Rhizopogon species are important ectomycorrhizal (ECM) symbionts of Pinaceae and play a vital role in seedling establishment. Although nearly three hundred Rhizopogon species have been recorded globally, Asian taxa remain poorly characterized. This study reported the first confirmed occurrence of Rhizopogon in Vietnam and the first evidence of its ECM association with Pinus kesiya. Field surveys in P. kesiya forests of Lam Dong Province (Vietnam) yielded three basidiomata and a cluster of ECM root tips. Both morphological features and ITS-based phylogenetic analysis identified the basidiomata and ECM fungal partner as Rhizopogon boninensis, which was previously considered endemic to the southern islands of Japan. Amplicon sequencing of bulk soil samples further confirmed the presence of R. boninensis propagules in the local forest ground. The in vitro co-culture of P. kesiya seedlings with R. boninensis successfully produced ECM root tips. The ECM seedlings exhibited significantly enhanced height, dried biomass, and root development, respectively 1.7, 2.9, and 3 times compared with non-inoculated controls. These results extend the known distribution of R. boninensis and highlight its potential as a native-compatible bioinoculant to support P. kesiya propagation and reforestation across Southeast Asia.

The Anna Karenina Principle (AKP) posits that healthy microbiomes converge toward similar compositional states, whereas dysbiotic microbiomes diverge into distinct and system-specific configurations. Despite its broad recognition in microbiome research, systematic evidence remains scarce as to whether pathogen stress drives plant microbiome assembly in accordance with AKP. To address this knowledge gap, we examined 1,410 samples from multiple compartments (bulk soil, rhizosphere soil, roots, stems, and seeds) across a continental-scale, comparing healthy and Fusarium stalk rot-infected maize using 16S rRNA gene sequencing, complemented with metagenomic sequencing of 93 selected rhizosphere and stem samples. By integrating variations of bacterial community diversity, beta dispersion, average variation degree, and a modified stochasticity ratio, we demonstrated that pathogen-induced microbiome shifts conform to AKP predictions. Notably, AKP-conforming stochastic assembly enriched oligotrophic taxa, resulting in microbial communities with higher GC content, smaller average genome size, and reduced 16S rRNA operon copy numbers. Moreover, the selective enrichment of specific functional traits (including peptidoglycan biosynthesis and degradation, chromatin structure and dynamics, and lipid transport and metabolism) was closely associated with AKP. Our findings support AKP as a useful framework for understanding plant microbiome assembly under pathogen pressure and provide new insights into plant-microbiome-pathogen interactions.

Mycological studies in China have achieved substantial and encouraging progress in recent decades. In this paper, the discoveries of novel fungal taxa published by Chinese mycologists and the documented records of fungi distributed in China are statistically summarized based on the data retrieved from Fungal Names and the Checklist of Fungi in the China database, respectively. Our analysis reveals that a total of 2875 Chinese scholars have published 20,826 new fungal taxa to date, 65% of which were published within the past decade. During the same period, Chinese mycologists placed great importance on archiving fungal diversity data and have completed the compilation of the national checklist of fungi. Based on 382,503 records derived from over 18,200 research articles and 300 books, a total of 31,180 fungal species, spanning 17 phyla, 65 classes, 240 orders, 840 families, and 4531 genera, have been documented in China. The southwestern region, especially Yunnan Province, exhibits the highest richness of documented species. These results provide a comprehensive overview of the current status of fungal biodiversity and taxonomic studies in China, providing a valuable foundation for future investigations.

Fungal secondary metabolism plays a critical role in pathogen-host interactions, yet the regulatory networks linking metabolic reprogramming to virulence remain poorly understood. This study identifies a conserved regulatory hub in the human pathogen Aspergillus fumigatus, where the RNA-binding protein (RBP) CsdA interacts with the global regulator LaeB in the nucleus to regulate biosynthesis of the secondary metabolite fumiquinazoline C (FqC). Disruption of the CsdA-LaeB interaction hyperactivates FqC production, enhancing fungal colonization and lethality in murine invasive aspergillosis models. Integrative metabolomic and transcriptomic analyses reveal that CsdA and LaeB function as co-regulators of a broader secondary metabolic gene cluster network, with FqC emerging as an effector that mediates virulence in vivo. Genetic validation confirms that FqC is strictly required for the increased virulence phenotype of CsdA- or LaeB-deficient strains, while analyses of clinical isolates demonstrate a striking inverse correlation: reduced CsdA and LaeB expression coincides with elevated FqC production, showing consistency with the infection outcomes of the deletion mutants. This work identifies the RBP-based interaction that regulates fungal metabolic virulence, shedding new light on the post-transcriptional regulatory logic linking secondary metabolism to pathogenicity and offering alternative strategies for diagnostic development and therapeutic intervention in invasive fungal diseases.

Seven previously undescribed compounds, acrenoids A-G (1-7), along with two known compounds (8 and 9), were isolated from the culture of the deep-sea-derived fungus Acremonium sclerotigenum LW14. The structures of these compounds were characterized by a combination of spectroscopic studies, ECD calculations, and ECD experiments induced by Rh2(OCOCF3)4. Acrenoid A (1) features a distinctive 5/5/7 tricyclic ring framework. Moreover, all isolates were evaluated for their antifungal activities. Notably, compound 9 exhibited potent antifungal activity against drug-resistant Candida auris 12766, with a MIC of 4 μg/mL. In addition, compound 9 exhibited low hemolytic toxicity. The antifungal mechanism of compound 9 involves cell membrane disruption and intracellular ROS accumulation. In addition to these effects, it also inhibited biofilm formation in C. auris 12766. These findings highlight compound 9 as a promising antifungal candidate for treating C. auris.

Colletotrichum species are major plant pathogens and emerging opportunistic human pathogens. Due to their vast genetic diversity, existing diagnostic tools often suffer from narrow specificity or labor-intensive workflows. In this study, we developed a rapid, universal, and highly sensitive genus-specific real-time PCR assay utilizing a TaqMan MGB probe targeting the conserved 28S rDNA region. The assay demonstrated exceptional specificity, with no cross-reactivity against closely related fungal taxa or common co-occurring pathogens. The method exhibited high sensitivity, achieving a limit of detection (LOD) of 680 fg of genomic DNA. Furthermore, the assay was successfully validated using simulated environmental samples, where it accurately identified Colletotrichum within complex fungal communities. By providing a robust platform for genus-level screening, this methodology significantly enhances the efficiency of phytosanitary inspections and clinical diagnostics, facilitating timely biosecurity interventions and therapeutic decisions.

Emerging pathogen races spreading via long-distance migration increasingly threaten global agricultural ecosystems. Understanding how pathogens migrate and adapt to new hosts via virulence evolution is crucial for developing strategies to mitigate future crop damage. Here we performed biosurveillance of Puccinia polysora, a global fungal pathogen causing southern corn rust (SCR), across China, Thailand and the Philippines. By analysing 193 field transcriptomic data, we detected both epidemic and endemic lineages co-circulating in each country and elucidated the crucial role of host selection in driving the diversification of endemic lineages. Gene flow assessments and trajectory tracking indicated that the SCR infection source in northern China is likely of domestic origin and pathogen migration from the Philippines/Thailand into China is restricted to Hainan, coastal Guangdong and southern Yunnan. We detected country-specific variants in 32 effector genes, with AvrRppC exhibiting the strongest positive selection. A phylogenetically distinct Luzon Island lineage (Philippines), carrying a novel AvrRppC allele capable of overcoming RppC-mediated resistance and represents a potentially invasive threat. Finally, we reviewed the global migration history of P. polysora in light of our findings. Our work represents the first step toward establishing an international surveillance network for P. polysora and emphasised a comprehensive control strategy integrating local governance and invasion prevention of international races.

Soil fungi play an indispensable role in maintaining soil ecosystem functions. However, how forest succession and soil depth interactively shape fungal community composition and diversity remains poorly understood. To address this, we investigated fungal communities across four successional stages and two soil depths (0–10 cm and 40–60 cm) in a subalpine forest on the eastern Qinghai–Tibetan Plateau using Illumina high-throughput sequencing. Results showed that the soil fungal community composition of different trophic modes varied significantly with both succession and soil depth. The α-diversity of symbiotic and saprotrophic fungi responded to succession in a depth-dependent manner, while β-diversity across all trophic modes was primarily driven by species turnover. Soil properties and vegetation factors collectively explained 69.85–82.91% of the variation in soil fungal community composition, with their effects being dependent on both soil depth and trophic mode. Specifically, in topsoil, the β-diversity of symbiotic fungi was influenced only by soil property heterogeneity, whereas that of saprotrophic and pathogenic fungi was shaped by both vegetation and soil property heterogeneity. In subsoil, symbiotic fungal β-diversity was co-regulated by vegetation and soil properties heterogeneity, while saprotrophic fungal β-diversity was driven solely by soil properties heterogeneity. This study demonstrates that soil depth modulates the successional dynamics of soil fungal communities and highlights the trophic-dependent drivers of fungal assembly in forest soils.

Circadian clocks are known to modulate host immune responses to pathogen infections, yet their role in influencing pathogen pathogenesis remains unclear. Here, we investigated the role of circadian clocks in regulating the pathogenesis of the fungal pathogen Fusarium oxysporum, which has multiple genes homologous to the Neurospora crassa frq due to gene duplication events, with Fofrq1 being the primary circadian clock gene. The pathogenesis of F. oxysporum in plants is controlled by its circadian clock, with infections causing severe disease symptoms at dawn. Notably, disruption of clock genes dramatically reduces fungal pathogenicity. Circadian clocks regulate the rhythmic expression of several transcription factors, including FoZafA, which enables the pathogen to adapt to zinc starvation within the plant, and FoCzf1, which governs the production of the toxin fusaric acid. Together, our findings highlight the critical roles of circadian clocks in F. oxysporum pathogenicity by regulating zinc starvation response and secondary metabolite production.

With the increase in cross-border transmission in the context of globalization, the necessity for developing rapid and accurate detection methods for plant pathogens has become critical. This study introduces a recombinase polymerase amplification (RPA) technique combined with CRISPR/Cas12a cleavage and fluorescence-based detection systems (FRB) or paper-based lateral flow strips (PLFS) for the rapid on-site detection of invasive alien fungi, specifically Alternaria triticina and Plenodomus libanotidis, which pose significant threats to agriculture and biodiversity. The results demonstrate that either RPA-CRISPR/Cas12a-FRB or RPA-CRISPR/Cas12a-PLFS can accurately detect the target species within 30 min, with a sensitivity of up to 10 pg/μL. These portable and easy-to-use assays are suitable for rapid on-site screening of plant pathogenic fungi in plant tissues, enabling applications in disease control and port quarantine.

The Qinghai-Xizang Plateau is a globally renowned biodiversity epicentre which plays an important role in maintaining the ecological health of China and the Asian region. Understanding the distribution of phytopathogenic fungi in the major agricultural zones of Qinghai-Xizang Plateau is crucial for the agricultural management of major crops (e.g., highland barley) in the region. The genus Fusarium and its relatives in the family Nectriaceae (Ascomycota, Hypocreales) encompass a diverse array of species with pathogenic and ecological significance, but previous studies to the region have been very limited. This study aims to investigate the diversity and distribution of species belonging to Fusarium and allied genera in Xizang. A hitherto most intensive collection of diseased crops and samples of sediments, soils, and water from adjacent environments of cropland was carried out at 56 sites in Xizang, resulting in the isolation of 916 strains of fusarioid fungi. Using the FUSARIUM-ID v.3.0 and the FUSARIOID-ID databases, these strains were preliminarily classified into six genera: Cosmospora (4 strains), Fusarium (867 strains), Fusicolla (17 strains), Neocosmospora (21 strains), Neonectria (1 strain), and Thelonectria (6 strains). The representative strains were then subjected to multi-locus phylogenetic analyses, resulting in the identification of 46 species, including 17 new species described in this study and 8 new records for China. Our results provided preliminary insights into the species diversity and distribution of Fusarium and related genera in the Xizang region, and also suggested that cropland, including crop material, as well as neighboring ploughed and irrigated environments constitute a major reservoir for fungal pathogens.

The forma specialis concept has been a cornerstone in Fusarium phytopathology for 85 years, classifying pathogens based on host specificity. However, its validity as a natural and practical framework has been increasingly questioned. In this study, we critically re-evaluate the forma specialis concept through an extensive survey of Fusarium wilt diseases across 37 crop hosts from 23 provinces of China. Through multi-locus phylogenetic analyses, morphological assessments, and pathogenicity tests on 659 strains isolated from 171 diseased samples, we identified 46 Fusarium species, including seven newly described taxa, and uncovered extensive cross-host pathogenicity, with up to 21 species associated with the same wilt disease. In addition, 57% of samples exhibited multiple species co-infections, revealing significant inconsistencies with the forma specialis framework. These findings challenge the long-standing paradigm of host specificity in Fusarium pathogens and advocate for a shift of perspective to a “pathobiome” framework, where disease dynamics are largely driven by community-level interactions rather than single-pathogen relationships. Applying these conceptual advances to Fusarium wilt research could fundamentally transform our comprehension of host-pathogen relationships and facilitate the development of more ecologically sustainable disease management approaches.

Irpex lacteus is a fungus typically found on angiosperm branches and trunks. Here, we report the isolation of a novel strain of I. lacteus from the cervix uteri of a female patient diagnosed with endometriosis and COVID-19 at Beijing Obstetrics and Gynecology Hospital, Capital Medical University. Using whole-genome sequencing, we generated a high-quality draft genome for this human-derived strain. Comparative genomic analysis revealed significant variations amongst I. lacteus strains colonizing distinct environments. Functional annotations indicated that environmental adaptation has influenced specific functional traits in the strains. Moreover, potential virulence factors were identified, implying a risk of opportunistic infections associated with I. lacteus. This study elucidates the adaptive characteristics of I. lacteus across ecological niches and provides genomic insights into its opportunistic colonization.

Understanding the population structure of pathogens and the genetic determinants driving virulence gains is crucial for managing epidemic plant diseases. Puccinia polysora , a giga-scale fungal pathogen causing southern corn rust, has posed significant threat to global food security recently. Traditionally, P. polysora was considered clonal with minimal genetic variation. However, our population genomic and transcriptomic studies conducted in China, the emerging epicentre of the disease, have challenged this view. By adopting variant analyses appropriate to the dikaryotic nature of the pathogen, we discovered an unexpectedly clear population structure with six distinct groups. A cryptic group exhibits high virulence, facilitated by group-specific variation, and diversification of effectors. Although the Chinese population of P. polysora is predominantly asexual, internuclear exchange on some chromosomes have introduced recombination signals. The comprehensive pan-effectorome analyses revealed substantial presence/absence variation and alternative splicing events on effectors, shaping a highly adaptive effector repertoire in P. polysora . In conclusion, our findings highlight the tandem mapping on exploring clear genetic structure of dikaryotic species and reported the emergence of a virulent group and an adaptive effectorome of P. polysora . Effective containment strategies must be flexible to counter the threats posed by the unexpectedly dynamic evolution of this pathogen. ### Competing Interest Statement The authors have declared no competing interest. Strategic Priority Research Program of Chinese Academy of Sciences, XDB0830000 the Key Collaborative Research Program of the Alliance of International Science Organizations, ANSO-CR-KP-2022-07 National Natural Science Foundation of China, 32472506

The Qinghai-Xizang Plateau (QXP), harboring the planet’s highest density of plateau lakes, offers an exceptional biogeographic environment for studying extremophilic microbial communities and their adaptation to salinity. Through deep metagenomic sequencing, we construct the Qinghai-Xizang Lake Sediment Genome (QXLSG) catalog, a high-resolution genomic catalog comprising 5,866 metagenome-assembled genomes (MAGs), 58.16 million non-redundant protein encoding genes, and 19,008 biosynthetic gene clusters. Notably, 80.78% of the 2,742 species-level MAGs represent undescribed taxa, significantly expanding the known microbial diversity. Salinity emerges as the primary environmental factor influencing microbial community. Functional annotation highlights that the “salt-out” strategy, particularly the uptake of glycine betaine, is the main mechanism for salinity tolerance. This strategy is prevalent in both hypersaline lake communities and the dominant microbial phyla. Overall, this study provides a crucial genetic resource for future bioprospecting and deepens our understanding of the fundamental mechanisms of microbial adaptation to extreme saline environments.

Thirteen previously unreported ascochlorin-type meroterpenoids, acrocholrins A-M (1-13), together with seven known analogues (14-20) were characterized from the deep-sea-derived fungus Acremonium sclerotigenum LW14 guided by LC-MS/MS-based molecular networking. Their structures and absolute configurations were determined unambiguously by spectroscopic analysis, electronic circular dichroism (ECD) calculations, and single-crystal X-ray diffraction experiments. Compounds 1/3, 2/14, 6/7, 8/17, and 15/16 are diastereomers isomerized at C-10. Additionally, compounds 5, 11, 12, and 13 represent rare ascochlorin analogues featuring an uncommon 19S configuration in the cyclohexanone ring. Compounds 9, 11, and 19 exhibited antifungal activity against Cryptococcus gattii 3271G1 with the same minimum inhibitory concentration (MIC) of 4 μg/mL. Preliminary mechanistic studies showed that compound 9 exhibited its anti-C. gattii activity by inhibiting capsule formation and increasing cell membrane permeability.

With the increase in cross-border transmission in the context of globalization, the necessity for developing rapid and accurate detection methods for plant pathogens has become critical. This study introduces a recombinase polymerase amplification (RPA) technique combined with CRISPR/Cas12a cleavage and fluorescence-based detection systems (FRB) or paper-based lateral flow strips (PLFS) for the rapid on-site detection of invasive alien fungi, specifically Alternaria triticina and Plenodomus libanotidis, which pose significant threats to agriculture and biodiversity. The results demonstrate that either RPA-CRISPR/Cas12a-FRB or RPA-CRISPR/Cas12a-PLFS can accurately detect the target species within 30 min, with a sensitivity of up to 10 pg/mu L. These portable and easy-to-use assays are suitable for rapid on-site screening of plant pathogenic fungi in plant tissues, enabling applications in disease control and port quarantine.

The Colletotrichum gloeosporioides species complex (CGSC) is one of the most devastating fungal phytopathogens, and is composed of three main clades: Kahawae, Musae, and Theobromicola. Despite the diversity of CGSC, there is limited understanding on their evolutionary mechanisms. By analysing 49 newly assembled genomes, we found that the expansion of transposable elements, especially long terminal repeat retrotransposons, facilitates the expansion of genome size and genetic variation. In-depth analyses suggested that an intra-chromosomal inversion may have been the driving force behind the divergence of Kahawae clade from its ancestor. Within the Kahawae clade, the narrow-hosted quarantine species C. kahawae has undergone extensive chromosomal rearrangements mediated by repetitive sequences, generating highly dynamic lineage-specific genomic regions compared to the closely related broad-hosted species C. cigarro. The findings of this study highlight the role of chromosomal rearrangements in promoting genetic diversification and host adaptation, and provide new perspectives for understanding the evolution of phytopathogenic fungi.

Two new butanolides asperbutanolides A (1) and B (2), and a new fatty acid derivative omphalotol C (3), along with 5 known compounds were isolated from the ethyl acetate (EtOAc) crude extract of the deep-sea-derived fungus Aspergillus tabacinus LW82 guided by OSMAC (One Strain Many Compounds) strategy. The structural elucidation and absolute configuration determination of these compounds were achieved by comprehensive spectroscopic analysis, including nuclear magnetic resonance (NMR), high-resolution electrospray ionization mass spectrometry (HRESIMS), and [Rh2(OCOCF3)4]-induced electronic circular dichroism (ECD) experiment. Compound 1 exhibited antibacterial activity against Pseudomonas syringae pv. Lachrymans with MIC value of 64 μg ml−1. Furthermore, compound 6 displayed significant antifungal efficacy against Cryptococcus gattii R265 and 3284G14, with both MIC values of 8 μg ml−1, comparable to the antifungal agent fluconazole.