The ectomycorrhizal status of a tropical black bolete, Phlebopus portentosus, assessed using mycorrhizal synthesis and isotopic analysis

Genomic and Multi-Omics Analysis of Phlebopus portentosus: Effects of Cultivation on Secondary Metabolites

Phlebopus portentosus is an edible and medicinal ectomycorrhizal mushroom with delicious and high nutritional value. However, the mechanism of secondary metabolite biosynthesis in P. portentosus is still unclear. In this study, the genomics, metabolomics, and transcriptomics were integrated to reveal the biosynthesis mechanism of secondary metabolites in P. portentosus under different cultivation conditions. The 31.4 Mb genome of P. portentosus YAF023 with 15 scaffolds was assembled by Illumina and Nanopore sequencing and annotated, and 206 cytochrome P450s, 201 carbohydrate-active enzymes, 186 transcription factors, 18 terpene synthases (TPSs), and 5 polyketide synthases (PKSs) were identified. Multi-omics analysis showed that PpPKS1 is probably involved in the biosynthesis of Ethyl orsellinate; PpPKS2 and PpPKS5 are probably involved in the synthesis of 6-Methylsalicylic acid and Cytochalasin Z5, respectively; PpTRI5 was involved in the tetracyclic sesquiterpene β-type trichodiene compounds; and PpSTCs was involved in the synthesis of β-copaene analogs or derivatives. Co-expression network analysis and binding site prediction of the promoter regions suggested that PpHOX4 and PpHSF1 regulated the gene expression of PpPKS1, and Ppzf-C2H2 32 and PpHSF5 regulated the gene expression of PpSTCs 8, and PpSTCs 3, respectively. This study will provide an important foundation for further development and utilization of secondary metabolites of P. portentosus.

Selection and validation of internal control genes for quantitative real-time RT‒qPCR normalization of Phlebopus portentosus gene expression under different conditions

Phlebopus portentosus (Berk. and Broome) Boedijn is an attractive edible mushroom and is considered the only bolete for which artificial cultivation in vitro has been achieved. Gene expression analysis has become widely used in research on edible fungi and is important for elucidating the functions of genes involved in complex biological processes. Selecting appropriate reference genes is crucial to ensuring reliable RT‒qPCR gene expression analysis results. In our study, a total of 12 candidate control genes were selected from 25 traditional housekeeping genes based on their expression stability in 9 transcriptomes of 3 developmental stages. These genes were further evaluated using geNorm, NormFinder, and RefFinder under different conditions and developmental stages. The results revealed that MSF1 domain-containing protein (MSF1), synaptobrevin (SYB), mitogen-activated protein kinase genes (MAPK), TATA-binding protein 1 (TBP1), and SPRY domain protein (SPRY) were the most stable reference genes in all sample treatments, while elongation factor 1-alpha (EF1), actin and ubiquitin-conjugating enzyme (UBCE) were the most unstably expressed. The gene SYB was selected based on the transcriptome results and was identified as a novel reference gene in P. portentosus. This is the first detailed study on the identification of reference genes in this fungus and may provide new insights into selecting genes and quantifying gene expression.

Biochemical, nutritional, and toxicological properties of the edible species Phlebopus beniensis with ethnomycological notes from Paraguay

Abstract In recent decades, mushrooms have been recognized as an important resource and efforts to characterize their potential to aid nutrition and human health have increased. Phlebopus beniensis specimen from a semi-urban community in Paraguay were analyzed for its biochemical properties, nutritional value, and toxicity. The species was identified by morpho-anatomical and molecular tools. Analyses for antioxidants by Ultraviolet-visible (UV-VIS) and nutritional content revealed that P. beniensis is a favorable source of antioxidants, proteins, carbohydrates, dietary fiber, and fats. Spectrometry through Gas Chromatography-Mass Spectrometry (GC-MS) further showcased other mycochemicals such as the specific phenolic, antioxidant, and fatty acid compounds that serve important biological roles in human diets. Applying an ethnomycological framework across local Paraguayan populations, we also report accounts of histories, knowledge, and usage of P. beniensis in South America among settlers and Paraguayan people.

Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom (Gomphus purpuraceus) Provide Insights into Its Potential Food Application and Artificial Domestication

Gomphus purpuraceus (Iwade) Yokoyama is a species of wild fungi that grows in southwest China, considered an edible and medicinal fungus with potential commercial prospects. However, the detailed mechanisms related to the development of mycelium and the formation of the fruiting body are unclear. To obtain a comprehensive overview of genetic features, whole-genome and comparative genomics analyses of G. purpuraceus were performed. High-quality DNA was extracted from the mycelium, which was isolated from a fresh fruiting body of G. purpuraceus. The DNA sample was subjected to sequencing using Illumina and Oxford Nanopore sequencing platforms. A genome assembly totaling 40.15 Mb in 50 contigs with an N50 length of 2.06 Mb was generated, and 8705 putative predicted genes were found. Subsequently, phylogenetic analysis revealed a close evolutionary relationship between G. purpuraceus and Gomphus bonarii. Moreover, a total of 403 carbohydrate-active enzymes (CAZymes) were identified in G. purpuraceus, which included 147 glycoside hydrolases (GHs), 85 glycosyl transferases (GTs), 8 polysaccharide lyases (PLs), 76 carbohydrate esterases (CEs), 57 auxiliary activities (AAs) and 30 carbohydrate-binding modules (CBMs). Compared with the other 13 fungi (Laccaria bicolor, Russula virescens, Boletus edulis, etc.), the number and distribution of CAZymes in G. purpuraceus were similar to other mycorrhizal fungi. Furthermore, the optimization of culture medium for G. purpuraceus showed the efficient utilization of disaccharides such as sucrose and maltose. The genome of G. purpuraceus provides new insights into its niche, food applications and potential artificial domestication.

Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales

We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales by comparing the genomes of 21 symbiotrophic species with their saprotrophic brown-rot relatives. Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae. Ectomycorrhizal Boletales have a reduced set of plant cell-wall-degrading enzymes (PCWDEs) compared with their brown-rot relatives. However, the various lineages retain distinct sets of PCWDEs, suggesting that, over their evolutionary history, symbiotic Boletales have become functionally diverse. A smaller PCWDE repertoire was found in Sclerodermatineae. The gene repertoire of several lignocellulose oxidoreductases (e.g. laccases) is similar in brown-rot and ectomycorrhizal species, suggesting that symbiotic Boletales are capable of mild lignocellulose decomposition. Transposable element (TE) proliferation contributed to the higher evolutionary rate of genes encoding effector-like small secreted proteins, proteases, and lipases. On the other hand, we showed that the loss of secreted CAZymes was not related to TE activity but to DNA decay. This study provides novel insights on our understanding of the mechanisms influencing the evolutionary diversification of symbiotic boletes.

Whole-Genome and Transcriptome Sequencing of Phlebopus portentosus Reveals Its Associated Ectomycorrhizal Niche and Conserved Pathways Involved in Fruiting Body Development

Phlebopus portentosus (Berk. and Broome) Boedijin, a widely consumed mushroom in China and Thailand, is the first species in the order Boletaceae to have been industrially cultivated on a large scale. However, to date, the lignocellulose degradation system and molecular basis of fruiting body development in P. portentosus have remained cryptic. In the present study, genome and transcriptome sequencing of P. portentosus was performed during the mycelium (S), primordium (P), and fruiting body (F) stages. A genome of 32.74 Mb with a 48.92% GC content across 62 scaffolds was obtained. A total of 9,464 putative genes were predicted from the genome, of which the number of genes related to plant cell wall-degrading enzymes was much lower than that of some saprophytic mushrooms with specific ectomycorrhizal niches. Principal component analysis of RNA-Seq data revealed that the gene expression profiles at all three stages were different. The low expression of plant cell wall-degrading genes also confirmed the limited ability to degrade lignocellulose. The expression profiles also revealed that some conserved and specific pathways were enriched in the different developmental stages of P. portentosus. Starch and sucrose metabolic pathways were enriched in the mycelium stage, while DNA replication, the proteasome and MAPK signaling pathways may be associated with maturation. These results provide a new perspective for understanding the key pathways and hub genes involved in P. portentosus development.

Comparative Evaluation of Chemical Composition, Phenolic Compounds, and Antioxidant and Antimicrobial Activities of Tropical Black Bolete Mushroom Using Different Preservation Methods

Tropical black bolete, Phlebopus portentosus, provides various nutritional benefits and natural antioxidants to humans. In this study, the chemical composition, phenolic compounds, and antioxidant and antimicrobial activities of fresh mushroom samples and samples stored for a period of one year using different preservation methods (drying, brining, and frozen) were investigated. The results indicated that the brining method significantly reduced the protein and fat contents of the mushrooms. The polyphenol and flavonoid contents of the frozen sample were not significantly different from that of the fresh sample. The results revealed that an inhibition value of 50% (IC₅₀) for the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay of the extract of the dried and frozen samples was not statistically different from that of the fresh sample. The IC₅₀ value of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) assay and ferric reducing antioxidant power (FRAP) value in the extract of the frozen sample were not found to be significantly different from those of the fresh sample. Furthermore, the lowest degree of antioxidant activity was found in the extract of the brined sample. Additionally, the antimicrobial activities of the extracts of the fresh and frozen samples were not significantly different and both extracts could have inhibited the growth of all tested Gram-positive bacteria and Pseudomonas aeruginosa.

A New Report on Edible Tropical Bolete, Phlebopus spongiosus in Thailand and Its Fruiting Body Formation without the Need for a Host Plant

Phlebopus spongiosus is a well-known edible ectomycorrhizal mushroom indigenous to southern Vietnam. The mushroom specimens collected from northern Thailand in this study were identified as P. spongiosus. This identification was based on morphological characteristics and the multi-gene phylogenetic analyses. Pure cultures were isolated and the relevant suitable mycelial growth conditions were investigated. The results indicated that the fungal mycelia grew well on L-modified Melin-Norkans, and Murashige and Skoog agar all of which were adjusted to a pH of 5.0 at 30 °C. Sclerotia-like structures were observed on cultures. The ability of this mushroom to produce fruiting bodies in the absence of a host plant was determined by employing a bag cultivation method. Fungal mycelia completely covered the cultivation substrate after 90-95 days following inoculation of mushroom spawn. Under the mushroom house conditions, the highest amount of primordial formation was observed after 10-15 days at a casing with soil:vermiculite (1:1, v/v). The primordia developed into a mature stage within one week. Moreover, identification of the cultivated fruiting bodies was confirmed by both morphological and molecular methods. This is the first record of P. spongiosus found in Thailand and its ability to form fruiting bodies without a host plant.

Relationship between the honeydew of mealy bugs and the growth of Phlebopus portentosus

BACKGROUND

Phlebopus portentosus and mealy bugs form a fungus-insect gall on the roots of host plants. The fungus and mealy bugs benefit mutually through the gall, which is the key link in the nutritional mechanism of P. portentosus. The cavity of the fungus-insect gall provides an ideal shelter for mealy bugs survival and reproduction, but how does P. portentosus benefit from this symbiotic relationship?

METHODOLOGY AND RESULTS

Anatomical examination of fungus-insect galls revealed that one or more mealy bugs of different generations were living inside the galls. The mealy bug's mouthpart could penetrate through the mycelium layer of the inside of the gall and suck plant juice from the host plant root. Mealy bugs excreted honeydew inside or outside the galls. The results of both honeydew agar medium and quartz tests showed that the honeydew can attract and promote the mycelial growth of P. portentosus. A test of the relationship between the honeydew and the formation of the fungus-insect gall showed that honeydew promoted gall formation.

CONCLUSIONS

All experimental results in this study show that the honeydew secreted by mealy bugs can attract and promote the mycelial growth of P. portentosus, forming a fungus-insect gall, because mealy bugs' honeydew is rich in amino acids and sugars.

Bacterial Profiling and Dynamic Succession Analysis of Phlebopus portentosus Casing Soil Using MiSeq Sequencing

Phlebopusportentosus (Berk. and Broome) Boedijin is a popular edible mushroom found in China and Thailand. To date, P. portentosus is the only species in the order Boletales that can be successfully cultivated worldwide. The use of a casing layer or casing soil overlaying the substrate is a crucial step in the production of this mushroom. In this study, bacterial profiling and dynamic succession analyses of casing soil during the cultivation of P. portentosus were performed. One hundred and fifty samples were collected, and MiSeq sequencing of the V3-V4 region of the 16S rRNA gene was conducted. After performing a decontamination procedure, only 38 samples were retained, including 6 casing soil-originated samples (OS), 6 casing soil samples (FHCS) and 5 upper substrate samples (FHCU) from the period of complete colonization by mycelia; 6 casing soil samples (PCS) and 5 upper substrate samples (PCU) from the primordium period; and 6 casing soil samples (FCS) and 4 upper substrate samples (FCU) from fruit body period. The results revealed that bacterial diversity increased sharply from the hyphal to the primordium stage and then decreased during harvesting. The non-metric multidimensional scaling (NMDS) ordination and analysis of similarities (ANOSIM) analysis suggested that the community composition during different stages was significantly different in casing soil. The most abundant phyla in all of the samples were Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Saccharibacteria, and Bacteroidetes. Burkholderia was the most abundant genus in all the samples except the OS samples. The relative abundance of Burkholderia in the FHCS samples (55.79%) decreased to 35.14% in the PCS samples and then increased to 45.60% in the FCS samples. The abundances of Acidobacterium, Rhizobium, Acidisphaera, Bradyrhizobium, and Bacillus increased from the FHCS to PCS samples. The linear discriminant analysis (LDA) effect size (LEfSe) suggested that Acidobacterium and Acidisphaera are micromarkers for PCS, whereas Bradyrhizobium, Roseiarcus, and Pseudolabrys were associated with fruit body stages. The network analyses resulted in 23 edges, including 4 negative and 19 positive edges. Extensive mutualistic interactions may occur among casing soil bacteria. Furthermore, these bacteria play important roles in mycelial elongation, primordium formations, and the production of increased yields.

The Dark Septate Endophytes and Ectomycorrhizal Fungi Effect on Pinus tabulaeformis Carr. Seedling Growth and their Potential Effects to Pine Wilt Disease Resistance

Pine wilt disease (PWD), a worldwide threat to pine forests, has caused tremendous damage to conifer forest in the world. However, little research has been conducted on the relationship between symbiosis functions of root associated fungi and pine wilt disease. In this study, we assessed the influence of seven ectomycorrhizal fungi (ECMF) and five dark septate endophytic fungi (DSE) on the growth traits and root morphology as well as the correlation of these parameters to the cumulative mortality and the morbidity rates in Pinus tabulaeformis Carr.showed the lowest cumulative mortality rates. We propose that the ECMF/DSE symbiosis enhanced the resistance of pine wilt disease via mitigation the dysfunction of water caused by PWN infection. Our research provided evidence that inoculation of ECMF/DSE could be a potential way for pine wilt disease prevention. To find highly efficient fungi for pine wilt disease management, more ECMF and DSE species should be tested.