Root-associated bacteria influencing mycelial growth of Tricholoma matsutake (pine mushroom)

Extraction of total flavonoids from Chaenomeles speciosa (Sweet) Nakai and its antioxidant and lipoxygenase inhibition effects

Ultrasound-assisted extraction technology was utilized to extract total flavonoids from Chaenomeles speciosa (Sweet) Nakai, and response surface methodology was employed to optimize the extraction process. The anti-oxidant and lipoxygenase inhibitory activities were evaluated, along with an analysis of the type of inhibition. The results revealed that the optimal extraction conditions for total flavonoids from Chaenomeles speciosa (Sweet) Nakai were as follows: an ethanol concentration of 62%, a liquid-to-solid ratio of 15:1 mL/g, an ultrasonic temperature of 68°C, and an ultrasonic time of 40 min, resulting in a total flavonoid extraction rate of 10.18%. Antioxidant assays demonstrated that the Chaenomeles speciosa (Sweet) Nakai extract exhibited significant radical scavenging activities against 1,1-diphenyl-2-picrylhydrazyl radicals, 2,2'-azinobis (3-ethylbenzothiazoline-6-sulfonic acid ammonium salt) radicals, and hydroxyl radicals, with IC50 values of 582 µg/mL, 538 µg/mL, and 1709 µg/mL, respectively. Furthermore, enzyme inhibition assays indicated that the Chaenomeles speciosa (Sweet) Nakai extract possesses notable inhibitory activity against lipoxygenase, with an IC50 value of 2658 µg/mL. This inhibition is mediated through a mixed reversible inhibition mechanism.

Species composition of root-associated mycobiome of ruderal invasive Anthemis cotula L. varies with elevation in Kashmir Himalaya

Investigating the microbial communities associated with invasive plant species can provide insights into how these species establish and thrive in new environments. Here, we explored the fungal species associated with the roots of the invasive species Anthemis cotula L. at 12 sites with varying elevations in the Kashmir Himalaya. Illumina MiSeq platform was used to identify the species composition, diversity, and guild structure of these root-associated fungi. The study found a total of 706 fungal operational taxonomic units (OTUs) belonging to 8 phyla, 20 classes, 53 orders, 109 families, and 160 genera associated with roots of A. cotula, with the most common genus being Funneliformis. Arbuscular mycorrhizal fungi (AMF) constituted the largest guild at higher elevations. The study also revealed that out of the 12 OTUs comprising the core mycobiome, 4 OTUs constituted the stable component while the remaining 8 OTUs comprised the dynamic component. While α-diversity did not vary across sites, significant variation was noted in β-diversity. The study confirmed the facilitative role of the microbiome through a greenhouse trial in which a significant effect of soil microbiome on height, shoot biomass, root biomass, number of flower heads, and internal CO2 concentration of the host plant was observed. The study indicates that diverse fungal mutualists get associated with this invasive alien species even in nutrient-rich ruderal habitats and may be contributing to its spread into higher elevations. This study highlights the importance of understanding the role of root-associated fungi in invasion dynamics and the potential use of mycobiome management strategies to control invasive species.

Promotion of Tricholoma matsutake mycelium growth by Penicillium citreonigrum

Tricholoma matsutake has been the most valuable ectomycorrhizal fungi in Asia because of its unique flavor and taste. However, due to the difficulty of artificial cultivation, the cultivation of T. matsutake has relied on natural growth in forests. To cultivate the T. matsutake artificially, microorganisms in fairy rings were introduced. In this study, we isolated 30 fungal species of microfungi from the soil of fairy rings. Among them, one single fungal strain showed a promoting effect on the growth of T. matsutake. The growth effect was confirmed by measuring the growth area of T. matsutake and enzyme activities including α-amylase, cellulase, and β-glucosidase. In comparison with control, microfungal metabolite increased the growth area of T. matsutake by 213% and the enzyme activity of T. matsutake by 110-200%. The isolated fungal strain was identified as Penicillium citreonigrum by BLAST on the NCBI database. The Discovery of this microfungal strain is expected to contribute to artificial cultivation of T. matsutake.

Draft Genome Sequence for the Symbiotic Pine Mushroom Tricholoma matsutake

We report the high-quality genome sequence of Tricholoma matsutake strain 2001, which was isolated from a mushroom fruiting body in South Korea. The genome has 80 contigs, a size of 162.6 Mb, and an N₅₀ value of 5,103,859 bp and will provide insight into the symbiotic association between T. matsutake and Pinus densiflora.

Responses of Bacterial Community Structure, Diversity, and Chemical Properties in the Rhizosphere Soil on Fruiting-Body Formation of Suillus luteus

Mycorrhiza helper bacteria (MHB) play an important role in driving mycorrhizal formation. There are few reports on the relationship between bacteria and fruiting growths. Taking mycorrhizal rhizosphere soil from sporocarps of the S. luteus and non-mycorrhizal rhizosphere soil of the host plant (Larix gmelinii), we measured the bacterial community structure and diversity and chemical properties to clarify the effect of bacteria on fruiting-body formation. The bacterial diversity was significantly higher in mycorrhizal rhizosphere soil (p < 0.05) than that in non-mycorrhizal rhizosphere soil. The relative abundance of Burkholderia, Bradyrhizobium, Pseudomonas, and Rhizobium was significantly higher (p < 0.05) in mycorrhizal rhizosphere soil than in non-mycorrhizal rhizosphere soil. The soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), ammonium nitrogen (AN), available phosphorus (AP), available potassium (AK), and the activity of catalase, urease, and phosphatase in mycorrhizal rhizosphere soil were significantly higher (p < 0.05) than those in non-mycorrhizal rhizosphere soil. A redundancy analysis (RDA) showed that dominant bacteria are closely related to soil enzyme activity and physicochemical properties (p < 0.05). The boletus recruits a large number of bacteria around the plant roots that speed up nutrient transformation and increase the soil nutrient content, providing an important guarantee for mycelium culture and fruiting-body formation. These findings provide ideas for the nutritional supply of boletus sporocarps and lay the theoretical foundation for the efficient artificial cultivation of boletus.

Isolation, genomic characterization, and mushroom growth-promoting effect of the first fungus-derived Rhizobium

Polyporus umbellatus is a well-known edible and medicinal mushroom, and some bacteria isolated from mushroom sclerotia may have beneficial effects on their host. These mushroom growth-promoting bacteria (MGPBs) are of great significance in the mushroom production. In this work, we aimed to isolate and identify MGPBs from P. umbellatus sclerotia. Using the agar plate dilution method, strain CACMS001 was isolated from P. umbellatus sclerotia. The genome of CACMS001 was sequenced using PacBio platform, and the phylogenomic analysis indicated that CACMS001 could not be assigned to known Rhizobium species. In co-culture experiments, CACMS001 increased the mycelial growth of P. umbellatus and Armillaria gallica and increased xylanase activity in A. gallica. Comparative genomic analysis showed that CACMS001 lost almost all nitrogen fixation genes but specially acquired one redox cofactor cluster with pqqE, pqqD, pqqC, and pqqB involved in the synthesis of pyrroloquinoline quinone, a peptide-derived redox participating in phosphate solubilization activity. Strain CACMS001 has the capacity to solubilize phosphate using Pikovskaya medium, and phnA and phoU involved in this process in CACMS001 were revealed by quantitative real-time PCR. CACMS001 is a new potential Rhizobium species and is the first identified MGPB belonging to Rhizobium. This novel bacterium would play a vital part in P. umbellatus, A. gallica, and other mushroom cultivation.

Isolation, Identification, and Analysis of Potential Functions of Culturable Bacteria Associated with an Invasive Gall Wasp, Leptocybe invasa

Symbioses between invasive insects and bacteria are one of the key drivers of insect invasion success. Gall-inducing insects stimulate host plants to produce galls, which affects the normal growth of plants. Leptocybe invasa Fisher et La Salle, an invasive gall-inducing wasp, mainly damages Eucalyptus plantations in Southern China, but little is known about its associated bacteria. The aim of this study was to assess the diversity of bacterial communities at different developmental stages of L. invasa and to identify possible ecological functions of the associated bacteria. Bacteria associated with L. invasa were isolated using culture-dependent methods and their taxonomic statuses were determined by sequencing the 16S rRNA gene. A total of 88 species belonging to four phyla, 27 families, and 44 genera were identified by phylogenetic analysis. The four phyla were Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, mainly from the genera Pantoea, Enterobacter, Pseudomonas, Bacillus, Acinetobacter, Curtobacterium, Sphingobium, Klebsiella, and Rhizobium. Among them, 72 species were isolated in the insect gall stage and 46 species were isolated from the adult stage. The most abundant bacterial species were γ-Proteobacteria. We found significant differences in total bacterial counts and community compositions at different developmental stages, and identified possible ecological roles of L. invasa-associated bacteria. This study is the first to systematically investigate the associated bacteria of L. invasa using culture-dependent methods, and provides a reference for other gall-inducing insects and associated bacteria.

Changes in soil bacteria functional ecology associated with Morchella rufobrunnea fruiting in a natural habitat

Morchella rufobrunnea is a saprobic edible mushroom, found in a range of ecological niches, indicating nutritional adjustment to different habitats and possible interaction with soil prokaryotic microbiome (SPM). Using the 16S rRNA gene, we examined the SPM of M. rufobrunnea that appeared in a natural habitat in Northern Israel. Three sample types were included: bare soil without mushroom, soil beneath young mushroom initials and soil beneath the mature fruiting body. Morchella rufobrunnea developmental stage was significantly associated with changes in bacterial populations (PERMANOVA, p < 0.0005). Indicator analysis with point-biserial correlation coefficient found 180 operational taxonomic units (OTU) uniquely associated with distinct stages of development. The Functional Annotation of Prokaryotic Taxonomy (FAPROTAX) database helped to infer ecological roles for indicator OTU. The functional ecological progression begins with establishment of a photoautotrophic N-fixing bacterial mat on bare soil. Pioneer heterotrophs including oligotrophs, acidifying nutrient mobilizers and nitrifiers are congruent with appearance of young M. rufobrunnea initials. Under the mature fruiting body, the population changed to saprobes, organic-N degraders, denitrifiers, insect endosymbionts and fungal antagonists. Based on this work, M. rufobrunnea may be able to influence SPM and change the soil nutritional profile.

Comparative analysis of transcriptomes revealed the molecular mechanism of development of Tricholoma matsutake at different stages of fruiting bodies

The purpose of the study is to investigate the molecular mechanisms of development of Tricholoma matsutake fruiting body at the primordial stage (TM-1), the intermediate stage (TM-2) and the mature stage (TM-3) using RNA-Seq sequencing technology. The analysis of gene expression level revealed that the Spn2 and Eef1a1 gene were the key genes in the primordial stage of T. matsutake by regulating cytokinesis, protein synthesis, and cell growth. And the Ubc, Atp6, Cytb, and Pth2 gene were the key genes in the mature stage of T. matsutake by regulating energy metabolism and protein synthesis. Differential expression genes (DEGs) analysis results showed that Cdc28, Rad53, Dun1, Pho85 and Pho81 were the key DEGs regulating cell cycle genes of T. matsutake from primordial stage to intermediate stage. And APC, Cyr1, Cdc45, Spo11 and Rec8 genes were the key DEGs for the meiosis and sporogenesis of T. matsutake from the intermediate stage to the mature stage.

Bioactive properties of streptomyces may affect the dominance of Tricholoma matsutake in shiro

Tricholoma matsutake is known to be the dominant fungal species in matsutake fruitbody neighboring (shiro) soil. To understand the mechanisms behind matsutake dominance, we studied the bacterial communities in matsutake dominant shiro soil and non-shiro soil, isolated the strains of Streptomyces from matsutake mycorrhizal root tips both from shiro soil and from the Pinus densiflora seedlings cultivated in shiro soil. Further, we investigated three Streptomyces spp. for their ability to inhibit fungal growth and Pinus densiflora seedling root elongation as well as two strains for their antifungal and antioxidative properties.

Our results showed that Actinobacteria was the most abundant phylum in shiro soil. However, the differences in the Actinobacterial community composition (phylum or order level) between shiro and non-shiro soils were not significant, as indicated by PERMANOVA analyses. A genus belonging to Actinobacteria, Streptomyces, was present on the matsutake mycorrhizas, although in minority. The two antifungal assays revealed that the broths of three Streptomyces spp. had either inhibitory, neutral or promoting effects on the growth of different forest soil fungi as well as on the root elongation of the seedlings. The extracts of two strains, including one isolated from the P. densiflora seedlings, inhibited the growth of either pathogenic or ectomycorrhizal fungi. The effect depended on the medium used to cultivate the strains, but not the solvent used for the extraction. Two Streptomyces spp. showed antioxidant activity in one out of three assays used, in a ferric reducing antioxidant power assay. The observed properties seem to have several functions in matsutake shiro soil and they may contribute to the protection of the shiro area for T. matsutake dominance.

Bacterial Community Selection of Russula griseocarnosa Mycosphere Soil

Russula griseocarnosa is a wild, ectomycorrhizal, edible, and medicinal fungus with high economic value in southern China. R. griseocarnosa fruiting bodies cannot be artificially cultivated. To better understand the effects of abiotic and biotic factors on R. griseocarnosa growth, the physicochemical properties of R. griseocarnosa and its associated bacterial communities were investigated in two soil types (mycosphere and bulk soil) from Fujian, Guangdong, and Guangxi Provinces. The results revealed that the diversity, community structure, and functional characteristics of the dominant mycosphere bacteria in all geographical locations were similar. Soil pH and available nitrogen (AN) are the major factors influencing the mycosphere-soil bacterial communities' structure. The diversity of soil bacteria is decreased in R. griseocarnosa mycosphere when compared with the bulk soil. Burkholderia-Paraburkholderia, Mycobacterium, Roseiarcus, Sorangium, Acidobacterium, and Singulisphaera may also be mycorrhiza helper bacteria (MHB) of R. griseocarnosa. The functional traits related to the two-component system, bacterial secretion system, tyrosine metabolism, biosynthesis of unsaturated fatty acids, and metabolism of cofactors and vitamins were more abundant in R. griseocarnosa mycosphere soil. The mycosphere soil bacteria of R. griseocarnosa play a key role in R. griseocarnosa growth. Application of management strategies, such as N fertilizer and microbial fertilizer containing MHB, may promote the conservation, propagation promotion, and sustainable utilization of R. griseocarnosa.

Mycorrhizosphere Bacterial Communities and their Sensitivity to Antibacterial Activity of Ectomycorrhizal Fungi

We investigated whether ectomycorrhizal (ECM) fungal species exhibit antibacterial activity towards culturable bacterial communities in mycorrhizospheres. Four hundred and thirty bacterial strains were isolated from the ECM root tips of Pinus densiflora and bulk soil, and 21 were co-cultured with six ECM fungal species. Three hundred and twenty-nine bacterial 16S rDNA sequences were identified in ECM roots (n=185) and bulk soil (n=144). Mycorrhizosphere isolates were dominated by Gram-negative Proteobacteria from 16 genera, including Burkholderia, Collimonas, Paraburkholderia, and Rhizobium. Paraburkholderia accounted for approximately 60%. In contrast, bulk soil isolates contained a high number of Gram-positive Firmicutes, particularly from Bacillus. Paraburkholderia accounted for ≤20% of the bacterial isolates from bulk soil, which was significantly lower than its percentage in ECM root tips. Co-cultures of six ECM fungal species with the 21 bacterial strains revealed that eight strains of three Gram-positive genera-Arthrobacter, Bacillus, and Lysinibacillus-were sensitive to the antibacterial activity of the fungi. In contrast, the Gram-negative strains, including five Paraburkholderia strains, two Burkholderia strains, and a Rhizobium sp., were not sensitive. The strength of fungal antibacterial activity varied in a species-dependent manner, but consistently affected Gram-positive bacteria. These results suggest that Gram-positive bacteria are excluded from the mycorrhizosphere by the antibacterial activity of ECM fungi, which develops specific soil bacterial communities in the mycorrhizosphere.

The Influence of Microfungi on the Mycelial Growth of Ectomycorrhizal Fungus Tricholoma matsutake

Pine mushroom (Tricholoma matsutake) is one of the most valued ectomycorrhizal fungi in Asia because of its unique pine-like aroma; however, due to exceptionally slow growth of its mycelia in artificial conditions, its cultivation has been largely deemed as not possible. Previous studies have shown that some bacteria and a few Trichoderma species associated with pine mushroom promoted the growth of T. matsutake isolate, but this effect is relatively unexplored. In this study, we investigated the diversity of microfungi in the fairy ring of T. matsutake and their effect on the growth of T. matsutake isolate. From 184 fungal isolates, 28 species were identified based on suitable molecular markers. Penicillium was most frequently observed (16 species), followed by Trichoderma (4 species). Five Zygomycota species showed a high promoting effect on the growth of T. matsutake while the effects of ascomycetes were mixed. The microfungi that promote the growth of T. matsutake can be useful for forest nursery and artificial cultivation of T. matsutake.

Biological and chemical diversity go hand in hand: Basidiomycota as source of new pharmaceuticals and agrochemicals

The Basidiomycota constitutes the second largest higher taxonomic group of the Fungi after the Ascomycota and comprises over 30.000 species. Mycelial cultures of Basidiomycota have already been studied since the 1950s for production of antibiotics and other beneficial secondary metabolites. Despite the fact that unique and selective compounds like pleuromutilin were obtained early on, it took several decades more until they were subjected to a systematic screening for antimicrobial and anticancer activities. These efforts led to the discovery of the strobilurins and several hundreds of further compounds that mainly constitute terpenoids. In parallel the traditional medicinal mushrooms of Asia were also studied intensively for metabolite production, aimed at finding new therapeutic agents for treatment of various diseases including metabolic disorders and the central nervous system. While the evaluation of this organism group has in general been more tedious as compared to the Ascomycota, the chances to discover new metabolites and to develop them further to candidates for drugs, agrochemicals and other products for the Life Science industry have substantially increased over the past decade. This is owing to the revolutionary developments in -OMICS techniques, bioinformatics, analytical chemistry and biotechnological process technology, which are steadily being developed further. On the other hand, the new developments in polythetic fungal taxonomy now also allow a more concise selection of previously untapped organisms. The current review is dedicated to summarize the state of the art and to give an outlook to further developments.

Paraburkholderia lacunae sp. nov., isolated from soil near an artificial pond

A Gram-stain-negative, strictly aerobic bacterial strain, designated strain S27^T, was isolated from soil near an artificial pond in South Korea. Cells were non-motile short rods showing oxidase- and catalase-positive activities. Growth of strain S27^T was observed at 20-40°C (optimum, 30°C), pH 5.0-7.0 (optimum, pH 6.0), and 0-0.5% (w/v) NaCl (optimum, 0%). Ubiquinone-8 was detected as the sole respiratory quinone and the major fatty acids were C_16:0, cyclo-C_17:0, and cyclo-C_19:0ω8c. The G + C content of the genomic DNA was 62.4 mol%. Phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminophospholipid were detected as the major polar lipids. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S27_T formed a clearly distinct phyletic lineage from closely related Paraburkholderia species within the genus Paraburkholderia. Strain S27^T was most closely related to Paraburkholderia rhynchosiae WSM3937^T, Paraburkholderia ginsengiterrae DCY85^T, Paraburkholderia fungorum NBRC 102489^T, and Paraburkholderia graminis C4D1M^T with 98.8%, 98.4%, 98.4%, and 97.7% 16S rRNA gene sequence similarities, respectively. The DNA-DNA relatedness level between strain S27^T and the type strain of P. rhynchosiae was 36.8 ± 2.6%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain S27^T represents a novel species of the genus Paraburkholderia, for which the name Paraburkholderia lacunae sp. nov. is proposed. The type strain is S27^T (KACC 19714 ^T = JCM 32721^T).

Diversity and effect of Trichoderma isolated from the roots of Pinus densiflora within the fairy ring of pine mushroom (Tricholoma matsutake)

Pine mushroom (PM, Tricholoma matsutake) is an important ectomycorrhizal fungus in Asia primarily due to its value as a food delicacy. Recent studies have shown that fairy rings of PM have distinctive fungal communities, which suggests that other fungi influence the growth of PM. Trichoderma is a well-known saprotrophic fungus commonly found in pine roots within PM fairy rings; however, little is known about the diversity of Trichoderma associated with PM and how these species influence PM growth. This study focused on diversity of Trichoderma isolated from pine roots within PM fairy rings and how these species affect the growth of PM isolate. Based on tef1a phylogenetic analyses, nine Trichoderma species (261 isolates) were identified. Trichoderma songyi and T. spirale were the dominant species, and Trichoderma community varied geographically. Growth experiments indicated that metabolites from five Trichoderma species had a significant influence on the growth of PM isolates. Metabolites of two Trichoderma species increased PM growth, while those of three Trichoderma species suppressed the growth. Within the fairy rings, Trichoderma that had a positive or neutral effect comprised the majority of Trichoderma communities. The results of this study suggest that various Trichoderma species co-exist within PM fairy rings and that these species influence PM growth.