Journal of Fungi

20 pages, 5162 KB

Open AccessArticle

Annual Dynamics of Mycobiota in Symptomatic Century-Old Trees of Aesculus hippocastanum, Fagus sylvatica, Populus alba, and Quercus robur

by Milan Spetik, Lucie Frejlichova, Jana Cechova, Pavel Bulir, Lenka Miksova, Lukas Stefl, Pavel Simek and Ales Eichmeier

J. Fungi 2026, 12(1), 50; https://doi.org/10.3390/jof12010050 (registering DOI) - 11 Jan 2026

Abstract

This study investigated the composition and temporal dynamics of wood-inhabiting fungal communities in four aging tree species in Lednice Castle Park (Czech Republic), located within the Lednice–Valtice Cultural Landscape, a UNESCO World Heritage Site. Forty wood cores were collected from 20 trees at [...] Read more.

This study investigated the composition and temporal dynamics of wood-inhabiting fungal communities in four aging tree species in Lednice Castle Park (Czech Republic), located within the Lednice–Valtice Cultural Landscape, a UNESCO World Heritage Site. Forty wood cores were collected from 20 trees at two time points (2023 and 2024). The hosts included horse chestnut (Aesculus hippocastanum L.), copper beech (Fagus sylvatica ‘Atropunicea’ L.), oak (Quercus robur L.), and poplar (Populus alba L.), each exhibiting visual signs of decline. Fungal assemblages were profiled using ITS2 high-throughput amplicon sequencing. Ascomycota dominated across all hosts (72–89% of reads), while Basidiomycota contributed 8–24%, largely represented by Agaricomycetes in F. sylvatica. Alpha diversity varied significantly among hosts (Shannon: F_3,36 = 10.61, p = 0.001 in 2023; F_3,36 = 10.00, p = 0.001 in 2024). Temporal shifts were host-dependent: F. sylvatica exhibited the strongest year-to-year decline in richness (Chao1: −83%, p = 0.007) and increased beta dispersion, while A. hippocastanum and P. alba showed significant increases in diversity (+65% and +42%, respectively). Community composition was shaped by host species (PERMANOVA Bray–Curtis: p = 0.001) and shifted over time (Jaccard: p = 0.001), with F. sylvatica showing the highest temporal turnover. Functional guild analysis revealed consistent dominance of saprotrophs (29–41%) and mixed pathotroph–saprotroph guilds (23–36%) across hosts, indicating active degradation processes inside functional xylem. These results indicate that, within the studied system, the wood mycobiome of aging trees is host-dependent and temporally dynamic rather than static or functionally neutral. Short-term temporal turnover observed between sampling years may contribute to shifts in fungal community composition and succession within wood, with potential implications for tree decline processes in managed historical park landscapes. Full article

(This article belongs to the Special Issue Innovations in Diagnosis and Management of Wood-Rotting Fungal Diseases)

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16 pages, 1104 KB

Open AccessArticle

Inhibitory Effect of Trichoderma longibrachiatum on Growth of Fusarium Species and Accumulation of Fumonisins

by Ruiqing Zhu, Ying Li, María Viñas, Qing Kong, Manlin Xu, Xia Zhang, Xinying Song, Kang He and Zhiqing Guo

J. Fungi 2026, 12(1), 49; https://doi.org/10.3390/jof12010049 (registering DOI) - 10 Jan 2026

Abstract

Fusarium spp. cause devastating crop diseases and produce carcinogenic mycotoxins such as fumonisins, threatening global food safety and human health. In this study, Trichoderma longibrachiatum A25011, isolated from apples in Aksu, Xinjiang, exhibited significant antagonistic activity with mycelial growth inhibition rates of 54.52% [...] Read more.

Fusarium spp. cause devastating crop diseases and produce carcinogenic mycotoxins such as fumonisins, threatening global food safety and human health. In this study, Trichoderma longibrachiatum A25011, isolated from apples in Aksu, Xinjiang, exhibited significant antagonistic activity with mycelial growth inhibition rates of 54.52% against F. verticillioides 48.62% against F. proliferatum, and 58.22% against F. oxysporum in confrontation assays. Enzyme activity detection revealed high chitinase (583.21 U/mg protein) and moderate cellulase (43.92 U/mg protein) production, which may have the capacity to degrade fungal cell walls. High-Performance Liquid Chromatography–Mass Spectrometry (HPLC-MS/MS) analyses enabled the quantification of fungal hormones including gibberellin A3 (GA3, 2.44 mg/L), cytokinins (cis-zeatin riboside (CZR): 0.69 mg/L; trans-zeatin riboside (TZR) : 0.004 mg/L; kinetin: 0.006 mg/L), and auxins (indole-3-acetic acid (IAA) : 0.35 mg/L; abscisic acid: 0.06 mg/L). Application of a T. longibrachiatum A25011 spore suspension around the roots of peanut plants enhanced growth by 13.20% (height), 5.65% (stem and leaf biomass), and 39.13% (root biomass). Notably, A25011 reduced F. proliferatum-derived fumonisin accumulation in rice-based cultures by 93.58% (6 d) and 99.35% (10 d), suggesting biosynthetic suppression. The results demonstrated that T. longibrachiatum strain A25011 exhibited excellent biocontrol capability against Fusarium spp., proving its dual role in simultaneously suppressing fungal growth and fumonisin accumulation while promoting plant growth. T. longibrachiatum A25011 could be applied as a multifunctional biocontrol agent in sustainable agriculture in the future. Full article

(This article belongs to the Special Issue Advances in the Control of Plant Fungal Pathogens)

20 pages, 42623 KB

Open AccessArticle

The Interference of Mnsod3 Enhances the Tolerance of Pleurotus ostreatus Mycelia to Abiotic Stress by Reshaping the Cell Wall

by Ludan Hou, Tonglou Li, Baosheng Zhang, Zehua Zhang, Bing Deng, Lijing Xu, Xueran Geng, Yanfen Cheng, Mingchang Chang and Junlong Meng

J. Fungi 2026, 12(1), 48; https://doi.org/10.3390/jof12010048 (registering DOI) - 10 Jan 2026

Abstract

In recent years, the response mechanism of Pleurotus ostreatus to abiotic stress has received widespread attention. MnSOD is an important antioxidant enzyme that has been widely studied in animals and plants because of its functions. However, there is little research on the function [...] Read more.

In recent years, the response mechanism of Pleurotus ostreatus to abiotic stress has received widespread attention. MnSOD is an important antioxidant enzyme that has been widely studied in animals and plants because of its functions. However, there is little research on the function and regulatory mechanism of MnSOD in the growth and development of edible fungi. This study investigated the role of Mnsod3 in the growth and development of P. ostreatus. The results showed that during the nutritional growth stage, heat stress can cause the cell wall of mycelia to shrink and the cells to exhibit cytoplasmic wall separation. RNA-seq revealed that Mnsod3 interference is strongly correlated with increased transcript levels of cell wall synthase genes and with increased tolerance to cell wall disruptors. During the primordium formation stage, the mycelial cell wall also significantly wrinkled under cold and light stresses. RNAi of Mnsod3 alleviated the cell wall wrinkling caused by cold and light stress, restored the smoothness of the cell walls, and increased mycelial tolerance to abiotic stress. This may be related to the slower formation rate of primordia, but the specific molecular mechanism still needs further research. and slowed the rate of primordium formation. In summary, Mnsod3 plays an important role in the growth and development of P. ostreatus under abiotic stress and plays a critical regulatory role in cell wall remodeling under abiotic stress. Full article

(This article belongs to the Section Fungal Cell Biology, Metabolism and Physiology)

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18 pages, 2041 KB

Open AccessArticle

Tuning FLO1 Expression via Promoter Engineering Modulates Flocculation Degree and Acetic Acid Stress Tolerance in Saccharomyces cerevisiae

by Pei-Liang Ye, Wei-Bin Wang, Liang Xiong, Guang-Xian Peng, Cheng Cheng and Xin-Qing Zhao

J. Fungi 2026, 12(1), 47; https://doi.org/10.3390/jof12010047 - 9 Jan 2026

Abstract

Robust yeast tolerance to inhibitors is essential for lignocellulosic biorefinery. Although cell flocculation is known to enhance acetic acid stress tolerance, the impact of its intensity remains unclear. In this study, engineered S. cerevisiae strains with distinct floc sizes were constructed through promoter [...] Read more.

Robust yeast tolerance to inhibitors is essential for lignocellulosic biorefinery. Although cell flocculation is known to enhance acetic acid stress tolerance, the impact of its intensity remains unclear. In this study, engineered S. cerevisiae strains with distinct floc sizes were constructed through promoter engineering. The native FLO1 promoter in the non-flocculating laboratory strain BY4741 was replaced with either the constitutive strong promoter PGK1p or the ethanol-inducible promoter TPS1p using CRISPR-Cas9-mediated genome editing, resulting in strongly and moderately flocculating strains BY4741 PGK1p-FLO1 and BY4741 TPS1p-FLO1, respectively. It was revealed that the BY4741 PGK1p-FLO1 showed a survival advantage in the late-stage fermentation and severe stress condition in the presence of 7.5 g/L acetic acid, while BY4741 TPS1p-FLO1 exhibited superior growth and fermentation performance under 5.0 g/L acetic acid stress. Further studies suggested that the enhanced acetic acid tolerance in flocculating cells was associated with their ability to maintain significantly higher intracellular ATP levels under stress. Our work highlights the importance of optimizing flocculation properties for robust industrial fermentation, and also provides a strategic basis for engineering stress-tolerant yeast strains for efficient fermentation in inhibitor-rich cellulosic hydrolysates. Full article

(This article belongs to the Special Issue Stress Tolerance in Yeast Biotechnology)

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23 pages, 12097 KB

Open AccessArticle

Structure Elucidation and Toxicity Analyses of the Degradation Products of Aflatoxin B₁ and Zearalenone by Trichoderma reesei GG-T40

by Yixuan Wang, Lixia Fan, Guidong Li, Changying Guo, Mingxiao Ning, Bingchun Zhang, Jiangyong Qu and Xianfeng Ren

J. Fungi 2026, 12(1), 46; https://doi.org/10.3390/jof12010046 - 8 Jan 2026

Abstract

Mycotoxin contamination in agricultural products poses a serious challenge to food safety, severely threatening human and animal health and causing significant economic losses. This study aimed to investigate the degradation and detoxification capabilities of Trichoderma reesei GG-T40 against two representative mycotoxins—aflatoxin B₁ [...] Read more.

Mycotoxin contamination in agricultural products poses a serious challenge to food safety, severely threatening human and animal health and causing significant economic losses. This study aimed to investigate the degradation and detoxification capabilities of Trichoderma reesei GG-T40 against two representative mycotoxins—aflatoxin B₁ (AFB₁) and zearalenone (ZEN). The results showed that the degradation rates of AFB₁ and ZEN by this strain reached 98.6% and 88.4%, respectively. Using ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF MS), the degradation products were systematically characterized, leading to the identification of six AFB₁ degradation products (C₁₇H₁₄O₇, AFD₁: C₁₆H₁₄O₅, C₁₁H₁₀O₄, C₁₄H₁₆O₄, C₁₅H₁₀O₄, and C₁₇H₁₄O₅) and two ZEN degradation products (α-ZOL and β-ZOL). Toxicity evaluation revealed that the key toxic structures of AFB₁ were disrupted, significantly reducing or even eliminating the toxicity of its degradation products; ZEN was mainly converted into β-ZOL (accounting for 91.5%), which has lower estrogenic activity. Further toxicological experiments in mice confirmed that the degradation products were non-toxic and non-pathogenic under actual testing conditions, demonstrating systematic verification of their safety. In conclusion, T. reesei GG-T40 can efficiently and safely degrade AFB₁ and ZEN, showing great potential for developing green control technologies for mycotoxin contamination in food and feed raw materials, with important application value for ensuring food safety. Full article

(This article belongs to the Section Fungi in Agriculture and Biotechnology)

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16 pages, 3746 KB

Open AccessArticle

T2T Colletotrichum lini Genomes with Hifiasm: ONT R9 and R10 Read Processing and Assembly Guidelines for Fungi

by Elizaveta A. Ivankina, Ekaterina M. Dvorianinova, Alexander A. Arkhipov, Antoniy M. Kaplun, Tatiana A. Rozhmina, Ludmila P. Kudryavtseva, Nikolai M. Barsukov, Olesya D. Moskalenko, Fedor D. Kostromskoy, Kirill A. Klimov, Andrei A. Artamonov, Elena V. Borkhert, Daiana A. Krupskaya, Elena N. Pushkova, Nataliya V. Melnikova and Alexey A. Dmitriev

J. Fungi 2026, 12(1), 45; https://doi.org/10.3390/jof12010045 - 7 Jan 2026

Abstract

The assembly of telomere-to-telomere (T2T) genomes is essential for understanding genomic architecture, especially in fungal pathogens with complex karyotypes, such as Colletotrichum lini, causing flax anthracnose disease. This study provides optimized guidelines for the T2T genome assembly using Oxford Nanopore Technologies (ONT) [...] Read more.

The assembly of telomere-to-telomere (T2T) genomes is essential for understanding genomic architecture, especially in fungal pathogens with complex karyotypes, such as Colletotrichum lini, causing flax anthracnose disease. This study provides optimized guidelines for the T2T genome assembly using Oxford Nanopore Technologies (ONT) R9.4.1 and R10.4.1 sequencing data processed with the Hifiasm 0.25.0 assembler (with --ont module). We analyzed ONT sequencing data for four C. lini strains and compared basecalling tools (Guppy and Dorado), read filtration strategies (quality thresholds Q10/Q15 and length cut-offs 5 kb/10 kb), and genome coverage levels from 5× to 160×. Our results demonstrated that Dorado-basecalled reads consistently had higher average quality, especially the R10.4.1 data, leading to improved telomere resolution and complete mitochondrial genome assembly. Moderate genome coverage (40–65×) combined with Q15 quality and 5 kb length filtration for R10.4.1 data, or Q10 and 5 kb for R9.4.1 data, produced the most contiguous and complete assemblies. Overfiltration of reads by length and quality or conversely excessive coverage (>90×) reduced assembly quality, causing fragmentation or erroneous chromosome merging. With optimized parameters of ONT R9.4.1 and R10.4.1 sequencing data preprocessing, Hifiasm efficiently generated T2T and near-T2T assemblies of C. lini genomes: 53.7–56.1 Mb length, 13–30 contigs, 12–13 chromosomes (including 3–12 T2T chromosomes), complete mitochondrial genome, and >98.5% BUSCO completeness. These findings provide a solid framework for ONT-based fungal genome assembly, facilitating future research on genomic variation and pathogenicity in Colletotrichum and related genera. Full article

(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction Between Pathogenic Fungi and Plants—Second Edition)

23 pages, 5527 KB

Open AccessArticle

Ozone Micro–Nano Bubbles Application Controls Disease Development and Maintains Quality of Fresh Radix astragali

by Yan Lv, Jihui Xi, Jinzhu Li, Cuixia Yang, Haijiao Chai, Huali Xue and Yang Bi

J. Fungi 2026, 12(1), 44; https://doi.org/10.3390/jof12010044 - 6 Jan 2026

Abstract

Ozone micro–nano bubbles (OMNBs) are an emerging preservation technology. However, there are few reports regarding their application in controlling postharvest diseases of agricultural products. Radix astragali, as a medicinal and edible plant, is particularly vulnerable to pathogenic microorganisms during postharvest storage, which [...] Read more.

Ozone micro–nano bubbles (OMNBs) are an emerging preservation technology. However, there are few reports regarding their application in controlling postharvest diseases of agricultural products. Radix astragali, as a medicinal and edible plant, is particularly vulnerable to pathogenic microorganisms during postharvest storage, which leads to diminishing the quality and commercial value. In this study, fresh R. astragali inoculated with Penicillium polonicum was treated with different concentrations (2, 3, 4, 5, 6, 8 mg/L) of OMNBs and stored at room temperature for 28 days. The results indicate that 3 mg/L OMNBs application for 8 min effectively inhibited the development of blue mold in fresh R. astragali and preserved its quality. Then, we compared the three different treatments of micro–nano bubbles (MNBs), 3 mg/L O₃, and 3 mg/L OMNBs on physiological and pathological parameters of un-inoculated fresh R. astragali during storage and analyzed the changes in the active ingredients by liquid chromatography and metabolomics. The results indicate that the 3 mg/L OMNBs treatment effectively inhibited the decline in weight loss rate, respiratory rate, firmness, browning index, and ABTS and DPPH radical-scavenging rates, as well as reduced the incidence rate and disease index of fresh R. astragali during storage. The metabolomics results suggest that the 3 mg/L OMNBs application activated the mevalonate pathway (MVA), the methylerythritol phosphate pathway (MEP), and the phenylpropanoid biosynthesis pathway to maintain the content of active ingredients such as terpenoids and flavonoids, and these findings are consistent with the results of HPLC-MS analysis. Full article

(This article belongs to the Special Issue Control of Postharvest Fungal Diseases, 2nd Edition)

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22 pages, 3368 KB

Open AccessArticle

Stress-Induced Cross-Protection and Combined Stress Responses in Extremotolerant Black Yeasts

by Klavdija Fortuna, Maja Kajin and Cene Gostinčar

J. Fungi 2026, 12(1), 43; https://doi.org/10.3390/jof12010043 - 6 Jan 2026

Abstract

Extremotolerant fungi inhabit environments with multiple overlapping stressors, yet most studies examine stresses individually. We tested whether preconditioning with salt, cold, or both improves survival after desiccation and freezing, and whether combined salinity and temperature effects on growth are additive or synergistic. We [...] Read more.

Extremotolerant fungi inhabit environments with multiple overlapping stressors, yet most studies examine stresses individually. We tested whether preconditioning with salt, cold, or both improves survival after desiccation and freezing, and whether combined salinity and temperature effects on growth are additive or synergistic. We studied Aureobasidium pullulans, Aureobasidium subglaciale, Aureobasidium melanogenum, and Hortaea werneckii (haploid and diploid). All preconditioning treatments significantly increased long-term desiccation survival in A. pullulans, reflecting its generalist capacity to activate cross-protective responses. H. werneckii displayed smaller improvements, consistent with a specialist strategy. Freezing survival without cryoprotectants remained ~100% in both species, indicating high intrinsic tolerance. Growth analyses revealed synergistic effects of salinity and temperature in Aureobasidium spp. Species differed in salinity sensitivity (A. melanogenum > A. pullulans > A. subglaciale) and thermal preferences. A. melanogenum and A. pullulans grew faster at higher temperatures, while A. subglaciale showed the opposite trend. In H. werneckii, salinity governed growth. Haploids slowed as salinity increased, while the diploid remained unaffected. This is the first confirmation of the long-standing suggestion that hybrid diploid genomes of many H. werneckii are an adaptation to osmotic stress. These findings illustrate two pathways to extremotolerance: inducible flexibility in Aureobasidium versus constitutive halotolerance in H. werneckii. Full article

(This article belongs to the Special Issue Stress Tolerance in Yeast Biotechnology)

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17 pages, 5150 KB

Open AccessArticle

Three New Species and Three New Records of Arthoniaceae (Ascomycota, Arthoniales) from China

by Chengyue Hao, Shuhua Jiang and Zefeng Jia

J. Fungi 2026, 12(1), 42; https://doi.org/10.3390/jof12010042 - 6 Jan 2026

Abstract

Based on morphological and phylogenetic analyses, during a study on the biodiversity of the lichenized fungi family Arthoniaceae in Yunnan, China, three new species of Arthonia, Eremothecella, and Synarthonia (Arthonia yunnanensis sp. nov., A. pararubella sp. nov., Eremothecella pruinocarpa sp. [...] Read more.

Based on morphological and phylogenetic analyses, during a study on the biodiversity of the lichenized fungi family Arthoniaceae in Yunnan, China, three new species of Arthonia, Eremothecella, and Synarthonia (Arthonia yunnanensis sp. nov., A. pararubella sp. nov., Eremothecella pruinocarpa sp. nov.) and three new Chinese records (A. rubella, E. calamicola, Synarthonia inconspicua) were reported in this present study. A phylogenetic analysis using maximum likelihood and Bayesian inference based on a two-gene dataset (mtSSU and RPB2) revealed that all these species form distinct independent clades. In addition, this study represents the first report of molecular sequences for the genus Eremothecella. Detailed descriptions, ecological and chemical characteristics, and illustrations for each species are provided. Full article

(This article belongs to the Special Issue Lichenized Fungi: A Themed Issue Dedicated to Academician Jiang-Chun Wei)

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23 pages, 4266 KB

Open AccessArticle

Symbiosis Among Naematelia aurantialba, Stereum hirsutum, and Their Associated Microbiome in the Composition of a Cultivated Mushroom Complex JinEr

by Kaixuan Zhang, Yingli Cai, Xiaofei Shi, Zhuyue Yan, Qiuchen Huang, Jesus Perez-Moreno, Dong Liu, Zhenyan Yang, Chengmo Yang, Fuqiang Yu and Wei Liu

J. Fungi 2026, 12(1), 41; https://doi.org/10.3390/jof12010041 - 4 Jan 2026

Abstract

The JinEr mushroom (“Golden Ear”), a globally rare edible and medicinal macrofungus, comprises a symbiotic complex formed by the symbiotic association of Naematelia aurantialba (Tremellomycetes) and Stereum hirsutum (Agaricomycetes). However, the interactions between these fungi and their associated microbiome [...] Read more.

The JinEr mushroom (“Golden Ear”), a globally rare edible and medicinal macrofungus, comprises a symbiotic complex formed by the symbiotic association of Naematelia aurantialba (Tremellomycetes) and Stereum hirsutum (Agaricomycetes). However, the interactions between these fungi and their associated microbiome remain poorly understood. This study employed high-throughput amplicon sequencing, in situ microbial isolation and culture, and microbial confrontation assays to analyze microbial diversity, community structure, and potential functional roles of the endomycotic bacterial community within JinEr basidiomata and its cultivation substrate. Molecular analysis confirmed the heterogenous composition of the basidiomata, revealing N. aurantialba constitutes less than 20% of the fungal biomass, while S. hirsutum predominates, accounting for approximately 80%. Endomycotic fungi accounted for 0.33% (relative abundance) of the fungal community. Prokaryotic analysis identified Delftia and Sphingomonas as the dominant endomycotic bacterial genera within basidiomata, comprising 85.42% of prokaryotic sequences. Endomycotic bacterial diversity differed significantly (p < 0.05) between basidiomata and substrate, indicating host-specific selection. Cultivation-based approaches yielded 140 culturable bacterial isolates (spanning four families and seven genera) from basidiomata core tissues. In vitro co-culture experiments demonstrated that eight representative bacterial strains exhibited compatible growth with both hosts, while one Enterobacteriaceae strain displayed antagonism towards them. These findings confirm that the heterogeneous JinEr basidiomata harbor a specific prokaryotic assemblage potentially engaged in putative symbiotic or commensal associations with the host fungi. This research advances the understanding of microbial ecology in this unique fungal complex and establishes a culture repository of associated bacteria. This collection facilitates subsequent screening for beneficial bacterial strains to enhance the JinEr cultivation system through the provision of symbiotic microorganisms. Full article

(This article belongs to the Section Fungi in Agriculture and Biotechnology)

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13 pages, 3624 KB

Open AccessArticle

Analysis of the Mating-Type Distribution and Fertility Variation in Magnaporthe oryzae Populations in China

by Han Yan, Jintao Liu, Han Xu, Jun Yang and Hai Dong

J. Fungi 2026, 12(1), 40; https://doi.org/10.3390/jof12010040 - 3 Jan 2026

Abstract

Magnaporthe oryzae exhibits significant genetic polymorphism in paddy fields. This study collected and isolated 832 single-spore isolates from major rice-producing areas of 17 provinces in six geographical regions across China, analyzing their mating-type distribution, fertility variation, and underlying mechanisms. Polymerase chain reaction (PCR) [...] Read more.

Magnaporthe oryzae exhibits significant genetic polymorphism in paddy fields. This study collected and isolated 832 single-spore isolates from major rice-producing areas of 17 provinces in six geographical regions across China, analyzing their mating-type distribution, fertility variation, and underlying mechanisms. Polymerase chain reaction (PCR) assays revealed a significantly higher proportion of the MAT1-2 mating type (79.21%) than MAT1-1 (20.79%), with severely skewed ratios in some regions. Correlation analysis indicated that mating-type distribution was significantly associated with effective accumulated temperature (≥10 °C). MAT1-1 was predominantly concentrated in regions with 4500–7000 degree-days, whereas MAT1-2 was mainly found in regions with 2500–5000 degree-days. Cross-culture fertility tests yielded an average fertility rate of 36.54% and mean perithecia production of 25.7 per isolate, suggesting generally low fertility, with MAT1-2 isolates showing significantly higher fertility than MAT1-1. This study demonstrates that regional M. oryzae populations in China exhibit both mating-type imbalances and fertility deficiency, suggesting rare genetic recombination in natural populations and evolution primarily driven by asexual reproduction. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Plant Fungal Disease and Control)

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23 pages, 3256 KB

Open AccessArticle

Genetic–Geographic–Chemical Framework of Polyporus umbellatus Reveals Lineage-Specific Chemotypes for Elite Medicinal Line Breeding

by Youyan Liu, Shoujian Li, Liu Liu, Bing Li and Shunxing Guo

J. Fungi 2026, 12(1), 39; https://doi.org/10.3390/jof12010039 - 3 Jan 2026

Abstract

Polyporus umbellatus is a valuable fungus with both dietary and medicinal applications. However, heterogeneous germplasm and chemical variability constrain its sustainable use. To elucidate the drivers of this variation, whole-genome resequencing and metabolic profiling were integrated. Genome-wide analysis of representative accessions revealed six [...] Read more.

Polyporus umbellatus is a valuable fungus with both dietary and medicinal applications. However, heterogeneous germplasm and chemical variability constrain its sustainable use. To elucidate the drivers of this variation, whole-genome resequencing and metabolic profiling were integrated. Genome-wide analysis of representative accessions revealed six distinct genetic clusters across China, identifying the Qinling–Daba Mountains as a putative center of diversity. Population analysis indicated severe genetic erosion with significant heterozygote deficits, likely driven by inbreeding and long-term clonal propagation. Multivariate analysis demonstrated that genetic lineage, rather than traditional commercial morphotypes (Zhushiling and Jishiling), is the primary determinant of metabolite accumulation. Specific lineages were identified as superior germplasm candidates: Group 2 consistently exhibited the highest genetic potential for accumulating steroids, whereas Group 4 attained the highest polysaccharide yield. Although the global genetic–chemical correlation was weak, implying environmental plasticity, the distinct clustering of superior lineages confirms that core accumulation patterns are genetically canalized. These findings advocate for shifting quality control from morphological grading to molecular-assisted selection. Ultimately, this framework provides an evidence-based foundation for urgent in situ conservation to restore genetic diversity and facilitates precision breeding of high-efficacy cultivars. Full article

(This article belongs to the Special Issue Edible and Medicinal Macrofungi, 4th Edition)

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17 pages, 2365 KB

Open AccessArticle

Fungal Reactive Oxygen Species Secreted by Candida albicans Induce Barrier Disruption and Cell Death in HaCaT Keratinocytes

by Jayshree Low Jit Sze, Xinyue Chen, Kanami Orihara and Susumu Kajiwara

J. Fungi 2026, 12(1), 38; https://doi.org/10.3390/jof12010038 - 2 Jan 2026

Abstract

Candida albicans is a pathogenic fungus that expresses a fungal NADPH oxidase known as C. albicans Cfl11, which produces reactive oxygen species (ROS). Secretion of these ROS triggers caspase 3–mediated cell death in hepatocytes, which was attenuated in a mutant with a disrupted [...] Read more.

Candida albicans is a pathogenic fungus that expresses a fungal NADPH oxidase known as C. albicans Cfl11, which produces reactive oxygen species (ROS). Secretion of these ROS triggers caspase 3–mediated cell death in hepatocytes, which was attenuated in a mutant with a disrupted CaCFL11 gene (designated Cacfl11Δ mutant). Here, we compared the effects of the C. albicans wild-type strain and the Cacfl11Δ mutant. Our findings revealed that C. albicans reduces the viability of HaCaT keratinocytes in a contact-independent manner. Furthermore, exposure to C. albicans increased intracellular ROS production and caspase 3 activity in HaCaT keratinocytes. These changes were attenuated when HaCaT keratinocytes were exposed to the Cacfl11Δ mutant or when HaCaT keratinocytes were treated with the known antioxidant N-acetylcysteine. Furthermore, wild-type C. albicans, but not the Cacfl11Δ mutant, disrupted transepithelial electrical resistance and modulated the downregulation of the tight-junction genes occludin and junction adhesion molecule 1 in HaCaT keratinocytes. Collectively, these results show that fungal ROS secretion via CaCFL11 is a potent virulence factor in mediating keratinocyte viability and barrier function. Full article

(This article belongs to the Special Issue Fungal Infections and Antifungals)

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14 pages, 5593 KB

Open AccessArticle

Biocontrol Efficacy of Bacillus velezensis FXJ Against Fusarium graminearum-Induced Fusarium Head Blight in Wheat

by Yihua Liao, Xiao Xu, Huijuan Peng, Ao Chen, Chenjingzi Hao and Chengcheng Li

J. Fungi 2026, 12(1), 37; https://doi.org/10.3390/jof12010037 - 2 Jan 2026

Abstract

Fusarium head blight (FHB), caused by Fusarium graminearum, poses a serious threat to wheat production and grain security. In this study, a strain of Bacillus velezensis was isolated from the plant Polygonatum sibiricum and designated FXJ. FXJ inhibited the mycelial growth of [...] Read more.

Fusarium head blight (FHB), caused by Fusarium graminearum, poses a serious threat to wheat production and grain security. In this study, a strain of Bacillus velezensis was isolated from the plant Polygonatum sibiricum and designated FXJ. FXJ inhibited the mycelial growth of F. graminearum by 52% and induced hyphal abnormalities including swelling and shrinkage. In vivo experiments demonstrated that FXJ treatment significantly reduced disease severity in wheat coleoptiles and spikes, decreased deoxynivalenol accumulation in grains, and down-regulated the expression. Transcriptomic analysis further revealed that FXJ suppressed fungal growth by interfering with energy metabolism and essential biosynthetic processes, particularly pathways related to fatty acid degradation and sugar metabolism. Overall, B. velezensis FXJ shows strong potential for integrated management of wheat Fusarium head blight through combined mechanisms, including the inhibition of mycelial growth, disruption of hyphal morphology, reduction in pathogen infection, and suppression of toxin synthesis. Full article

(This article belongs to the Special Issue Growth and Virulence of Plant Pathogenic Fungi, 2nd Edition)

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18 pages, 4594 KB

Open AccessArticle

Colletotrichum fructicola CfGti1 Transcriptionally Regulates Penetration, Colonization, and Pathogenicity on Apple

by Wenkui Liu, Wei Zhang, Wenxin Shi, Yecan Pan, Pengbo Dai, Chen Yang, Yanjie Wang, Mark L. Gleason, Rong Zhang, Guangyu Sun and Bianqing Hao

J. Fungi 2026, 12(1), 36; https://doi.org/10.3390/jof12010036 - 2 Jan 2026

Abstract

Glomerella leaf spot (GLS), mainly caused by Colletotrichum fructicola, is a destructive disease of apple. However, the underlying pathogenesis mechanisms of GLS are still largely obscure. Previous infection transcriptome analysis showed that transcription factor CfGti1 was induced during leaf infection. The present [...] Read more.

Glomerella leaf spot (GLS), mainly caused by Colletotrichum fructicola, is a destructive disease of apple. However, the underlying pathogenesis mechanisms of GLS are still largely obscure. Previous infection transcriptome analysis showed that transcription factor CfGti1 was induced during leaf infection. The present study confirms that the CfGti1 gene is strongly expressed in conidia and early infection. To identify functions performed, we generated gene deletion mutant ΔCfGti1 by homologous recombination. Phenotypic analysis revealed that ΔCfGti1 lost pathogenicity to apple leaves by blocking appressorium-mediated host penetration, although penetration pegs still developed on cellophane. In addition, ΔCfGti1 colonization and hyphal extension in wounded apple fruit were dramatically decreased. The ΔCfGti1 mutant exhibited defects in growth and development of hyphae, which may be partly responsible for its inability to colonize apple. Comparative transcriptome and qRT-PCR analyses suggested that CfGti1 regulated appressorium-mediated host penetration by modulating genes related to metabolism of appressorial lipid droplets. Interestingly, CfGti1 also regulated the expression of ybtS and AKT1 or AFT1-1 related to biosynthesis of AK and AF host-specific toxins. This study demonstrated that CfGti1 is a pivotal regulator for apple GLS pathogenesis in C. fructicola. Full article

(This article belongs to the Special Issue Fungal Growth and Development Based on Functional Genomics and Microbiomics)

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23 pages, 14339 KB

Open AccessArticle

Integrative Genomic and Transcriptomic Analysis of White-Rot Fungi Ganoderma tsugae Growing on Both Coniferous and Broad-Leaved Trees

by Yifei Sun, Mengxue Lv, Meiqin Luo, Ziqi Yao, Miao Zhou, Yuxuan Fang, Dongmei Wu, Neng Gao and Baokai Cui

J. Fungi 2026, 12(1), 35; https://doi.org/10.3390/jof12010035 - 1 Jan 2026

Abstract

Ganoderma tsugae is a typical white-rot fungus capable of decaying both coniferous and broad-leaved trees and is also used in traditional Chinese medicine for its immunomodulatory and anticancer properties. To elucidate the molecular basis of its broad substrate adaptability, we performed integrated genomic [...] Read more.

Ganoderma tsugae is a typical white-rot fungus capable of decaying both coniferous and broad-leaved trees and is also used in traditional Chinese medicine for its immunomodulatory and anticancer properties. To elucidate the molecular basis of its broad substrate adaptability, we performed integrated genomic and transcriptomic analyses of two G. tsugae strains (collected from Xingjiang on Betula and Jilin on Larix). The high-quality genomes of G. tsugae Wu 2022 from Xinjiang (40.8 Mb, 12,496 genes) and G. tsugae Cui 14110 from Jilin (45.6 Mb, 13,450 genes) were obtained. There are enriched gene families related to carbohydrate-active enzymes (CAZymes) in two G. tsugae strains. Notably, specific CAZyme families implicated in hemicellulose (GH16), chitin metabolism (GH18), and ester bond cleavage (CE10) were prominently expanded. Transcriptome analyses under the induction of Betula and Larix sawdust revealed a core adaptive response. A total of 5558 genes were differentially expressed, including 2094 up-regulated and 3464 down-regulated genes. Most differentially expressed genes (DEGs) were annotated as “catalytic activity”, “metabolic processes” and specific functions such as nutrient transport (“MFS transporter”), and lipid metabolism (“3-oxoacyl-[acyl-carrier protein] reductase”). In addition, a conserved suite of the eleven shared DEGs were annotated as “Heat shock protein 9/12”, “alcohol dehydrogenase”, and “Cytochrome p450” related to secondary metabolites biosynthesis, transport, and catabolism. Based on the annotation results, the wood degradation mechanism of G. tsugae can be described as synthesizing and secreting degradation enzyme system to obtain energy, using protective enzyme systems to ensure its own health, and employing a transport enzyme system to recycle metabolic capacity. This progress ensures the environmental adaptability and high degradation efficiency of G. tsugae during wood degradation. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics, 2nd Edition)

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9 pages, 501 KB

Open AccessCommunication

Antifungal Susceptibility Testing Experience in the Management of Culture-Positive Mucormycosis: Observation from a Large Healthcare System

by Maryam Naveed, Tirdad T. Zangeneh, Nathan P. Wiederhold, William Lainhart and Mohanad M. Al-Obaidi

J. Fungi 2026, 12(1), 34; https://doi.org/10.3390/jof12010034 - 1 Jan 2026

Abstract

Background: Mucormycosis, an invasive fungal infection with high morbidity and mortality rates, requires prompt surgical and antifungal therapies; however, the role of antifungal susceptibility testing (AFST) in clinical management of mucormycosis remains underexplored. We aimed to describe the experience of using AFST in [...] Read more.

Background: Mucormycosis, an invasive fungal infection with high morbidity and mortality rates, requires prompt surgical and antifungal therapies; however, the role of antifungal susceptibility testing (AFST) in clinical management of mucormycosis remains underexplored. We aimed to describe the experience of using AFST in the clinical management of mucormycosis. Methods: We conducted a retrospective study from 1 October 2017 to 8 February 2023. We included non-pregnant patients aged ≥ 18 years old with a positive culture for Mucorales and with proven or probable mucormycosis. We collected clinical and microbiological data using a chart review. Results: Over the study period, a total of 119 patients were included, with 36 (30%) undergoing AFST. Of all patients, the median age was 54 years, with 80 (67%) being White and not Hispanic and 73 (61%) being male. Fifty-three (45%) patients had DM, 27 (23%) had hematological malignancy, 15 (13%) had SOT, and 23 (19%) had COVID-19. Half of the cases met the criteria of proven invasive mucormycosis, with pulmonary involvement being the most common presentation (46, 39%), followed by rhino-cerebral-orbital involvement (35, 29%). The majority of Mucorales isolates were Rhizopus species (79, 66%). Among the 36 who underwent AFST, posaconazole minimal inhibitory concentrations (MICs) were lower than isavuconazole (range 0.03 to 2 µg/mL versus 0.1 to 16 µg/mL, respectively). AFST resulted in a change in antifungal therapy from isavuconazole to posaconazole in 3/36 (8%) cases. There was no statistically significant difference in the mortality between the patients whose isolates received AFST versus those who did not have AFST performed. Conclusions: AFST led to a change in antifungal therapy in a minority of mucormycosis cases. Further studies to understand the epidemiological range of antifungal MICs and the effect of AFST-informed antifungal therapy are needed. Full article

(This article belongs to the Special Issue Host–Fungal Interplay: Virulence, Immunity, Antifungal Resistance, and Therapeutic Strategies)

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16 pages, 2853 KB

Open AccessArticle

Quantitative Morphological Profiling and Isolate-Specific Insensitivity of Cacao Pathogens to Novel Bio-Based Phenolic Amides

by Ezekiel Ahn, Masoud Kazem-Rostami, Sunchung Park, Richard D. Ashby, Helen Ngo and Lyndel W. Meinhardt

J. Fungi 2026, 12(1), 33; https://doi.org/10.3390/jof12010033 - 1 Jan 2026

Abstract

Fungal pathogens, including Colletotrichum gloeosporioides and Pestalotiopsis spp., are significant threats to global cacao production. Understanding their varying responses to novel antifungal agents is crucial for developing sustainable plant protection strategies. This study investigated the quantitative morphological responses and isolate-specific sensitivity of three [...] Read more.

Fungal pathogens, including Colletotrichum gloeosporioides and Pestalotiopsis spp., are significant threats to global cacao production. Understanding their varying responses to novel antifungal agents is crucial for developing sustainable plant protection strategies. This study investigated the quantitative morphological responses and isolate-specific sensitivity of three cacao pathogen isolates (one Pestalotiopsis sp. and two C. gloeosporioides) to four novel bio-based phenolic-branched fatty acids and their corresponding amides derived from renewable feedstocks. We observed a high degree of isolate-specific susceptibility. A phenol-branched soy oil-derived fatty amide (PhSOAM) proved most potent, significantly inhibiting the growth of Pestalotiopsis sp. and one C. gloeosporioides isolate. In contrast, the second C. gloeosporioides isolate displayed complete insensitivity to all tested compounds, highlighting significant intraspecific variation. Notably, quantitative image analysis revealed that PhSOAM uniquely altered fungal colony morphology by significantly increasing the length-to-width ratio, suggesting a mechanism of action involving the disruption of polarized growth. Multivariate analyses and machine learning models (R² up to 0.74) effectively classified these responses, identifying the specific pathogen-compound pairing as the most critical determinant of the interaction outcome. This work not only highlights the potential of bio-based amides but also establishes a powerful analytical framework, combining morphological profiling with predictive modeling, to gain deeper insights into the complex, isolate-specific nature of fungal–antifungal interactions. Full article

(This article belongs to the Special Issue Integrated Management of Plant Fungal Diseases—2nd Edition)

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18 pages, 775 KB

Open AccessCase Report

Cutaneous Alternariosis Caused by Alternaria infectoria: A Case Report in Kidney Transplant Recipient and Literature Review

by Maria Antonietta Grignano, Marilena Gregorini, Tefik Islami, Maria Carmela Esposto, Camilla Vassallo, Angela Di Matteo, Elena Seminari, Palma Minutillo, Eleonora Francesca Pattonieri, Emma Diletta Stea, Giuseppe Lanotte, Valentina Portalupi, Andreana De Mauri, Elisabetta Margiotta, Alessandro Tragni, Grazia Soccio, Caterina Cavanna and Teresa Rampino

J. Fungi 2026, 12(1), 32; https://doi.org/10.3390/jof12010032 - 31 Dec 2025

Abstract

Cutaneous infections caused by dematiaceous fungi are rare in the general population but are increasingly recognized in solid organ transplant recipients as a consequence of prolonged immunosuppression. When Alternaria species are confirmed as the causative agents of a skin infection, the condition is [...] Read more.

Cutaneous infections caused by dematiaceous fungi are rare in the general population but are increasingly recognized in solid organ transplant recipients as a consequence of prolonged immunosuppression. When Alternaria species are confirmed as the causative agents of a skin infection, the condition is referred to as alternariosis. These infections may clinically resemble bacterial or neoplastic lesions and require accurate diagnosis and individualized therapy. We report one case of cutaneous alternariosis in a kidney transplant recipient receiving tacrolimus-based immunosuppression. The patient was a 47-year-old woman who sustained minor trauma to her knee three months after transplantation. She developed an ulcerated, crusted lesion, which coincided with severe neutropenia. Histology, culture and molecular identification confirmed A. infectoria. Treatment included systemic azole therapy (voriconazole followed by isavuconazole) and surgical excision, resulting in resolution without recurrence. This case highlights the importance of early recognition of alternariosis in transplant recipients. Successful management typically requires combined surgical and systemic antifungal therapy, with careful monitoring of drug interactions and immunosuppressive levels to prevent toxicity or rejection. Full article

(This article belongs to the Section Fungal Pathogenesis and Disease Control)

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