The online version contains supplementary material available at 10.1007/s13205-026-04743-w.

The characteristics of metabolites accumulation and their connections with endophytic fungi in roots and stems of Ephedra sinica with different cultivation ages.

Stochastic process dominated community assembly during high-temperature Daqu storage, leading to reduced microbial co-occurrence network complexity.

ABSTRACT The Brazilian savanna designated as Cerrado is one of the most biodiverse biomes in the world, yet it has lost nearly 50% of its native vegetation since the mid-20th century, mostly due to agricultural expansion. This rapid degradation makes it one of the most threatened biodiversity hot spots worldwide, highlighting the urgent need for intensified conservation and biodiversity research efforts. The systematic study of rust fungi (Pucciniales) in the Brazilian Cerrado began around 140 years ago with the temporary emigration from Germany of the explorer and collector Ernst Heinrich Georg Ule (*1854–†1915) to Brazil where he was hired as a “visiting naturalist” serving in the National Museum of Rio de Janeiro from 1891 until 1895. Since then, approximately 270 species of rust fungi have been documented in the Cerrado. Historically, taxonomic classifications of rust fungi relied strongly on the interpretation of morphological traits, which are prone to subjective bias that has led to taxonomic instability and is reflected in complex taxonomic histories. Furthermore, recent molecular phylogenetic studies have revealed a high frequency of homoplasious traits in rust fungal morphology, further complicating accurate taxonomic decisions when such traits are considered in isolation. In this study, we conducted morphological and molecular phylogenetic analyses on several rarely collected and studied genera of Cerrado rust fungi, evaluating phylogenetic relationships and discussing their taxonomy. We describe a new Puccinia species infecting the genus Coracoralina (Eriocaulaceae: Poales), Puccinia coracoralinae, sp. nov. along with a new genus Dietelomyces, gen. nov. and several new combinations, i.e. Cerradopsora pouteriae, nom. nov. Dietelomyces copaiferae, comb. nov. besides defining the suprageneric status of Esalque holwayi, Dietelia duguetiae, Kimuramyces cerradensis, and Mimema venturae. Additionally, we discuss the effects of identified homoplasious traits on rust fungal systematics based on our phylogenetic analyses. Considering published estimates of rust fungal diversity in other regions, we conclude that with approximately 12 356 documented vascular plant species in the Cerrado, at least ca. 2300 rust fungal species can be expected to be present. This suggests that, to date, ca. of 13% of the rust fungi occurring in the Cerrado has been documented. Given the alarming threat status of the Cerrado and its extremely significant biodiversity, we also emphasize and discuss the potential implications of systematic rust fungal research for future conservation policies in this unique ecosystem. By addressing key taxonomic and phylogenetic gaps, this study highlights rust fungi as a critically understudied component of Cerrado biodiversity and reinforces the urgent need to expand field collections and integrate fungal systematics with conservation strategies as habitat loss accelerates.

Atmospheric deposition threatens aquatic ecosystems, yet its effects on the microbial diversity, composition, and function in rivers remain unclear. Here, we examined the responses of microbial communities to atmospheric pollutants across 105 Chinese rivers. We found that PM2.5 and PM10 were associated with reduced bacterial and fungal diversity and richness. Structural equation modeling revealed that atmospheric deposition (e.g., PM2.5, SO2, NO2, and organic matter aerosol) was directly and indirectly associated with bacterial and fungal community composition through cascading pathways mediated by dissolved oxygen, pH, Mn, inorganic nitrogen, nitrate nitrogen, ammonium nitrogen, and chlorophyll-a. Compared with fungal communities, bacterial communities exhibited broader environmental thresholds and greater sensitivity to atmospheric pollutants. Ecological network analysis further revealed that deposition preferentially disrupted mutualistic motifs in bacterial networks but intensified competitive interactions in fungal networks. Metagenomic analysis revealed that atmospheric pollution is significantly associated with key microbial functional genes involved in carbon degradation (e.g., glucoamylase, pullulanase, and β-glucosidase), nitrogen assimilation and reduction (e.g., nifD, narB, and nirS), and sulfur reduction (e.g., sat, aprA, and dsrA) in rivers. Our findings underscore the importance of air quality mitigation in terms of protecting river ecosystem health.

ABSTRACT ‘Fungus blindness’ is a persistent underappreciation of fungi’s importance and has significant implications for building regenerative futures. This study explores public perceptions of fungi in a predominantly ‘fungi-blind’ society and whether experiential engagement can challenge them. Two formats were examined: (1) a hands-on workshop, encouraging noticing fungi at macro and micro scales, and (2) an immersive audio experience giving voice to afictional fungus, prompting reflection on ecological interconnectedness. Using Personal Meaning Mapping, the mental models of 70 participants were captured pre- and post-intervention, revealing both affective and cognitive dimensions. Analysis focused on the breadth of participant understanding around ‘fungi’. Pre-intervention findings revealed narrow perceptions dominated by ‘Mushroom’, ‘Food’ and ‘Poison’, alongside limited knowledge of fungal diversity, morphology, and classification. Participants expressed minimal awareness of fungi’s ecological and biotechnological significance alongside a fascination with their strangeness. Post-intervention, ecological learning expanded across both cases, with contextual elements (e.g. ‘trees’ and ‘soil’) facilitating emerging understanding of fungi. Modest shifts towards eco-centric perspectives were also observed, demonstrating the value of experiential approaches in encouraging human-fungi and broader nature-connection. This study advocates educational reform, targeted outreach, and proposes a refined definition of fungus blindness with actionable learning aims.

The Fairy ring (FR) is a circular formation created by the mycelium of the FR fungus during its dynamic proliferation in the soil. FRs were categorized into three types based on their varying effects on adjacent plants. Type I FRs (T1) cause extensive damage with wilting and necrosis, Type II FRs (T2) promote growth with dark-green zones, and Type III FRs (T3) feature fruiting bodies with minimal impact on vegetation. T2 FR often display conspicuous growth-promoting zones and thus are studied more frequently than other types. Here we compare three FR types-Agrocybe sp. (T1), Agaricus campestris (T2), and Clitocybe sp. (T3)-across zones (ON (beneath the fruiting body)/IN (20cm inward from the ON zone) /OUT (20cm outward from the ON zone) and depths (0-10/10-20cm) in Tibetan alpine meadows using 16S and ITS amplicon sequencing. We infer putative microbe-fungus associations from diversity patterns, differential abundances, and co-occurrence analyses. Our research revealed that bacterial diversity was minimal in the ON zones; in contrast, fungal diversity was maximal, which may be attributable to the selection and interspecific competition among FR fungi. Taxa enriched in ON zones differed among FR types: T1 exhibited enrichment of Nitrospiria (nitrification) and Phycisphaerae (organic matter decomposition); T2 demonstrated enrichment of Actinobacteria and Proteobacteria, correlating with plant-growth enhancement; T3 displayed diminished recruitment, consistent with negligible vegetation influence. Cross-kingdom co-occurrence networks demonstrated increased microbial collaboration in ON zones, especially in surface soils for T1/T3 and in subsurface layers for T2. Different types of FR fungi exert varying effects on soil microorganisms at different depths. This study provides comparative data on three types of fairy rings and their associated soil microorganisms, offering insights into elucidating the potential mechanisms of fungal-bacterial-plant interactions. However, further validation through metabolomics and controlled experiments is still required.

During an investigation of lignicolous freshwater fungi on the Qinghai–Xizang Plateau, two hyphomycetous isolates were obtained from submerged wood in freshwater habitats. Morphological studies combined with multi-gene phylogenetic analyses based on ITS, LSU, and TEF1-α sequences revealed that the isolates belong to the genus Codinaea (Chaetosphaeriaceae). Based on both molecular and morphological evidence, a new species, C. linzhiensis, is introduced and described herein from its asexual morph. Detailed morphological descriptions and justifications for the establishment of this new species are provided. This discovery further expands the known diversity of freshwater fungi on the Qinghai–Xizang Plateau.

Fungal communities exhibit strong spatial and environmental structuring across forest ecosystems, yet the drivers shaping their diversity patterns remain incompletely understood. In this study, we combined multivariate ordination, clustering analyses, and Zeta diversity (ζ-diversity) metrics to characterize fungal assemblages across environmental gradients. Canonical Correspondence Analysis (CCA) revealed that fungal community composition was significantly associated with climatic variables, particularly seasonal precipitation, thermal variation, and elevation. Hierarchical and K-means clustering identified coherent community clusters that differed in species richness and alpha diversity. Bray–Curtis distances and a Ward-based dendrogram further supported this separation, revealing a clear hierarchical structure in community similarity. Zeta diversity analysis indicated a slower species turnover, suggesting niche assimilation and habitat homogenization. Furthermore, the grouping of fungal assemblages followed a power-law model, emphasizing the role of deterministic environmental filtering. Critically, our findings reveal that only 1208 (33.5%) of the 3606 recorded species are present within existing Protected Natural Areas (PNAs), indicating a significant conservation gap. Together, these results provide an integrated ecological understanding of fungal diversity patterns, highlighting how climate–topography interactions structure communities and emphasizing the urgent need to align conservation strategies with these environmental drivers.

Traditional cultivation of medicinal Cyclocarya paliurus has consistently failed to resolve the growth-secondary metabolism trade-off, affecting yield and quality. Utilizing dark septate endophyte, which induces host plant endogenous hormone synthesis and enhances stress resistance, offers a feasible and effective method to balance this trade-off relationship. In this study, sterile C. paliurus seedlings were subjected to dark septate endophyte inoculation, jasmonic acid (JA) spraying and JA inhibitor treatments. We demonstrated that dark septate endophyte inoculation increased seedling height by 59.46% and biomass by 15.94%. This treatment established an antioxidant barrier in plants, maintained reactive oxygen species homeostasis and alleviated membrane lipid peroxidation, thereby boosting plant stress resistance. ITS gene sequencing confirmed that dark septate endophyte enhanced root fungal diversity. Integrated multi-omics analysis revealed that dark septate endophyte promoted flavonoid biosynthesis (total flavonoids increased by 15.30%) through triggering the JA signaling pathway to activate MYC2-mediator complex subunit 25, significantly increasing vitexin content. Our results identify dark septate endophyte as a pivotal metabolic checkpoint for synergistically enhancing medicinal plant yield and quality. This study provides novel insights into eco-efficient cultivation strategies and lays the foundation for the broader application of beneficial dark septate endophyte in agroforestry practices.

The impact of silo-bag storage on Fusarium diversity, mycotoxin contamination, and grain deterioration in bread wheat genotypes.

Copper and synthetic pesticides are major drivers of soil bacterial and fungal communities.

ABSTRACT Fungi are ubiquitous organisms that play a crucial role in ecosystem functioning and biotechnology. New fungal discoveries from diverse parts and habitats worldwide significantly contribute to the understanding of fungal diversity. Micro- and macro-fungi samples collected from terrestrial habitats in China, India, Italy, and Pakistan were subjected to morphological and multi-locus phylogenetic analyses. The results revealed several new species and new records. Based on the results, we introduce 16 new fungal species, viz. Agaricus ferruginosquamulis, Amanita bengalensis, Candolleomyces striatus, Conferticium yunnanense, Diplodia yunnanensis, Hymenopellis himalayana, H. kashmirensis, Kirschsteiniothelia hongheensi, Phaeoisaria xishuangbannaensis, Phaeosphaeriopsis agave, Phialoarthrobotryum jeewonii, Pseudocercospora cordifoliana, Pseudosperma aranyakum, Roussoella bambusicola, Sporidesmium duyunense, and Tropicoporus chennaiensis. There are seven new host or geographical records for Agaricus thujae, Candolleomyces eurysporus, C. sulcatotuberculosus, Diplodia acerigena, Phaeographis decipiens, Pseudocoleodictyospora sukhothaiensis, and Russula yanshanensis. Descriptions, illustrations, and phylogenetic analyses results for the 23 taxa are provided, and the new taxa are compared with their closely related taxa.

Pine wilt disease (PWD), caused by Bursaphelenchus xylophilus, is a destructive forest disease leading to rapid mortality. Although Chongqing is a major epidemic region in China, the population genetic structure of B. xylophilus and the ecological interactions among nematode occurrence, blue stain formation, and microbial community dynamics remain insufficiently clear. This study systematically surveyed nematode incidence and performed morphological and molecular identification, revealing strong correlations between nematode presence, blue stain, and insect infestation (p < 0.0001). Within Monochamus alternatus, nematodes were mainly distributed in the abdomen and thorax (p < 0.0001). High-throughput sequencing showed significantly higher fungal (e.g., Leptographium) and bacterial (e.g., Burkholderia-Caballeronia-Paraburkholderia) diversity in diseased than healthy pinewood, indicating pronounced microbial shifts during disease progression. mtCOI-based genetic analyses of 162 nematodes from 11 populations revealed five haplotypes, with Hap1 shared across all populations. AMOVA indicated that over 80% of genetic variation occurred within populations, and neutrality and mismatch analyses suggested recent expansion in some populations (Beibei, Jiangbei, Rongchang). These findings clarify nematode epidemiology, microbial shifts, and genetic characteristics in Chongqing, providing a scientific basis for precise sampling, rapid detection, and integrated management of PWD, and suggest that microbial community changes may contribute to rapid pine decline.

Abstract Despite decades of research, the associations between plants and their mycorrhizal fungi remain poorly understood. In ecosystems with a mix of arbuscular mycorrhizal (AM) and ectomycorrhizal (EM)‐associated trees, tree species richness and tree mycorrhizal association may shape mycorrhizal fungal communities and below‐ground processes. Utilizing a long‐term biodiversity–ecosystem function experiment at the Smithsonian Environmental Research Center (SERC), we investigated how tree species richness (1, 4, 12 species) and tree mycorrhizal association (AM, EM, mixed) influence the diversity and composition of the soil microbiome. We further assessed how above‐ and below‐ground taxonomic and functional diversity influence soil characteristics. We hypothesized that soil microbial communities would be more strongly driven by tree mycorrhizal association than tree species richness and that both tree mycorrhizal association and fungal diversity would affect soil characteristics. Tree mycorrhizal type influenced EM fungal richness, diversity and turnover more strongly than tree species richness, with tree mycorrhizal association effects on turnover 2.4 times greater. Conversely, tree species richness led to a significant increase in AM hyphal length, while AM fungal relative abundance was linked to mycorrhizal association. Neither tree species richness nor tree mycorrhizal association directly impacted soil characteristics. Instead, shifts in fungal diversity and composition affected soil characteristics. 3. AM fungal richness was positively associated with acid phosphatase (AP) extracellular enzyme activity (EEA), whereas AM fungal hyphal lengths were positively associated with N ‐acetyl‐glucosaminidase (NAG) EEA. The AP EEA was negatively correlated with inorganic phosphate (PO 4 3− ) concentrations in soils whereas NAG EEA was positively correlated with inorganic nitrate (NO 3 − ). 4. Shifts in the composition of saprotrophic and pathogenic fungi correlated with soil organic carbon (SOC) stocks, suggesting SOC decomposition rate, rather than accumulation, drove carbon storage in these plots. Synthesis . By jointly manipulating tree species richness and tree mycorrhizal association, we demonstrated that mycorrhizal associations drive EM fungal diversity and composition and AM fungal abundance while indirectly influencing soil characteristics via below‐ground microbiomes. As global change alters plant and fungal diversity and guild structure, understanding the universality of these above‐ and below‐ground linkages will be critical for predicting ecosystem‐level responses.

Abstract Soil fungi play major roles in ecosystem functioning and plant resilience to environmental stresses. However, they are often overlooked in ecosystem restoration plans. In the Coastal Range of southern Chile, the endangered conifer Alerce ( Fitzroya cupressoides ) is the second longest-lived tree species on Earth and one of the largest in South America. These Alerce forests are currently facing major threats due to habitat destruction and climate change. Using ITS2 and SSU soil metabarcoding, we characterized soil and mycorrhizal fungal communities in an Alerce forest comprising a millennial tree (the ‘Alerce Abuelo’) estimated to be over 2400 years old. We also compared the performance of reference DNA sequence databases (i.e. MaarjAM, UNITE and EUKARYOME) for the taxonomic identification of mycorrhizal fungi in metabarcoding data. Beneath the Alerce Abuelo, soil fungal richness was 2.25 higher than the mean richness per sample, harboring 361 unique fungal OTUs. Likewise, arbuscular mycorrhizal (AM) fungal richness was 1.75 times higher than the mean richness per sample. Soil and AM fungal richness positively correlated with diameter at breast height (DBH) and tree biomass, and negatively with available phosphorus, which was the best predictor of fungal community composition. Finally, EUKARYOME detected more mycorrhizal taxa compared to MaarjAM for SSU (AM fungi) and UNITE for ITS2 (ectomycorrhizal fungi). We therefore recommend to carefully evaluate the approaches used for assigning mycorrhizal guilds in comparative studies. Our study illustrates the importance of millennial trees in sustaining fungal diversity in forest soils. By accumulating fungal diversity as they age, large-diameter Alerce trees can act as umbrella species for soil and mycorrhizal fungi, thereby protecting fungal communities for future forest restoration efforts.

Soil microbiome drives soil multifunctionality across slope positions in a mountain tea plantation ecosystem.

Phoenix Nirvana and rebirth-pyrophilous microbes reconstruct soil microbial communities in a short term post-fire forest.

Ecosystems worldwide are undergoing unprecedented changes, and as a result amphibians are experiencing devastating population declines driven by subsequent habitat loss and emerging pathogens. The skin microbiota is an important first line of defence for amphibians against pathogens. Here, for the first time, we characterised the bacteria and fungi comprising the skin microbiota of 56 individual golden Alpine salamanders (Salamandra atra aurorae, Trevisan, 1982), a highly endemic and endangered amphibian subspecies. In addition, we investigated the impact of the 2018 Vaia windstorm on skin microbiota of salamanders in plots classified as impacted or non-impacted based on windthrows. Salamander sex, weather during sampling, and dominant tree species in plots were also investigated as influencers of microbiota. Beta diversity estimates revealed greater variation in bacterial microbiota composition among individuals from non-impacted plots compared to plots impacted by Vaia. Notably, we found differential abundances of five genera of bacteria and eight genera of fungi in the skin microbiota of salamanders from impacted compared with non-impacted plots. Further analyses revealed that median relative abundances of Aeromonas hydrophila, the causative agent of the potentially fatal red-leg syndrome, were significantly higher in microbiota of salamanders from impacted plots. Weather conditions during sampling significantly influenced both alpha and beta diversity of the skin microbiota, and explained up to 9% of bacterial and 6% of fungal variation. Bacterial richness and phylogenetic diversity were lower during rainfall, whereas fungal beta diversity increased, suggesting contrasting moisture preferences. These findings suggest that extreme weather events, as well as moderate daily weather fluctuations, may be associated with the microbial communities of amphibian skin, potentially affecting their resilience to pathogens. This study underscores the importance of considering both natural and human-mediated disturbances in conservation strategies for vulnerable species like the golden Alpine salamander.

Characterization and analysis of the skin mycobiome in keloid: A case-control study.