Leaves, due to their high exposure, are particularly susceptible to environmental influences. Foliar endophytic fungi play important roles in plant resilience and adaptation yet remain poorly documented in the Zingiberaceae. This study investigated the colonisation and diversity patterns of culturable foliar endophytic fungi associated with nine host species, representing four genera of Zingiberaceae, collected from urban environments in Bogor, Indonesia. Endophytic fungi were isolated using a standardised surface sterilisation method. Colonisation rates, isolation frequencies, and diversity indices of endophytic fungi were calculated. Molecular identification was conducted via Sanger sequencing of the internal transcribed spacer (ITS) region. Host taxonomic relatedness was represented by a categorical taxonomic distance matrix derived from nomenclatural classification and used to assess its relationship with fungal colonisation and community patterns using Mantel tests. Colonisation rates differed significantly among host species and were positively correlated with host taxonomic distance, indicating that closely related hosts tended to harbour similar levels of endophytic colonisation. In contrast, fungal diversity indices and species-level distribution patterns showed no significant relationship with host taxonomy. At the genus level, endophytic communities were consistently dominated by Colletotrichum, followed by Phyllosticta and Diaporthe, whereas species-level assemblages showed no clear clustering by host. These results demonstrate that host taxonomic relatedness influences colonisation rates but does not structure species-level distribution patterns of foliar endophytic fungi in the Zingiberaceae. By focusing on culturable endophytes, this study provides new insights into host-endophyte associations and establishes a baseline for future ecological and functional studies in tropical plant systems.

The aim of our research is to explore the multifaceted and escalating impact of mold proliferation within urban environments, critically examining its implications for both microbial and macroscopic biodiversity, ecosystem function, and human well-being. As urbanization intensifies, the complex interplay between anthropogenically altered landscapes and indoor environments has precipitated a significant shift in fungal communities. This analysis moves beyond the traditional focus on merely identifying pathogenic mold to understanding its broader ecological ramifications. Specifically, we discuss how the documented increase in indoor fungal biomass and richness correlates directly with elevated water availability—a condition exacerbated by common urban infrastructure issues such as aging plumbing, poor ventilation, and the increasing frequency of extreme weather events. We investigate the hypothesis that this shift in urban mycobiomes is characterized by a proliferation of larger-spored, potentially pathogenic taxa that significantly contribute to adverse human health outcomes, including respiratory ailments and allergies. However, the scope of this research extends to the broader ecological impact on urban biodiversity. We analyze how these altered fungal communities disrupt delicate urban ecosystem services by influencing the diversity and function of other microbial and macro-organisms. Recent findings indicate a substantial reduction in both aerial and soil fungal diversity within urban areas compared to natural habitats, suggesting a profound ecological imbalance. This involves a nearly twofold reduction in species richness and a fivefold decrease in fungal DNA abundance even at small scales, underscoring a critical loss of ecological functionality necessary for urban regeneration. The prevailing indoor microbiome often comprises airborne species of outdoor origin that passively collect on surfaces rather than arising from endogenous growth. This challenges traditional views of indoor microbial sources and highlights the limitations of relying solely on mechanical systems such as heating, ventilation, and air conditioning (HVAC) to manage indoor air quality. Instead, we advocate for a holistic approach that incorporates sustainable building materials and responsive architectural design to foster resilient, diverse microbial communities. A major limitation in elucidating these complex interactions is the current reliance on 18S rRNA gene sequencing, which often lacks the taxonomic resolution required for genus-level identification. We propose that future research should employ shotgun metagenomic sequencing and RNA-based methods to distinguish viable organisms from dead cells, thereby providing a more comprehensive view of microbial diversity and metabolic pathways. Furthermore, integrating advanced "omic" approaches, ecological modeling, and machine learning will allow for the development of predictive frameworks. These frameworks are essential for understanding how urban development influences fungal successions and for informing interventions that promote beneficial microbial communities. Finally, this presentation addresses the potential of fungal bioremediation, or mycoremediation, as a sustainable solution for environmental contaminants. While current limitations in scaling exist due to knowledge gaps regarding fungal potential, biotechnological innovations offer promising avenues. We explore how genetic engineering can enhance fungal capabilities by constructing novel fungi with improved metabolic pathways for utilizing emerging contaminants. Additionally, the integration of nanotechnology with mycoremediation could significantly enhance the specificity and efficiency of contaminant degradation. By combining fungal biology with nanotechnological advancements, we can develop potent strategies for addressing persistent organic pollutants. Ultimately, this research aims to move beyond simplistic pathogen identification to embrace a functional ecological perspective, crucial for designing healthier, more resilient urban environments that balance human health needs with long-term ecosystem stability.

The application of nitrification inhibitors (Nis) with nitrogen fertilizers is increasingly used as a management strategy to improve nitrogen use efficiency in crop production systems. To evaluate the effects of Ni dicyandiamide (DCD) and 1,2,4-triazole (TZ) on the rhizosphere microbiome and strawberry yield (Fragaria × ananassa Duch.), a two-year field experiment was conducted with three treatments: unfertilized control (C), mineral nitrogen fertilizer (N) applied in two doses (40 + 40 kg N ha−1 year−1), and a single nitrogen application (80 kg N ha−1 year−1) combined with nitrification inhibitors (N + Ni). Soil microbiota were assessed using cultivation-based methods and metabarcoding of 16S rRNA and ITS2 regions. Total bacterial counts on complex media increased from 5.85 to 6.15 log CFU g−1 in the N treatment, while remaining 5.89 in N + Ni. Microscopic fungi increased in fertilized treatments during spring but decreased in July of the second year. Microbial community composition differed among treatments, although sampling time explained a larger proportion of variability than fertilization. Relative abundance of Gemmatimonas decreased under N + Ni, whereas Nitrososphaera increased. Fungal Shannon diversity decreased in N + Ni, while prokaryotic diversity did not differ significantly. Despite similar levels of mineral nitrogen measured before harvest, strawberry yield increased significantly in the N + Ni treatment in the second year, reaching 109% higher values than the control and 80% higher than the N treatment. This may indicate that the fertilization regime including nitrification inhibitors influenced nitrogen availability earlier in the growing season.

This study investigated how fertilization regimes and ridge furrow planting patterns influence the soil nutrient conditions and microbial taxonomic composition and function in the rhizosphere of spring maize in Northeast China. Three treatments were compared: CK (compound fertilizer, small ridge), KF (formula fertilization, small ridge), and BMP (formula fertilization, large double-row ridge). High-throughput sequencing was used to characterize the soil bacterial and fungal community composition and diversity. The results showed that the combination of formula fertilizer and wide-ridge cultivation synergistically improved soil physicochemical properties and significantly increased maize yield (p < 0.05). Compared with CK, both BMP and KF significantly improved the composition and diversity of microbial communities. Notably, the BMP treatment increased the relative abundances of Ascomycota and Basidiomycota-key decomposers of soil organic matter, lignin, and cellulose-which suggested enhanced nutrient cycling potential under this integrated management practice. Among the three treatments, BMP (N:P2O5:K2O = 1:2:1, 130 cm wide-ridge double-row planting) achieved the highest maize yield (859 ± 14 kg ha-1), representing an 11.0% increase over conventional practices (CK, 774 ± 13 kg ha-1). We propose that integrating optimized fertilization with ridge configuration is an effective strategy for improving soil quality, microbial functionality, and crop productivity in Northeast China's black soil region.

Annually, aspergillosis, candidiasis, cryptococcosis, and mucormycosis result in approximately 1,500,000, 650,000, 120,000, and 59,000 deaths, respectively. Mortality rates among patients receiving antifungal drug treatment range from 30% to 90%. Therefore, there is an urgent need to improve the efficacy of antifungal drug therapies against infections by these high-priority fungal diseases. Aspergillus fumigatus, Candida albicans, Cryptococcus neoformans, and Rhizopus delemar are the most common causative pathogens. We have previously developed DectiSomes, which are liposomes loaded with antifungal drugs and coated with the carbohydrate recognition domains of mouse Dectin-1 and/or Dectin-2. We demonstrated that the murine DectiSomes efficiently bound and killed these pathogens growing in vitro and/or in mouse disease models. With the plan to move DectiSomes into the clinic with the human Dectin orthologs, we were concerned that the significant sequence divergence between mouse and human Dectin-1 and Dectin-2 carbohydrate recognition domains could have altered pathogen specificity. Herein, we compared the functionality of the human and mouse Dectin-1 and Dectin-2 orthologs in targeting DectiSomes to these pathogens. Binding and growth inhibition data on A. fumigatus and C. neoformans supported their functional similarity, while results with C. albicans and R. delemar indicated some functional divergence. Despite these differences, our results demonstrate that both human and mouse DectiSomes are effective at binding and killing all four diverse fungal pathogens.

Agriophyllum squarrosum (L.) Moq., a pioneer species in desert ecosystems, is renowned for its remarkable capabilities in wind erosion control and adaptation to extreme environmental conditions. While plant-associated microbiota plays pivotal roles in host development and resilience to abiotic stress, the composition and ecological functions of endophytic microbial communities in A. squarrosum remain largely unexplored. In this study, we employed high-throughput sequencing of 16 S rRNA and internal transcribed spacer 1 (ITS1) regions, combined with functional prediction analyses, to comprehensively characterize the spatial differentiation of endophytic microbial communities across root, shoot, and leaf tissues, and to infer their potential ecological roles in host–environment interactions. Our findings revealed tissue-specific patterns in microbial community assembly, with the highest bacterial diversity observed in roots, and relatively greater fungal diversity in shoots and leaves. Taxonomically, Proteobacteria and Ascomycota emerged as the dominant bacterial and fungal phyla, respectively, with each tissue harboring distinct endophytic taxa of varying abundance. Notably, microbial communities in shoots and leaves exhibited higher compositional similarity. Co-occurrence network analyses demonstrated predominantly positive interactions among endophytic taxa, with root-associated networks displaying greater complexity and robustness. Functional predictions suggested that microbial processes such as nitrogen cycling, carbon assimilation, and cryptic oxygen metabolism—as well as pathways like ABC transporters and two-component systems—may contribute to the adaptive capacity of A. squarrosum in arid desert environments. Collectively, our study elucidates the spatial heterogeneity and ecological potential of endophytic microbial communities across different plant tissues, offering new insights into the microbial mechanisms underlying drought adaptation in desert pioneer plants.

Two medicinal mushroom species, Pleurotus tuber-regium (Lentinus tuber-regium) (commonly known as the sclerotium-forming oyster mushroom) and Ganoderma suae (a resinous polypore recently described from Southeast China in 2024)—are reported for the first time in Vietnam. The taxonomic histories of both genera, Ganoderma and Pleurotus are complex due to morphologically similarities among closely related species, posing challenges for accurate identification. In this study, specimens collected from National resources of Vietnam were identified combining detailed morphological examination with molecular analysis using rDNA ITS markers for phylogenetic confirmation. This report enhances the understanding of fungal diversity in Vietnam and provides a basis for further studies on cultivation, bioactivity, and value-added applications.

For the western Patagonia region (Argentina), climate change models predict a 1–3 °C increase in temperature and a 10%–30% reduction in precipitation. Patagonia native forests are home to a variety of soil fungi, including ectomycorrhizal fungi (EcM), which play a crucial role in drought-tolerant trees. However, the responses of soil fungi to changes in rainfall remain poorly understood. To evaluate shifts in soil fungal communities’ response under reduced precipitation scenarios and identify potentially drought-tolerant EcM species, we took 144 composite soil samples associated with Nothofagus forests along an east–west rainfall gradient. We used environmental DNA to estimate alpha and beta diversity of soil fungi and EcM. Soil fungal richness did not differ across precipitation treatments, whereas EcM richness declined with decreasing precipitation. Shannon and inverse Simpson indices of EcM decreased under reduced precipitation, whereas no significant effects were observed on soil fungi, highlighting the EcM vulnerability to water limitation. Soil fungi community composition changes along the rainfall gradient due to species replacement. Tarzetta sp., Cortinarius sp., and Russula sp. were found in drier plots, indicating a potential association with drought tolerance. Selecting native drought-tolerant EcM for forest management and restoration can improve seedling establishment and ecosystem resilience under climate change.

Maize (Zea mays L.) is the world’s third most important cereal crop, valued for its roles in human food, animal feed, industrial products, and biofuels. Its seeds harbor diverse endophytic fungi that can affect seed quality, plant health, and resilience. Given the vertical transmission of seed microbiota, this study investigated the diversity of seed-borne fungal endophytes in Egyptian maize cultivars across 18 governorates and assessed their associations with regional climate. In addition, the study evaluated the antagonistic activity of native Trichoderma isolates as potential biocontrol agents against Fusarium verticillioides, a major seed-borne pathogen threatening maize production. A total of 34 endophytic fungal species from 23 genera were identified. Aspergillus niger, Penicillium spp., A. flavus, and F. verticillioides were the most prevalent, with A. niger occurring in 97.2% of sites and F. verticillioides in 89.6%. Relative abundances were highest for Penicillium spp. (20.08%), A. niger (18.15%), and F. verticillioides (14.93%). Diversity metrics varied regionally, with species richness ranging from 8 to 22 and Shannon diversity indices (H) from 1.02 to 2.46. Canonical correspondence analysis revealed that temperature, solar radiation, and humidity collectively explained 63.6% of fungal community variation. Trichoderma longibrachiatum (T14) demonstrated the strongest antagonistic effect, inhibiting F. verticillioides growth by 74.03% in vitro and exhibiting pronounced mycoparasitic features. This study highlights the dominance of a core group of seed-borne endophytes in Egyptian maize and underscores the significant role of climate in structuring fungal communities. However, as this study was based on single-season, culture-dependent data with limited molecular validation, further multi-seasonal and molecular-based investigations are needed to confirm these patterns and fully characterize the maize seed mycobiome. Notably, T. longibrachiatum demonstrated strong biocontrol potential against F. verticillioides, offering promise as a native, eco-friendly biocontrol agent for maize production systems in semi-arid environments.

Abstract Mycorrhizal association networks, which represent community-level bitrophic interactions between plants and fungi, consistently exhibit distinct topological patterns across ecosystems. Clarifying their elevation-related dynamics is crucial for predicting the effects of climate change on plant community assembly and ecosystem resilience. On the basis of a systematic sampling of plant roots across ten elevational belts in an oak-dominated forest, we investigated the effects of elevation on mycorrhizal network specialization as well as the relative contributions of climate, plant, and soil characteristics. Our results revealed that (1) plant diversity decreased and mycorrhizal fungal diversity increased as the elevation increased. (2) Ten mycorrhizal network displayed elevated specialization (H’2) at mid-elevation zones and subalpine treelines and exhibited a hollow-shaped variation in terms of the standard effect size of H’2 (SES(H’2)) and species specialization of plants (SES(d’)), indicating that the high H’2 at subalpine treelines was mainly caused by passive sampling. (3) The SES(H’2) exhibited significantly positive relationships with plant diversity, litter thickness, and soil moisture, whereas soil parameters had negligible effects. (4) Fungal species specialization (SES(d’)) increased along with increases in the plant diversity, litter thickness, plant crown density, and soil moisture, implying that plant and climate filters governed fungal partner selection. Our findings indicate that the plant diversity and climate condition—rather than edaphic factors—serves as determinants of mycorrhizal network specialization in temperate forest ecosystems.

Despite the significant improvement in survival rates due to antiretroviral therapy, opportunistic infections continue to pose a major health risk for individuals living with HIV. As a key anatomical intersection of the upper respiratory and digestive tracts, the pharyngeal microbiome during HIV infection remains poorly characterized. This study aimed to compare the composition of bacterial and fungal communities in the pharynx between HIV-infected individuals and healthy controls, and to investigate their association with host immune status. Throat swab samples were collected from 70 HIV-infected individuals—stratified into severe, moderate, and no/mild immunosuppression groups based on CD4⁺ T-cell counts—and 18 healthy controls. Microbial composition was assessed using 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing. Bacterial alpha diversity was significantly reduced in the severe immunosuppression group (CD4⁺ T cells < 200/µL) compared to other groups, whereas fungal alpha diversity did not differ significantly across groups. Beta-diversity analysis revealed a distinct bacterial community structure in the severe immunosuppression group. Fungal communities, however, differed significantly between all HIV-infected individuals and healthy controls. At the genus level, the severe immunosuppression group exhibited a decrease in commensal bacteria such as Prevotella and an increase in Halomonas. Additionally, Candida was significantly enriched in the severe immunosuppression group, while Exophiala levels were elevated across all HIV-infected groups. The pharyngeal microbiome of HIV infected individuals undergoes significant changes, with bacterial community disorder associated with immune suppression, while the fungal community changes are more closely related to the HIV infection status of the individuals. The enrichment of Candida in individuals with severe immune suppression is more appropriately interpreted as a manifestation of fungal dysbiosis associated with advanced immunosuppression and a potential indicator of increased susceptibility to oropharyngeal candidiasis, rather than as a diagnostic biomarker of overt disease. Not applicable.

Hypogeous fungi play important ecological roles and have significant economic value. However, the hypogeous habit of these organisms hinders our understanding of their diversity and vulnerability. The first comprehensive assessment of the hypogeous fungal diversity in Korea was conducted using environmental DNA metabarcoding, encompassing 643 soil samples collected from 162 nationwide grids. A total of 186 phylotypes of hypogeous fungi (representing 32 genera) were identified through phylogeny-based identification using a curated ITS reference database that comprised 3,359 sequences from 693 species (83 genera). This number largely exceeds the 30 species recorded in Korea. The environmental preference analysis revealed two distinct ecological clusters of hypogeous fungal genera, respectively vulnerable to climate warming and to soil eutrophication. Based on geographic range criteria (Area of Occupancy and Extent of Occurrence), 10 of 15 phylotypes exhibited distribution patterns consistent with Endangered or Vulnerable thresholds. These findings reveal extensive cryptic diversity, establish baseline conservation data for hypogeous fungi, and provide a replicable methodology for global hypogeous fungal assessments in soil ecosystems.

Background and Aim: Tilapia aquaculture is rapidly expanding across Southeast Asia and plays a critical role in regional food security. While bacterial microbiomes of farmed fish have been widely investigated, the fungal component of aquatic microbial communities remains poorly characterized, particularly at the biologically important interface between rearing water and fish gills. Fungi may influence fish health, environmental microbial ecology, and occupational exposure risks within aquaculture systems. This study aimed to characterize fungal mycobiomes associated with rearing water and gills of clinically healthy red tilapia (Oreochromis spp. hybrids) cultured in Central Thailand using internal transcribed spacer (ITS) rRNA amplicon sequencing and to determine how habitat type, farming system, and environmental variables shape fungal community structure. Materials and Methods: Samples were collected from ten tilapia farms located in five provinces of Central Thailand, representing two aquaculture systems: open river cages and closed earthen ponds. A total of 27 rearing water samples and 30 composite gill samples were analyzed. Fungal DNA was extracted and the ITS1 region was amplified and sequenced using the Illumina MiSeq platform. Sequence processing and amplicon sequence variant inference were performed in QIIME2 using the DADA2 pipeline. Alpha diversity indices and beta diversity analyses were used to evaluate community structure, while multivariate statistical approaches assessed the influence of habitat type, geographic location, farming style, and physicochemical water parameters. Results: Fungal communities displayed considerable taxonomic diversity and differed significantly between habitats. Rearing water samples exhibited significantly higher alpha diversity than gill-associated communities. Dominant genera included Cladosporium, Candida, Aspergillus, Fusarium, and Rhodotorula. Gill communities were relatively enriched in Candida and Fusarium, whereas rearing water contained higher abundances of Cladosporium and Rhodotorula. Beta diversity analyses demonstrated significant effects of sampling source, province, and farming system on fungal community composition. Environmental parameters such as pH, nitrate concentration, and ionic strength were associated with variations in fungal diversity, particularly in rearing water. Several detected genera included taxa with known opportunistic pathogenic potential for fish and humans. Conclusion: This study provides the first ITS-based baseline characterization of fungal mycobiomes associated with red tilapia aquaculture systems in Central Thailand. Distinct fungal assemblages occur at the water–gill interface, with environmental conditions and aquaculture practices influencing community composition. The presence of opportunistic fungal genera highlights the importance of incorporating fungal community monitoring into aquaculture biosecurity and One Health surveillance frameworks to support sustainable fish production, environmental health, and occupational safety. Keywords: aquaculture microbiome, fish gills, fungal diversity, fungal mycobiome, ITS rRNA sequencing, One Health, red tilapia, water microbiome.

This study systematically identified the pathogenic fungi affecting Areca catechu in Hainan. Using diseased tissues from five regions, isolates were obtained using molecular methods, and their pathogenicity was confirmed using Koch’s postulates. We obtained 44 distinct fungal isolates from 9 genera. Fusarium (27.27%) and Colletotrichum (38.12%) were the dominant genera across all tissues. Twenty isolates were confirmed as pathogens. Key findings include the first report of Alternaria angustiovoidea and A. pogostemonis as areca leaf spot pathogens in China and the first confirmation of pathogenicity for three Fusarium species complexes (FSSC, FFSC, FIESC). Five Fusarium species are newly reported as pathogens in China. Cladosporium tenuissimum and Plectosphaerella cucumerina were confirmed for the first time to cause leaf spot. Fusarium, Colletotrichum, and Alternaria were core pathogens, all exhibiting high polygalacturonase and cellulase activity. The FFSC and Colletotrichum gloeosporioides species complex (CGSC) showed broad-spectrum pathogenicity on tropical fruits. Fungicide sensitivity assays ranked efficacy as prochloraz &gt; difenoconazole &gt; tebuconazole &gt; ethylicin &gt; pyraclostrobin, with genus-specific responses observed. This research fills a systematic knowledge gap on areca fungal diseases in China, providing a crucial basis for precise control strategies and integrated management.

The remarkable ability to survive desiccation and persist in a dry state is among nature's most fascinating adaptations, enabling certain organisms to withstand extreme dehydration without damage. This phenomenon has been widespread across diverse life forms, including plants, fungi, and nematodes. However, our understanding of its molecular basis, particularly in animals, remains limited. Aphelenchus avenae nematodes are notable for their exceptional tolerance to dehydration, and multiple genes related to this trait have been identified. However, the absence of a chromosome-scale, high-contiguity genome for A. avenae has been a limitation in the genome-wide identification of gene families potentially involved in desiccation tolerance. In this study, we assemble a high-quality, telomere-to-telomere haplotype genome of A. avenae Transcriptomic analyses reveal distinct sets of genes involved in responses to desiccation and freezing stress. Notably, under desiccation stress, several desiccation-tolerance genes exhibit allelic imbalance expression. Among these, we identify the stress response gene P5CS in A. avenae nematodes. Aap5cs RNAi experiments demonstrate that knockdown of Aap5cs results in increased accumulation of reactive oxygen species under desiccation stress and reduced desiccation survival time, suggesting that Aap5cs plays a role in the stress response of A. avenae This finding also raises the possibility of functional parallels between plant and nematode responses to dehydration. This study enhances our understanding of nematode resistance to desiccation stress and provides valuable genetic resources for investigating the intricate regulatory pathway that organisms use for dehydration stress adaptation.

Understanding how soil microbial communities respond to forest succession is essential for predicting ecosystem functions and biogeochemical stability. We investigated bacterial and fungal communities across three successional stages (early, mid, late) and three soil depths (0–10, 10–20, 20–50 cm) in forests of Pakistan and China using high-throughput amplicon sequencing of 108 soil samples. This cross-regional, depth-resolved study aimed to determine whether microbial successional trajectories and soil–microbe relationships are general or region-specific. Preliminary results showed that the forest succession was accompanied higher soil organic carbon (SOC), total nitrogen (TN) and declined soil pH in Pakistan. It indicates consistent acidification and potential phosphorus limitation in mature stands. Whereas SOC and total potassium (TK) exhibited mid-successional peaks in China, that indicates different resource/nutrient dynamics. Mid-forest successional stages showed maximum bacterial diversity, whereas late succession revealed the highest fungal diversity (kingdom-specific responses). Community composition shifted from copiotrophic taxa in early stages to oligotrophic taxa in mature forests. Soil pH was the most influential factor shaping microbial composition in Pakistan, whereas potassium availability was the most influential factor in China. These cross-regional, depth-resolved results reveal both successional patterns and region-specific environmental controls, offering new insights into microbial community composition during forest development and providing guidance for forest restoration and soil-carbon management across biogeographically diverse regions.

Coffee leaf rust (CLR), caused by Hemileia vastatrix, is one of the biggest economic challenges for coffee cultivation and leads to high economic losses each year. Co-occurring fungal microbial communities and their diversity in the presence of CLR are widely understudied but may harbor potential agents or indicators to reduce CLR infections. In this study, the fungal communities associated with CLR pustules in Coffea arabica L. plants across different regions of Costa Rica were analyzed. To this end, individual pustules were excised from infected leaf tissue and used as source material for DNA extraction and subsequent amplification and sequencing of the fungal taxonomic marker region ITS1. Effects of altitude and location on fungal community structure were also observed. High taxonomic variance within regions and a large proportion of unclassified taxa were detected as well as similar community structures across regions, possibly reflecting small effects of the analyzed regions on the identified taxa. However, altitude was a significant factor on the detected community structure, indicating either less favorable growth conditions for the pathogen in higher regions or favorable conditions for co-occurring taxa. This emphasizes that taxonomic identification of co-occurring fungi and their ecological relevance (e.g., potential mycoparasites) during CLR infection requires further research. This study provides a foundational framework for global coffee research by emphasizing the untapped potential of fungal community analyses to develop innovative, microbiome-informed strategies for managing coffee leaf rust and improving crop resilience.

tRNA are adapter molecules with an integral role in translation and further roles in stress adaptation. Processing of tRNA is tightly regulated and includes the enzymatic addition of several post-transcriptional modifications that are required for translation efficiency, recognition, selective translation, and structure. We currently lack a multispecies wide view of tRNA modifying enzymes across eukaryotes. Here, we performed a comparative analysis of tRNA gene sequence, modification enzymes, and modification profiles across the Saccharomycotina subphylum. We employed machine learning methods to explore tRNA sequence conservation and to annotate modifying enzymes known to exist in fungi, humans, and prokaryotes. We then applied Nano-tRNAseq to three species (Saccharomyces cerevisiae, Hanseniaspora uvarum, and Yarrowia lipolytica) to profile modification signatures and compare modification patterns. We identified substantial lineage-specific conservation of tRNA sequences despite the highly conserved tRNA structure. We found significant variation in tRNA modifying enzyme repertoires across Saccharomycotina, including lineage-specific losses, and annotated a prokaryotic-associated enzyme, tilS. Integrating genomic and sequencing data enabled us to link enzyme repertoires with tRNA gene sequences. tRNA sequencing revealed distinct modification signatures across the three focal species, and further analysis using General Linearized modelling suggested tRNA enzyme loss is associated with target tRNA nucleotide absence in gene sequences. This work provides the first integrated view of tRNA gene and modification diversity in eukaryotes and expands the field of tRNA diversity in fungi.

Substances derived from the combustion of Carpinus betulus and Salix viminalis wood may have the potential to selectively modulate the structure and diversity of soil fungi. Therefore, the aim of this study was to evaluate their effects on the structure and diversity of the mycobiome, the physicochemical and thermodynamic properties of proteins, and the biomass of Zea mays. The pot experiment was conducted for 60 days on Eutric Cambisols soil developed from sandy loam (pHKCl = 4.37). Changes in the taxonomic profile of fungi were analyzed using the ITS region sequencing. Ascomycota dominated the control soil, while the addition of substances from the combustion of S. viminalis reduced their relative abundance, and C. betulus increased it. The growth of fungi of the genera Penicillium, Fusarium, Fusicolla, Chaetomium, and Mortierella was inhibited, whereas Iodophanus was stimulated by both additives. The abundance of Vishniacozyma spp. decreased after the addition of C. betulus and increased after the addition of S. viminalis. The most thermodynamically stable proteins were observed in the genera Fusarium and Penicillium, and the least stable in Mortierella and Vishniacozyma. Substances derived from tree biomass combustion significantly altered the diversity and evenness of fungal communities and exerted an inhibitory effect on both above-ground and root biomass of plants. These results suggest that the presence of these substances in the soil influences the structure and functional activity of fungi.

Recent research has underscored the significant role of skin fungi in human health and disease. The advent of next-generation sequencing has facilitated the identification of previously unrecognized fungi; however, a standardized sampling method for the skin mycobiome has yet to be established. Given that fungi are distributed across all layers of the skin, this study aimed to establish and compare the fungal profiles obtained from paired skin swabs (skin surface) and tissue specimens (skin dermis), utilizing ITS rRNA gene sequencing. Fungal diversity and composition varied between swabs and tissue specimens from the same individual. Tissue specimens exhibited greater fungal diversity relative to skin swabs, as indicated by the Chao1 estimator (P=0.028) and Shannon index (P=0.0136). Notably, Malassezia species was more abundant in swabs (P=0.002), whereas Trichoderma species was more prevalent in tissue samples (P=0.0001). Compared to swabs, tissue sampling also demonstrated superior sensitivity in detecting non-Malassezia species. These findings suggest that skin swabs and tissue specimens provide different views of the skin mycobiome: Swabs are effective for studies targeting surface-dwelling fungi, while tissue sampling remains necessary when investigating deeper skin fungi and potential systemic infections. Future research should carefully consider appropriate sampling method based on target fungal location to mitigate procedural artifacts.Level of Evidence III This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .