulatus genome, especially Gypsy-like long terminal repeats, and there has also been an expansion in helicases. The metagenome is a complex community dominated by bacteria in Bradyrhizobiaceae, and there is evidence to suggest that the community may be reduced in functional capacity as estimated by KEGG pathways. Through the sequencing of sporocarp tissue, this study has provided insights into Elaphomyces phylogenetics, genomics, metagenomics and the evolution of the ectomycorrhizal association.

A quest for indigenous truffle helper prokaryotes

Tuber aestivum is the most common European truffle with significant commercial exploitation. Its production originates from natural habitats and from artificially inoculated host tree plantations. Formation of Tuber ectomycorrhizae in host seedling roots is often inefficient. One possible reason is the lack of indigenous associative microbes. Here we aimed at metagenetic characterization and cultivation of indigenous prokaryotes associated with T. aestivum in a field transect cutting through the fungus colony margin. Several operational taxonomic units (OTUs) showed close association with the T. aestivum in the ectomycorrhizae and in the soil, but there was no overlap between the associative prokaryotes in the two different habitats. Among those positively associated with the ectomycorrhizae, we identified several bacterial genera belonging to Pseudonocardineae. Extensive isolation efforts yielded many cultures of ectomycorrhizae-associative bacteria belonging to Rhizobiales and Streptomycineae, but none belonging to the Pseudonocardineae. The specific unculturable Tuber-associated prokaryotes are likely to play important roles in the biology of these ectomycorrhizal fungi, including modulation of competition with other symbiotic and saprotrophic microbes, facilitation of root penetration and/or accessing mineral nutrients in the soil. However, the ultimate proof of this hypothesis will require isolation of the microbes for metabolic studies, using novel cultivation approaches.