Search Results (245)

The taxonomy of Laccaria laccata, the type species of the genus Laccaria, has long been ambiguous due to the absence of a reference sequence and the reliance on early, morphology-based descriptions. To resolve this issue, we selected a Code-compliant lectotype for Agaricus laccatus—the basionym of L. laccata—from Schaeffer’s 1762 illustration cited in Fries’ sanctioning work. Given the limitations of this historical material for modern species interpretation, we also designated an epitype based on Singer’s collection C4083 (BAFC) from Femsjö, Sweden, which was previously but not effectively designated as the “lectotype” by Singer. This epitype is supported by detailed morphological descriptions, iconography, and newly generated nrITS, nrLSU, and RPB2 sequences, which have also been newly obtained from additional collections. Phylogenetic analyses consistently place the epitype of L. laccaria within a well-supported clade, herein designated as/Laccaria laccata, which includes sequences previously reported as falling within the “proxima 1 clade”. This integrative approach, combining historical typification with modern molecular and morphological data, stabilizes the nomenclature of L. laccata and provides a robust foundation for future studies of this ecologically and economically important genus of ectomycorrhizal fungi. Full article

This study addresses the understanding of fungal diversity and their bioremediation roles in an integrated aquaculture wastewater bioremediation system, an area less explored compared to bacteria, viruses, and protozoa. Despite the rapid advancement and affordability of molecular tools, insights into fungal communities remain vague, and interpreting environmental studies in an ecologically meaningful manner continues to pose challenges. To bridge this knowledge gap, we developed an integrated aquaculture wastewater bioremediation system, incorporating photosynthetic bacteria, and utilizing internal transcribed spacer (ITS) sequencing to analyze fungal community composition. Our findings indicate that the fungal community in aquaculture wastewater is predominantly composed of the phyla Ascomycota and Chytridiomycota, with dominant genera including Aspergillus, Hortea, and Ciliphora. FUNGuild, a user-friendly trait and character database operating at the genus level, facilitated the ecological interpretation of fungal functional groups. The analysis revealed significant negative correlations between nutrient levels (COD_mn, NH₄⁺-N, NO₃⁻-N, NO₂⁻-N, and PO₄⁻³-P) and specific fungal functional groups, including epiphytes, animal pathogens, dung saprotrophs, plant pathogens, and ectomycorrhizal fungi. The removal rate for the COD_mn, NH₄⁺-N, NO₃⁻-N, NO₂⁻-N, and PO₄⁻³-P were 71.42, 91.37, 88.80, 87.20, and 91.72% respectively. This study highlights the potential role of fungal communities in bioremediation processes and provides a framework for further ecological interpretation in aquaculture wastewater treatment systems. Full article

Plant microbiomes are vital for the growth and health of their host. Tree-associated microbiomes are shaped by multiple factors, of which the host is one of the key determinants. Whether different host genotypes affect the structure and diversity of the tissue-associated microbiome and how specific taxa enriched in different tree tissues are not yet well illustrated. Chinese fir (Cunninghamia lanceolata) is an important tree species for both economy and ecosystem in the subtropical regions of Asia. In this study, we investigated the tissue-specific fungal community structure and diversity of nine different Chinese fir genotypes (39 years) grown in the same field. With non-metric multidimensional scaling (NMDS) analysis, we revealed the divergence of the fungal community from rhizosphere soil (RS), fine roots (FRs), and thick roots (TRs). Through analysis with α-diversity metrics (Chao1, Shannon, Pielou, ACE, Good‘s coverage, PD-tree, Simpson, Sob), we confirmed the significant difference of the fungal community in RS, FR, and TR samples. Yet, the overall fungal community difference was not observed among nine genotypes for the same tissues (RS, FR, TR). The most abundant fungal genera were Russula in RS, Scytinostroma in FR, and Subulicystidium in TR. Functional prediction with FUNGuild analysis suggested that ectomycorrhizal fungi were commonly enriched in rhizosphere soil, while saprotroph–parasite and potentially pathogenic fungi were more abundant in root samples. Specifically, genotype N104 holds less ectomycorrhizal and pathogenic fungi in all tissues (RS, FR, TR) compared to other genotypes. Additionally, significant correlations of several endophytic fungal taxa (Scytinostroma, Neonothopanus, Lachnum) with the growth traits (tree height, diameter, stand volume) were observed. This addresses that the interaction between tree roots and the fungal community is a reflection of tree growth, supporting the “trade-off” hypothesis between growth and defense in forest trees. In summary, we revealed tissue-specific, as well as host genotype-specific and genotype-common characters of the structure and functions of their fungal communities. Full article

In this review, we aim to provide a comprehensive overview of the roles of fungi in horticultural crops. Their beneficial roles and pathogenic effects are investigated. In addition, the recent advancements in fungal detection and management strategies (especially the use of spectral analysis) are summarized. Beneficial fungi, including plant growth-promoting fungi (PGPF), ectomycorrhizal fungi (ECM), and arbuscular mycorrhizal fungi (AMF), enhance nutrient uptake, promote root and shoot development, improve photosynthetic efficiency, and support plant resilience against biotic and abiotic stresses. Additionally, beneficial fungi contribute to flowering, seed germination, and disease management through biofertilizers, microbial pesticides, and mycoinsecticides. Conversely, pathogenic fungi cause significant diseases affecting roots, stems, leaves, flowers, and fruits, leading to crop yield losses. Advanced spectral analysis techniques, such as Fourier Transform Infrared Spectroscopy (FTIR), Near-Infrared Spectroscopy (NIR), Raman, and Visible and Near-Infrared Spectroscopy (Vis-NIR), alongside traditional methods like Polymerase Chain Reaction (PCR) and Enzyme-Linked Immunosorbent Assay (ELISA), have shown promise in detecting and managing fungal pathogens. Emerging applications of fungi in sustainable agriculture, including biofertilizers and eco-friendly pest management, are discussed, underscoring their potential to enhance crop productivity and mitigate environmental impacts. This review provides a comprehensive understanding of the complex roles of fungi in horticulture and explores innovative detection and management strategies. Full article

The land-use conversion of Masson pine forests to tea fields is extensively practiced across subtropical China, primarily driven by its economic benefit. However, the effects of this conversion on soil fungal communities and functional guilds are poorly understood. Herein, a field experiment was conducted in a Masson pine forest (F), a 5-year-old tea plantation without (FT-CK) fertilization or with (FT-N), and a 30-year-old tea plantation (FT-O) to assess the impact of Masson pine forest-to-tea conversion on soil fungal abundance, community structure, and functional guilds by using qPCR and high-throughput sequencing. Compared to F, fungal abundance significantly decreased by 95%, 68%, and 79% in FT-CK, FT-N, and FT-O, respectively, probably caused by the decreased total nitrogen content and habitat disruption. Fungal alpha diversity significantly increased in FT-N and FT-O compared to FT-CK. FT-O presented the highest percentages of Mortierella among treatments, which favours soil organic carbon accumulation. FUNGuild-based predictions showed that FT-CK and FT-N had higher relative abundances of plant pathogens than F and FT-O. FT-O presented the highest percentages of litter and soil saprotrophs but exhibited the lowest percentages of ectomycorrhizal fungi among treatments, likely driven by increased soil organic carbon, total nitrogen, and total phosphorus content. Our findings demonstrate that Masson pine forest-to-tea conversion significantly degrades soil fungal community and function, highlighting the urgent need for soil management strategies (e.g., organic amendments) to enhance soil health in tea agroecosystems. Full article

Many macrofungi are impractical or impossible to culture. Consequently, DNA for long-read sequencing required for the assembly of high-quality genomes must be isolated from samples taken from the environment. Collection is often in remote locations, limiting the options for stabilising samples to methods that do not require refrigeration. Fungi contain species-specific arrays of metabolites that may complicate purification techniques and call for judgement to be made to apply appropriate modifications to the DNA extraction protocol in specific cases. The protocols and commentary we describe are informed by the preparation of DNA from a range of Australasian ectomycorrhizal and saprotrophic macrofungi. We collect samples into isopropanol at ambient temperature and employ a strategy of chromatin isolation followed by the sequential removal of unwanted molecular components to purify DNA. Full article

Hydnum, a well-defined genus in the family Hydnaceae (order Cantharellales), is characterized by its distinctive spine-bearing hymenophores. In this study, we performed a multi-locus phylogenetic analysis (ITS-nrLSU-tef1) of Hydnum species. Integrating morphological examinations and phylogenetic evidence, we identified and delineated five Hydnum species in China, which include four novel species (Hydnum crassipedum, H. albomarginatum, H. fulvostriatum, and H. bifurcatum) and the first record (H. orientalbidum) in Anhui Province. This study provides a comprehensive morphological description (including macroscopic morphology and microscopic structure), hand-drawn illustrations (encompassing basidiocarps, basidiospores, basidia, and pileipellis hyphae), morphological comparative analysis with similar species, and comparative phylogenetic analysis with related taxa. Furthermore, we developed a dichotomous key for identifying Hydnum species distributed in China. Full article

The Qinghai-Xizang Plateau is among the most ecologically vulnerable and responsive areas worldwide. Studying the characteristics of soil microbial communities along altitudinal gradients on plateaus and revealing the response mechanisms and vertical distribution patterns of microbial communities in alpine ecosystems is of significant academic value for assessing the ecological stability of the Qinghai-Xizang Plateau. This research examines the Lhasa River Basin by employing Illumina NovaSeq high-throughput sequencing to investigate how soil bacterial and fungal communities shift across elevation gradients in the Duilong Qu subbasin. This study also explored the key environmental drivers behind these microbial distribution patterns. The results indicate the following: (1) Key bacterial groups in the Duilong Qu Basin soil include Proteobacteria, Acidobacteria, and Actinobacteria, with Ascomycota, Mortierellomycota, and Basidiomycota as the prevalent fungal phyla. (2) Soil bacterial richness fluctuates with increasing elevation, and diversity exhibits a V-shaped distribution; fungal richness increases monotonically with elevation, whereas diversity shows no altitudinal dependence. (3) Principal coordinate analysis (PCoA) revealed that bacterial community structures exhibit separation trends across different elevations, with high intragroup consistency; fungal community structures at mid-elevations (4000–5000 m) show clustering similarity, whereas those at 3650–5000 m and 5500 m remain highly distinct from those at other elevations. (4) RDA reveals that factors such as accessible phosphorus, potassium, and organic content have a major effect on how bacterial communities are arranged. On the other hand, soil conductivity, along with available and total phosphorus levels, as well as pH, plays a key role in shaping fungal communities. (5) Functional prediction analysis suggests that soil bacteria shift from aerobic and biofilm-forming to facultatively anaerobic, stress-tolerant, and pathogenic traits with increasing elevation. Fungi are predominantly undefined saprotrophs, transitioning from ectomycorrhizal and pathogenic functions to saprotrophic functions at relatively high elevations. Full article

The order Pezizales (Ascomycota) consists of cup and truffle fungi growing in a wide range of habitats and geographical zones worldwide, exhibiting diverse nutritional behaviors. In Israel, morphological studies have designated most Pezizales as saprotrophs. We re-screened Pezizales mushrooms collected in northern Israel between 2020–2022 using molecular tools based on DNA sequences of partial large subunit rRNA (28S), internal transcribed spacer (ITS), and partial heat shock protein (Hsp90) regions, along with macro images of each freshly collected samples. Trophic mode was determined through available literature and δ¹³C and δ¹⁵N stable isotope analysis along with a quadratic discriminator analysis (QDA) model to predict trophic modes: 112 collections were positively identified with identification of 23 genera; 23 taxa were resolved to the species level, 11 to approximate species, and 15 to the genus level. Helvella was the most species-rich genus; 25 species and species approximations were newly reported for Israel. Further molecular phylogenetic studies are needed to resolve species identity of the Israeli Pezizales. Most Pezizales collections were determined by trophic mode studies to be ectomycorrhizal, with a few saprotrophs. The QDA model yielded several samples with undefined nutritional behavior or a different trophic mode than previously inferred, suggesting that more in-depth study is needed to understand their trophic ecology. This study improves knowledge regarding species diversity, ecology, and evolution of Israeli Pezizales. Full article

Background/Objectives: In South China, Lithocarpus species dominate mixed evergreen broadleaf forests, forming symbiotic relationships with ectomycorrhizal fungi and serving as food resources for diverse fauna, including frugivorous birds and mammals. The limited understanding of chloroplast genomes in this genus restricts our insights into its species diversity. This study investigates the chloroplast genome (cp genome) sequences from seven Lithocarpus species, aims to elucidate their structural variation, evolutionary relationships, and functional gene content to provide effective support for future genetic conservation and breeding efforts. Methods: We isolated total DNA from fresh leaves and sequenced the complete cp genomes of these samples. To develop a genomic resource and clarify the evolutionary relationships within Lithocarpus species, comparative chloroplast genome studies and phylogenetic investigations were performed. Results: All studied species exhibited a conserved quadripartite chloroplast genome structure, with sizes ranging from 161,495 to 163,880 bp. Genome annotation revealed 130 functional genes and a GC content of 36.72–37.76%. Codon usage analysis showed a predominance of leucine-encoding codons. Our analysis identified 322 simple sequence repeats (SSRs), which were predominantly palindromic in structure (82.3%). All eight species exhibited the same 19 SSR categories in similar proportions. Eight highly variable regions (ndhF, ycf1, trnS-trnG-exon1, trnk(exon1)-rps16(exon2), rps16(exon2), rbcL-accD, and ccsA-ndh) have been identified, which could be valuable as molecular markers in future studies on the population genetics and phylogeography of this genus. The phylogeny tree provided critical insights into the evolutionary trajectory of Fagaceae, suggesting that Lithocarpus was strongly supported as monophyletic, while Quercus was inferred to be polyphyletic, showing a significant cytonuclear discrepancy. Conclusions: We characterized and compared the chloroplast genome features across eight Lithocarpus species, followed by comprehensive phylogenetic analyses. These findings provide critical insights for resolving taxonomic uncertainties and advancing systematic research in this genus. Full article

Forest plantations in the Neotropics aim to alleviate pressure on primary forests. This study synthesizes knowledge on pine species used in these plantations, emphasizing the challenges and potential of ectomycorrhizal fungi and bacteria as inoculants. An analysis of 98 articles identifies 23 pine species in Mexico and Central America and about 16 fast-growing species in South America. While pine plantations provide a habitat for generalist species, they reduce the richness of specialist species. Ectomycorrhizal fungi and bacterial diversity in plantations with introduced pines is up to 20% lower compared to native ecosystems. Suillus and Hebeloma are commonly used as mycorrhizal inoculants for Neotropical and introduced species, including Pinus ponderosa and Pinus radiata in South America. Commercial inoculants predominantly feature the fungal species Pisolithus tinctorius, alongside bacterial genera such as Bacillus, Cohnella, and Pseudomonas. This study emphasizes the importance of leveraging native microbial communities and their synergistic interactions with ECM fungi and bacteria to enhance seedling growth and quality. Such a combined approach can improve plantation survival, boost resilience to environmental stressors, and promote long-term productivity. These findings underscore the need to incorporate native fungi and bacteria into inoculant strategies, advancing sustainable forestry practices and ecosystem adaptation in the Neotropics. Full article

Pinus tabuliformis is a well-recognized woody mycorrhizae host plant growing in North China. EM fungi contribute to the host health and the stability of the forest ecosystem. However, ectomycorrhiae (EM) fungal community associated with this species is less documented. In this study, we examined EM fungal diversity and composition of P. tabuliformis from three sites in Inner Mongolia, China by using Illumina MiSeq sequencing on the rDNA ITS2 region. Our results showed that a total of 105 EM fungal operational taxonomic units (OTUs) were identified from 15 composite root samples, and the dominant lineages were /suillus-rhizopogon, /tomentella-thelephora, /tricholoma, /amphinema-tylospora, /wilcoxina, /inocybe, and /Sebacina. A high proportion of unique EM fungal OTUs (33, 31.4% of total OTUs) were detected, and some abundant OTUs preferred to exist in specific sites. The composition of EM fungal communities was significantly different among the sites, with soil, climatic, and spatial variables being related to the community variations. The EM fungal community assembly was mainly driven by environmental factors in deterministic processes. These findings suggest that this endemic Pinaceae species in China also harbored a rich and distinctive EM fungal community and deterministic processes played more important roles than stochastic in shaping the symbiotic fungal community. Our study improves our understanding of EM fungal diversity and community structure from the perspective of a single host plant that has not been investigated exclusively before. Full article

Pine wilt disease (PWD) poses a significant threat to pine forest health, making sanitation thinning of infected trees and cultivation of disease-resistant pine stands crucial measures for forest ecosystem restoration. To date, limited studies have systematically investigated how post-sanitation planting of pine-wilt-disease-resistant Pinus species affects soil microbiome, especially regarding bacterial and fungal diversity characteristics, functional succession patterns, and community assembly processes. In this study, we performed a comparative analysis of soil microbial community characteristics and biochemical properties between experimental plots subjected to sanitation thinning and those replanted with disease-resistant pine species. The results indicated that compared to the sanitation-thinned experimental plot, the disease-resistant experimental plots (Pinus taeda experimental plot and Pinus thunbergii experimental plot) exhibited significantly higher activities of β-glucosidase (S-β-GC), N-acetyl-β-D-glucosidase (S-NAG), and soil arylsulfatase (S-ASF). Compared with the sanitation logging stands, our analysis revealed that the Pinus taeda experimental plot and Pinus thunbergii experimental plot exhibited significantly higher fungal community evenness (OTUs), greater species abundance (OTUs), and more unique fungal taxa. Furthermore, the edaphic properties—specifically soil moisture content (SMC), pH levels, and total potassium (TK)—significantly influenced the structures of soil bacterial and fungal communities. Compared to the sanitation-thinned experimental plot, wood saprotrophic fungi and ectomycorrhizal fungi exhibited increased abundance in both the P. taeda experimental plot and Pinus thunbergii experimental plot. Furthermore, the null models indicated that both the P. taeda experimental plot and P. thunbergii experimental plot enhanced the undominated processes of bacteria and fungi. In summary, our data elucidate the differences in bacterial and fungal responses between pine forests undergoing thinning due to infected trees and those cultivated for disease resistance. This deepens our understanding of microbial functions and community assembly processes within these ecosystems. Full article

Ectomycorrhizal fungi of the genus Tuber (Ascomycota) produce hypogeous ascomata commonly known as truffles. Despite their high ecological and economic importance, a considerable gap of knowledge exists concerning the diversity of Tuber species in the eastern Mediterranean region. In the frame of this study, more than 200 Tuber collections, originating from various regions of Greece, were examined. A new species to science, i.e., Tuber leptodermum, is formally described. Tuber leptodermum is grouped in the Maculatum clade, as revealed by the ITS and LSU rDNA concatenated phylogenetic tree, and appears as sister to T. foetidum. In addition, T. leptodermum exhibits distinct morphoanatomic features: it produces medium-sized, dark-brown ascomata with a thin pseudoparenchymatous peridium, composed of globose-to-angular cells and forms one-to-four-spored asci containing reticulate–alveolate, ellipsoid ascospores with broad meshes. Thirty other phylogenetic species are identified: seven of them (i.e., T. anniae, T. buendiae, T. conchae, T. dryophilum, T. monosporum, T. regianum and T. zambonelliae) constitute new records for the Greek mycobiota, while the presence of five other species is molecularly confirmed for the first time. Moreover, the existence of ten undescribed phylogenetic species is revealed, six of which are reported for the first time in Greece. Several taxonomic and phylogenetic issues and discrepancies in the genus Tuber are discussed in relation to the new findings. Full article

This study explored how potted treatments (with and without Scleroderma bovista inoculation) shape rhizosphere microbial diversity in hazel across five soils using split-root cultivation. Three treatments (control, split-root, split-root with S. bovista) were analyzed for root growth and microbial dynamics. S. bovista inoculation consistently enhanced root parameters (number, tips) in all soils. Potted treatments (with and without S. bovista inoculation) altered microbial features (OTU/ASV), with only 0.9–3.3% of features remaining unchanged. At the class level, potting increased Agaricomycetes abundance while reducing Sordariomycetes, a trend amplified by S. bovista. Potting decreased species richness estimates (ACE and Chao1), while both treatments lowered diversity index (Shannon index). Potted treatments without S. bovista inoculation drove stronger shifts in species composition than inoculation. Findings reveal potting and S. bovista synergistically recruit symbiotic fungi via root exudates, establishing disease-suppressive communities that selectively inhibit pathotrophic fungi (particularly plant pathogen Coniothyrium and fungal parasite Cladobotryum) while roughly maintaining non-pathogenic saprotrophic microbes essential for organic matter decomposition. This work provides insights for optimizing hazel orchard management and ectomycorrhizal agent development. Full article