Journal of Fungi

20 pages, 1812 KiB

Open AccessSystematic Review

Pine Forest Plantations in the Neotropics: Challenges and Potential Use of Ectomycorrhizal Fungi and Bacteria as Inoculants

by Yajaira Baeza-Guzmán, Sara Lucía Camargo-Ricalde, Dora Trejo-Aguilar and Noé Manuel Montaño

J. Fungi 2025, 11(5), 393; https://doi.org/10.3390/jof11050393 (registering DOI) - 20 May 2025

Abstract

Forest plantations in the Neotropics aim to alleviate pressure on primary forests. This study synthesizes knowledge on pine species used in these plantations, emphasizing the challenges and potential of ectomycorrhizal fungi and bacteria as inoculants. An analysis of 98 articles identifies 23 pine [...] Read more.

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

(This article belongs to the Special Issue Mycological Research in Mexico)

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22 pages, 7024 KiB

Open AccessArticle

Isolation and Identification of Colletotrichum nymphaeae as a Causal Agent of Leaf Spot on Rhododendron hybridum Ker Gawl and Its Effects on the Ultrastructure of Host Plants

by Yajiao Sun, Yunjing Tian, Jian Liu, Huali Li, Junjia Lu, Mengyao Wang and Shuwen Liu

J. Fungi 2025, 11(5), 392; https://doi.org/10.3390/jof11050392 - 19 May 2025

Abstract

Rhododendron hybridum Ker Gawl, a widely cultivated horticultural species in China, is highly valued for its ornamental and medicinal properties. However, with the expansion of its cultivation, leaf spot disease has become more prevalent, significantly affecting the ornamental value of R. hybridum Ker [...] Read more.

Rhododendron hybridum Ker Gawl, a widely cultivated horticultural species in China, is highly valued for its ornamental and medicinal properties. However, with the expansion of its cultivation, leaf spot disease has become more prevalent, significantly affecting the ornamental value of R. hybridum Ker Gawl. In this study, R. hybridum Ker Gawl from the Kunming area was selected as the experimental material. The tissue isolation method was employed in this study to isolate pathogenic strains. The biological characteristics of the pathogens were determined using the mycelial growth rate method. The pathogens’ influence on the host plant’s ultrastructure was investigated using transmission electron microscopy (TEM). Colletotrichum nymphaeae was identified as the pathogen implicated in the development of leaf spot disease in R. hybridum Ker Gawl across three regions in Kunming City through the integration of morphological traits and phylogenetic analyses of multiple genes (ITS, ACT, GAPDH, HIS3, CHS1, and TUB2). Its mycelial growth is most effective at a temperature of 25 °C. pH and light have relatively minor effects on the growth of mycelium. The preferred carbon and nitrogen sources were identified as mannitol and yeast extract, respectively. Additionally, TEM observations revealed significant damage to the cell structure of R. hybridum Ker Gawl leaves infected by the pathogen. The cell walls were dissolved, the number of chloroplasts decreased markedly, starch granules within chloroplasts were largely absent, and the number of osmiophilic granules increased. This is the first report of leaf spot disease in R. hybridum Ker Gawl caused by C. nymphaeae. The results of this study provide valuable insights for future research on the prevention and control of this disease. Full article

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18 pages, 7007 KiB

Open AccessArticle

by Thilini Weerasinghe, Josh Li, Xuanye Chen, Jiayang Gao, Lei Tian, Yan Xu, Yihan Gong, Weijie Huang, Yuelin Zhang, Liwen Jiang and Xin Li

J. Fungi 2025, 11(5), 391; https://doi.org/10.3390/jof11050391 - 19 May 2025

Abstract

Sclerotinia sclerotiorum is a devastating fungal pathogen that can colonize numerous crops. Despite its economic importance, the regulation of its development and pathogenicity remains poorly understood. From a forward genetic screen in S. sclerotiorum, six UV mutants were identified with loss-of-function mutations [...] Read more.

Sclerotinia sclerotiorum is a devastating fungal pathogen that can colonize numerous crops. Despite its economic importance, the regulation of its development and pathogenicity remains poorly understood. From a forward genetic screen in S. sclerotiorum, six UV mutants were identified with loss-of-function mutations in SsATG1, SsATG2, SsATG4, SsATG5, SsATG9, and SsATG26. Functional validation through gene knockouts revealed that each ATG is essential for sclerotia formation, although the morphology of appressoria was not significantly altered in the mutants. Different levels of virulence attenuation were observed among these mutants. Autophagy, monitored using GFP-ATG8, showed dynamic activities during sclerotia development. These findings suggest that macroautophagy and pexophagy contribute to sclerotia maturation and virulence processes. Future work will reveal how autophagy controls target organelle or protein turnover to regulate these processes. Full article

(This article belongs to the Special Issue Current Research in Soil Borne Plant Pathogens)

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14 pages, 2135 KiB

Open AccessArticle

Neocotylidia gen. nov. (Hymenochaetales, Basidiomycota) Segregated from Cotylidia Based on Morphological, Phylogenetic, and Ecological Evidence

by Jinxin Ma, Yizhe Zhang, Jiaqi Liang, Yue Li, Heng Zhao, Zhirui Shang, Jing Si and Haijiao Li

J. Fungi 2025, 11(5), 390; https://doi.org/10.3390/jof11050390 - 19 May 2025

Abstract

Taxonomic and phylogenetic studies of Cotylidia (Hymenochaetales, Basidiomycota) were performed. A phylogenetic estimate based on six genetic markers revealed that Cotylidia in the current sense includes species belonging to three distantly related clades in the Hymenochaetales. Based on morphology, phylogeny, and ecological habitat, [...] Read more.

Taxonomic and phylogenetic studies of Cotylidia (Hymenochaetales, Basidiomycota) were performed. A phylogenetic estimate based on six genetic markers revealed that Cotylidia in the current sense includes species belonging to three distantly related clades in the Hymenochaetales. Based on morphology, phylogeny, and ecological habitat, the name Cotylidia s.s. is proposed for the first clade, including the type species C. undulata and C. carpatica. Neocotylidia gen. nov. is proposed for the second clade, which includes N. diaphana, N. fibrae, the new species N. bambusicola, and two accessions recorded as Cotylidia aurantiaca var. alba and C. aurantiaca. Contrary to the findings in earlier studies, C. pannosa demonstrated a weak grouping affinity with Globulicium hiemale, Hastodontia hastata, Atheloderma mirabile, Tsugacorticium kenaicum, Lawrynomyces capitatus, and Lyoathelia laxa. The morphological characteristics of Cotylidia s.s. are restricted to species with hymenial cystidia, pileocystidia, and caulocystidia, as well as a muscicolous habitat. Neocotylidia species differ from Cotylidia s.s. in the lack of pileocystidia and caulocystidia and substrate preference for soil or wood. Illustrated descriptions of the new species and genus, as well as an identification key to the worldwide species of Cotylidia s.l. are provided. Full article

(This article belongs to the Special Issue Taxonomy, Systematics and Evolution of Forestry Fungi, 2nd Edition)

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21 pages, 4432 KiB

Open AccessArticle

Soil Fungal Diversity, Community Structure, and Network Stability in the Southwestern Tibetan Plateau

by Shiqi Zhang, Zhenjiao Cao, Siyi Liu, Zhipeng Hao, Xin Zhang, Guoxin Sun, Yuan Ge, Limei Zhang and Baodong Chen

J. Fungi 2025, 11(5), 389; https://doi.org/10.3390/jof11050389 - 19 May 2025

Abstract

Despite substantial research on how environmental factors affect fungal diversity, the mechanisms shaping regional-scale diversity patterns remain poorly understood. This study employed ITS high-throughput sequencing to evaluate soil fungal diversity, community composition, and co-occurrence networks across alpine meadows, desert steppes, and alpine shrublands [...] Read more.

Despite substantial research on how environmental factors affect fungal diversity, the mechanisms shaping regional-scale diversity patterns remain poorly understood. This study employed ITS high-throughput sequencing to evaluate soil fungal diversity, community composition, and co-occurrence networks across alpine meadows, desert steppes, and alpine shrublands in the southwestern Tibetan Plateau. We found significantly higher fungal α-diversity in alpine meadows and desert steppes than in alpine shrublands. Random forest and CAP analyses identified the mean annual temperature (MAT) and normalized difference vegetation index (NDVI) as major ecological drivers. Mantel tests revealed that soil physicochemical properties explained more variation than climate, indicating an indirect climatic influence via soil characteristics. Distance–decay relationships suggested that environmental heterogeneity and species interactions drive community isolation. Structural equation modeling confirmed that the MAT and NDVI regulate soil pH and carbon/nitrogen availability, thereby influencing fungal richness. The highly modular fungal co-occurrence network depended on key nodes for connectivity. Vegetation coverage correlated positively with network structure, while soil pH strongly affected network stability. Spatial heterogeneity constrained stability and diversity through resource distribution and niche segregation, whereas stable networks concentrated resources among dominant species. These findings enhance our understanding of fungal assemblage processes at a regional scale, providing a scientific basis for the management of soil fungal resources in plateau ecosystems. Full article

(This article belongs to the Section Environmental and Ecological Interactions of Fungi)

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20 pages, 3840 KiB

Open AccessArticle

Vacuolar Proteases of Candida auris from Clades III and IV and Their Relationship with Autophagy

by Daniel Clark-Flores, Alvaro Vidal-Montiel, Ricardo Mondragón-Flores, Eulogio Valentín-Gómez, César Hernández-Rodríguez, Margarita Juárez-Montiel and Lourdes Villa-Tanaca

J. Fungi 2025, 11(5), 388; https://doi.org/10.3390/jof11050388 - 18 May 2025

Abstract

Candida auris is a multidrug-resistant pathogen with a high mortality rate and widespread distribution. Additionally, it can persist on inert surfaces for extended periods, facilitating its transmissibility in hospital settings. Autophagy is a crucial cellular mechanism that enables fungal survival under adverse conditions. [...] Read more.

Candida auris is a multidrug-resistant pathogen with a high mortality rate and widespread distribution. Additionally, it can persist on inert surfaces for extended periods, facilitating its transmissibility in hospital settings. Autophagy is a crucial cellular mechanism that enables fungal survival under adverse conditions. A fundamental part of this process is mediated by vacuolar proteases, which play an essential role in the degradation and recycling of cellular components. The present work explores the relationship between C. auris vacuolar peptidases and autophagy, aiming to establish a precedent for understanding the survival mechanisms of this emerging fungus. Thus, eight genes encoding putative vacuolar peptidases in the C. auris genomes were identified: PEP4, PRB1, PRC1, ATG42, CPS, LAP4, APE3, and DAP2. Analysis of the protein domains and their phylogenetic relationships suggests that these enzymes are orthologs of Saccharomyces cerevisiae vacuolar peptidases. Notably, both vacuolar protease gene expression and the proteolytic activity of cell-free extracts increased under nutritional stress and rapamycin. An increase in the expression of the ATG8 gene and the presence of autophagic bodies were also observed. These results suggest that proteases could play a role in yeast autophagy and survival during starvation conditions. Full article

(This article belongs to the Special Issue Candidiasis: Changes and Challenges in Its Epidemiology, Pathogenesis, Diagnosis, Treatment and Prevention)

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20 pages, 34946 KiB

Open AccessArticle

Feasibility of Bamboo Sawdust as Sustainable Alternative Substrate for Auricularia heimuer Cultivation

by Ya-Hui Wang, Cong-Sheng Yan, Yong-Jin Deng, Zheng-Fu Zhu, Hua-An Sun, Hui-Ping Li, Hong-Yuan Zhao and Guo-Qing Li

J. Fungi 2025, 11(5), 387; https://doi.org/10.3390/jof11050387 - 17 May 2025

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Abstract

With the increasing scarcity of traditional hardwood sawdust resources, developing sustainable substrates for edible fungi cultivation has become an urgent industrial priority. This study systematically evaluated the effects of bamboo sawdust substitutions (20%, 30%, 40%, and 50%) on mycelial growth, fruiting body development, [...] Read more.

With the increasing scarcity of traditional hardwood sawdust resources, developing sustainable substrates for edible fungi cultivation has become an urgent industrial priority. This study systematically evaluated the effects of bamboo sawdust substitutions (20%, 30%, 40%, and 50%) on mycelial growth, fruiting body development, and nutritional quality of Auricularia heimuer, while elucidating the underlying molecular mechanisms through transcriptome sequencing. The results demonstrated that bamboo substitution of ≤30% maintained normal mycelial growth and fruiting body differentiation, with 20% and 30% substitutions increasing yields by 5.30% and 3.70%, respectively, compared to the control. However, 50% substitution significantly reduced yield by 9.49%. Nutritional analysis revealed that 20–40% bamboo substitution significantly enhanced the contents of crude protein, polysaccharides, and essential minerals (calcium, iron, and selenium) in fruiting bodies. Transcriptome analysis identified upregulation of glycosyl hydrolase family genes and downregulation of redox-related genes with increasing bamboo proportions. Biochemical assays confirmed these findings, showing decreased oxidative substances and increased reductive compounds in mycelia grown with high bamboo content, which indicate disrupted cellular redox homeostasis. This study provides both a practical solution to alleviate the “edible mushrooms derived from lignicolous fungi–forest conflict” and fundamental insights into fungal adaptation mechanisms to non-wood substrates, thus establishing a theoretical foundation for the valorization of agricultural and forestry wastes. Full article

(This article belongs to the Special Issue Fungi in Sustainable Applications and the Circular Economy: A Themed Issue Dedicated to Academician Yu Li)

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19 pages, 11989 KiB

Open AccessArticle

PEG-Mediated Protoplast Transformation of Penicillium sclerotiorum (scaumcx01): Metabolomic Shifts and Root Colonization Dynamics

by Israt Jahan, Qilin Yang, Zijun Guan, Yihan Wang, Ping Li and Yan Jian

J. Fungi 2025, 11(5), 386; https://doi.org/10.3390/jof11050386 - 17 May 2025

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Abstract

Protoplast-based transformation is a vital tool for genetic studies in fungi, yet no protoplast method existed for P. sclerotiorum-scaumcx01 before this study. Here, we optimized protoplast isolation, regeneration, and transformation efficiency. The highest protoplast yield (6.72 × 10⁶ cells/mL) was obtained [...] Read more.

Protoplast-based transformation is a vital tool for genetic studies in fungi, yet no protoplast method existed for P. sclerotiorum-scaumcx01 before this study. Here, we optimized protoplast isolation, regeneration, and transformation efficiency. The highest protoplast yield (6.72 × 10⁶ cells/mL) was obtained from liquid mycelium after 12 h of enzymatic digestion at 28 °C using Lysing Enzymes, Yatalase, cellulase, and pectinase. Among osmotic stabilizers, 1 M MgSO₄ yielded the most viable protoplasts. Regeneration occurred via direct mycelial outgrowth and new protoplast formation, with a 1.02% regeneration rate. PEG-mediated transformation with a hygromycin resistance gene and GFP tagging resulted in stable GFP expression in fungal spores and mycelium over five generations. LC/MS-based metabolomic analysis revealed significant changes in glycerophospholipid metabolism, indicating lipid-related dynamics influenced by GFP tagging. Microscopy confirmed successful colonization of tomato roots by GFP-tagged scaumcx01, with GFP fluorescence observed in cortical tissues. Enzymatic (cellulase) seed pretreatment enhanced fungal colonization by modifying root surface properties, promoting plant–fungal interaction. This study establishes an efficient protoplast transformation system, reveals the metabolic impacts of genetic modifications, and demonstrates the potential of enzymatic seed treatment for enhancing plant–fungal interactions. Full article

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

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28 pages, 4056 KiB

Open AccessArticle

Morphological, Physiological, Biochemical, and Molecular Characterization of Fungal Species Associated with Papaya Rot in Cameroon

by Moussango Victor Davy, Voundi Olugu Steve, Tchabong Raymond Sammuel, Marie Ampères Bedine Boat, Ntah Ayong Moise, Anna Cazanevscaia Busuioc, Priscile Ebong Mbondi, Andreea Veronica Dediu Botezatu, Manz Koule Jules, Maria Daniela Ionica Mihaila, Rodica Mihaela Dinica and Sameza Modeste Lambert

J. Fungi 2025, 11(5), 385; https://doi.org/10.3390/jof11050385 - 17 May 2025

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Abstract

Post-harvest decay of Carica papaya L. is the primary cause of deterioration in papaya quality and the low economic impact of this sector in Cameroon. Field surveys conducted by teams from the Ministry of Agriculture and Rural Development (MINADER) in Cameroon have primarily [...] Read more.

Post-harvest decay of Carica papaya L. is the primary cause of deterioration in papaya quality and the low economic impact of this sector in Cameroon. Field surveys conducted by teams from the Ministry of Agriculture and Rural Development (MINADER) in Cameroon have primarily associated these decays with fungal attacks. However, to date, no methodological analysis has been conducted on the identification of these fungal agents. To reduce post-harvest losses, rapid detection of diseases is crucial for the application of effective management strategies. This study sought to identify the fungal agents associated with post-harvest decay of papaya cv Sunrise solo in Cameroon and to determine their physiological and biochemical growth characteristics. Isolation and pathogenicity tests were performed according to Koch’s postulate. Molecular identification of isolates was achieved by amplification and sequencing of the ITS1 and ITS4 regions. Phylogenetic analysis was based on the substitution models corresponding to each fungal genus determined by jModeltest, according to the Akaike information criterion (AIC). Fungal explants of each identified species were subjected to variations in temperature, pH, water activity, and NaCl concentration. The ability to secrete hydrolytic enzymes was determined on specific media such as skimmed milk agar for protease, peptone agar for lipase, and carboxymethylcellulose for cellulase. These experiments allowed the identification of three fungi responsible for papaya fruit decay, namely Colletotrichum gloeosporioides, Fusarium equiseti, and Lasiodiplodia theobromae. All three pathogens had maximum mycelial growth at a temperature of 25 ± 2 °C, pH 6.5, NaCl concentration of 100 µM, and water activity (aw) equal to 0.98. The three fungal agents demonstrated a strong potential for secreting cellulases, lipases, and proteases, which they use as lytic enzymes to degrade papaya tissues. The relative enzymatic activity varied depending on the fungal pathogen as well as the type of enzyme secreted. This study is the first report of F. equiseti as a causal agent of papaya fruit decay in Cameroon. Full article

(This article belongs to the Special Issue Genomics of Fungal Plant Pathogens, 3rd Edition)

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15 pages, 5980 KiB

Open AccessArticle

Prevalence of Neofusicoccum parvum Associated with Fruit Rot of Mango in South Italy and Its Biological Control Under Postharvest Conditions

by Laura Vecchio, Alessandro Vitale, Dalia Aiello, Chiara Di Pietro, Lucia Parafati and Giancarlo Polizzi

J. Fungi 2025, 11(5), 384; https://doi.org/10.3390/jof11050384 - 17 May 2025

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Abstract

Botryosphaeriaceae species were recently found to be responsible for heavy mango crop losses worldwide. In 2020, mango fruit samples showing fruit decay symptoms were collected from Glenn, Kent, Irwin, Palmer, Brokaw 2, and Gomera 3 accessions in 4 orchards located in Sicily (Italy). [...] Read more.

Botryosphaeriaceae species were recently found to be responsible for heavy mango crop losses worldwide. In 2020, mango fruit samples showing fruit decay symptoms were collected from Glenn, Kent, Irwin, Palmer, Brokaw 2, and Gomera 3 accessions in 4 orchards located in Sicily (Italy). A molecular analysis of the ITS and tub2 regions performed on 41 representative isolates allowed for the identification of mainly Neofusicoccum parvum and occasionally Botryosphaeria dothidea (1/41) as the causal agents of fruit decay. Pathogenicity proofs were satisfied for both fungal pathogens. Ripe and unripe Gomera 3 mango fruits were used to compare the virulence among the N. parvum isolates. Postharvest experiments performed on Gomera 3 fruits and by using different biocontrol agents (BCAs) showed that the performance of treatments in reducing fruit decay depends on N. parvum virulence. The data show that unregistered Wickerhamomyces anomalus WA-2 and Pichia kluyveri PK-3, followed by the trade bioformulate Serenade™ (Bacillus amyloliquefaciens QST713), were the most effective in managing mango fruit rot. This paper shows, for the first time, the potential of different BCAs, including Trichoderma spp., for the controlling of postharvest decay caused by N. parvum on mango fruits. Full article

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

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20 pages, 7153 KiB

Open AccessArticle

Integrative Transcriptome and Metabolome Analysis Reveals Candidate Genes Related to Terpenoid Synthesis in Amylostereum areolatum (Russulales: Amylostereaceae)

by Lixia Wang, Ningning Fu, Ming Wang, Zhongyi Zhan, Youqing Luo, Jianrong Wu and Lili Ren

J. Fungi 2025, 11(5), 383; https://doi.org/10.3390/jof11050383 - 16 May 2025

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Abstract

Amylostereum areolatum (Chaillet ex Fr.) Boidin (Russulales: Amylostereaceae) is a symbiotic fungus of Sirex noctilio Fabricius that has ecological significance. Terpenoids are key mediators in fungal–insect interactions, yet the biosynthetic mechanisms of terpenoids in this species remain unclear. Under nutritional conditions [...] Read more.

Amylostereum areolatum (Chaillet ex Fr.) Boidin (Russulales: Amylostereaceae) is a symbiotic fungus of Sirex noctilio Fabricius that has ecological significance. Terpenoids are key mediators in fungal–insect interactions, yet the biosynthetic mechanisms of terpenoids in this species remain unclear. Under nutritional conditions that mimic natural growth, A. areolatum was sampled during the lag phase (day 7), exponential phase (day 14), and stationary phase (day 21). Metabolome (solid-phase microextraction (SPME) combined with gas chromatography–mass spectrometry (GC-MS) and liquid chromatography–mass spectrometry (LC-MS)) and transcriptome (Illumina NovaSeq) profiles were integrated to investigate terpenoid–gene correlations. This analysis identified 103 terpenoids in A. areolatum, substantially expanding the known repertoire of terpenoid compounds in this species. Total terpenoid abundance progressively increased across three developmental stages, with triterpenoids and sesquiterpenoids demonstrating the highest diversity and abundance levels. Transcriptomic profiling (61.66 Gb clean data) revealed 26 terpenoid biosynthesis-associated genes, establishing a comprehensive transcriptional framework for fungal terpenoid metabolism. Among 11 differentially expressed genes (DEGs) (|log2Fold Change| ≥ 1, adjusted p < 0.05), HMGS1, HMGR2, and AaTPS1-3 emerged as key regulators potentially governing terpenoid biosynthesis. These findings provide foundational insights into the molecular mechanisms underlying terpenoid production in A. areolatum and related basidiomycetes. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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21 pages, 3361 KiB

Open AccessArticle

Three New Species and a New Record of Arbuscular Mycorrhizal Fungi of the Genus Acaulospora Associated with Citrus from South China

by Haisi Huang, Xiaojuan Qin, Yihao Kang, Jie Xu, Pengxiang Shang, Tingsu Chen, Tong Cheng and Jinlian Zhang

J. Fungi 2025, 11(5), 382; https://doi.org/10.3390/jof11050382 - 16 May 2025

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Abstract

Arbuscular mycorrhizal (AM) fungi are root symbionts that play an important role in the growth of vascular plants. Four AM fungi, including three new species, Acaulospora citrusnsis, A. guangxiensis, A. jiangxiensis, and a new country record from China, Acaulospora herrerae, are reported [...] Read more.

Arbuscular mycorrhizal (AM) fungi are root symbionts that play an important role in the growth of vascular plants. Four AM fungi, including three new species, Acaulospora citrusnsis, A. guangxiensis, A. jiangxiensis, and a new country record from China, Acaulospora herrerae, are reported based on morphological characteristics and molecular phylogenetic analysis. They were isolated and propagated from spores extracted from the rhizosphere soils of citrus. A. citrusnsis is characterized by forming hyaline to pale yellow globose to subglobose spores of (70.0–)85.0(−100.0) μm in diameter. Spores of A. guangxiensis are pale yellow to pale yellowish brown, with spherical to sub-spherical appearance and (103.1–)122.1(–147.1) μm in diameter. Young spores of A. jiangxiensis are hyaline, gradually turning pale yellow as they mature, with spherical to sub-spherical appearance and (78.7–)85.6(–90.0) μm in diameter. Spores of A. herrerae are hyaline and 86.3–127.2 μm in diameter. Four species have three spore wall layers, and spores form individually in the soil. The phylogenetic tree was constructed and inferred from sequences of 18S-ITS1-5.8S-ITS2-28S datasets by Bayesian inference and maximum likelihood analysis. Voucher specimens are deposited in the Center for Subtropical Arbuscular Mycorrhizal Fungi Culture Collection (CSMC). Full article

(This article belongs to the Section Fungal Evolution, Biodiversity and Systematics)

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16 pages, 5753 KiB

Open AccessArticle

Biocontrol Potential of Entomopathogenic Fungi Against Plant-Parasitic Nematodes: A Caenorhabditis elegans-Based Screening and Mechanistic Study

by Cheng Cheng, Renjun Zhang, Yanzhen Wang, Shuo Yang, Wenhao Yu and Yuxian Xia

J. Fungi 2025, 11(5), 381; https://doi.org/10.3390/jof11050381 - 16 May 2025

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Abstract

Plant-parasitic nematodes and insect pests critically threaten agricultural productivity, but chemical pesticides face limitations due to resistance and environmental concerns, necessitating eco-friendly biopesticides targeting both pests and nematodes. Here, we developed a high-throughput screening platform using Caenorhabditis elegans to identify entomopathogenic fungi exhibiting [...] Read more.

Plant-parasitic nematodes and insect pests critically threaten agricultural productivity, but chemical pesticides face limitations due to resistance and environmental concerns, necessitating eco-friendly biopesticides targeting both pests and nematodes. Here, we developed a high-throughput screening platform using Caenorhabditis elegans to identify entomopathogenic fungi exhibiting nematocidal activity against Meloidogyne incognita. Among 32 tested strains, nine Metarhizium spp. and one Beauveria strain demonstrated dual efficacy against C. elegans and M. incognita. Metarhizium anisopliae CQMa421 showed the highest virulence, suppressing nematode reproduction by 42.7% and inducing >80% mortality. Pot experiments revealed a 50% reduction in the root galling index and 50.3% fewer root galls in Solanum lycopersicum. The CQMa421 filtrate caused irreversible locomotor deficits and reduced egg hatching rates by 28%. Concurrently, intestinal damage, elevated oxidative stress and autophagy were observed in C. elegans. This was accompanied by a transcriptome-wide modulation of genes involved in detoxification and immune defense pathways. These findings demonstrate the efficacy of our C. elegans-based screening method for identifying fungi with nematocidal potential. CQMa421’s virulence against M. incognita suggests its promise for pest management, while molecular insights highlight pathways that may contribute to the future design of future nematicides. This study advances fungal biocontrol agents and offers a sustainable strategy for agriculture. Full article

(This article belongs to the Special Issue Pathogenic Mechanisms and Biological Control in Entomopathogenic Fungi)

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16 pages, 17023 KiB

Open AccessArticle

Fungal Species Associated with Tuber Rot of Foshou Yam (Dioscorea esculenta) in China

by Haifeng Liu, Aye Aye Htun, Sein Lai Lai Aung, Hyunkyu Sang, Jianxin Deng and Yaqun Tao

J. Fungi 2025, 11(5), 380; https://doi.org/10.3390/jof11050380 - 16 May 2025

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Abstract

Foshou yam (Dioscorea esculenta) is a tuber food crop in China. It is a rare species of the yam family and known for its high nutritional value. From 2019 to 2021, tuber rot was observed in Foshou yam in Wuxue, Hubei [...] Read more.

Foshou yam (Dioscorea esculenta) is a tuber food crop in China. It is a rare species of the yam family and known for its high nutritional value. From 2019 to 2021, tuber rot was observed in Foshou yam in Wuxue, Hubei Province, China. Fungal strains were isolated from diseased tubers, and ten representative strains were identified based on microscopical characterization and multi-locus phylogenetic analysis. A total of five different species were identified, including Curvularia geniculata, Curvularia muehlenbeckiae, Fusarium commune, Penicillium oxalicum, and Penicillium sclerotigenum. Pathogenicity test revealed that these fungi are the pathogens of tuber rot in Foshou yam. Among them, P. oxalicum exhibited the strongest pathogenicity. To our knowledge, this is the first report of tuber rot in D. esculenta caused by these five species worldwide. This study provides important information for the future management of tuber rot in Foshou yam. Full article

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

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26 pages, 10258 KiB

Open AccessArticle

Bacillus velezensis Isolate X5 Stimulates the Resistance of Resistant and Susceptible Banana Varieties to Foc Through Different Mechanisms

by Yunlong Xu, Jun Wang, Guangxiang Tian, Changcong Liang, You Zhou, Lijia Guo, Yang Yang and Laying Yang

J. Fungi 2025, 11(5), 379; https://doi.org/10.3390/jof11050379 - 16 May 2025

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Abstract

Banana wilt disease is an important disease in banana production, causing significant losses. Herein, we investigated the mechanism by which Bacillus velezensis isolate X5 enhances the resistance of different resistant banana cultivars to Fusarium oxysporum f. sp. cubense race 4 (Foc4). From the [...] Read more.

Banana wilt disease is an important disease in banana production, causing significant losses. Herein, we investigated the mechanism by which Bacillus velezensis isolate X5 enhances the resistance of different resistant banana cultivars to Fusarium oxysporum f. sp. cubense race 4 (Foc4). From the perspectives of metabolism, transcriptome, and key genes in important pathways, this study analyzed the composition and content changes of other types of signaling molecules, such as free amino acids and soluble sugars, in resistant/susceptible varieties. The results indicate that under pathogen stress, the contents of root-secreted metabolite components in both resistant and susceptible varieties increase significantly overall, and the increase in susceptible varieties is generally higher. For example, the free amino acid components in susceptible varieties are significantly more than those in resistant varieties. However, the addition of biocontrol bacteria can inhibit this increase. Exogenous addition experiments prove that differential metabolites can either promote or inhibit Foc4 and X5 at certain concentrations. The results of KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment and GO (Gene Ontology) annotation show that resistant varieties have more defense pathways compared to susceptible varieties. Under X5 treatment, more defense genes in resistant varieties are activated or their expression is enhanced, promoting the plant roots to secrete more substances related to plant resistance, such as phenylpropanoids and lignin. This research revealed the effects of Bacillus velezensis on bananas and pathogens, allowing valuable conclusions to be drawn. The results have good application potential to understand the relationships among the three species, defining the biocontrol effect and mechanism of Bacillus velezensis, and providing a theoretical basis for the biological control of soil-borne diseases such as banana wilt disease. Full article

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25 pages, 2383 KiB

Open AccessReview

Linking the Metabolic Activity of Plastic-Degrading Fungi to Their Taxonomy and Evolution

by Anusha H. Ekanayaka, Namali T. De Silva, Entaj Tarafder, Xue-Mei Chen, Dong-Qin Dai, Steven L. Stephenson, Suhail Asad, Saowaluck Tibpromma and Samantha C. Karunarathana

J. Fungi 2025, 11(5), 378; https://doi.org/10.3390/jof11050378 - 15 May 2025

Viewed by 129

Abstract

Plastic, a ubiquitous part of our daily lives, has become a global necessity, with annual production exceeding 300 million tons. However, the accumulation of synthetic polymers in our environment poses a pressing global challenge. To address this urgent issue, fungi have emerged as [...] Read more.

Plastic, a ubiquitous part of our daily lives, has become a global necessity, with annual production exceeding 300 million tons. However, the accumulation of synthetic polymers in our environment poses a pressing global challenge. To address this urgent issue, fungi have emerged as potential agents for plastic degradation. In our previous manuscript, ‘A Review of the Fungi That Degrade Plastic’, we explored the taxonomic placement of plastic-degrading fungi across three main phyla: Ascomycota, Basidiomycota, and Mucoromycota. In this review, we built upon that foundation and aimed to further explore the taxonomic relationships of these fungi in a comprehensive and detailed manner, leaving no stone unturned. Moreover, we linked metabolic activity and enzyme production of plastic-degrading fungi to their taxonomy and summarized a phylogenetic tree and a detailed table on enzyme production of plastic-degrading fungi presented here. Microbial enzymes are key players in polymer degradation, operating intra-cellularly and extra-cellularly. Fungi, one of the well-studied groups of microbes with respect to plastic degradation, are at the forefront of addressing the global issue of plastic accumulation. Their unique ability to hydrolyze synthetic plastic polymers and produce a wide range of specific enzymes is a testament to their potential. In this review, we gather and synthesize information concerning the metabolic pathways of fungi involved in the degradation of plastics. The manuscript explores the diverse range of specific enzymes that fungi can produce for plastic degradation and the major pathways of plastic metabolism. We provide a listing of 14 fungal enzymes (Esterase, Cutinase, Laccase, Peroxidases, Manganese peroxidase, Lignin peroxidase, Oxidoreductases, Urease, Protease, Lipase, Polyesterase, Dehydrogenase, Serine hydrolase, and PETase) involved in pathways for plastic degradation alongside the relevant fungi known to produce these enzymes. Furthermore, we integrate the fungi’s enzyme-producing capabilities with their taxonomy and phylogeny. Taxonomic and phylogenetic investigations have pinpointed three primary fungal classes (Eurotiomycetes, Sordariomycetes (Ascomycota), and Agaricomycetes (Basidiomycota)) as significant plastic degraders that produce the vital enzymes mentioned earlier. This paper provides a foundational resource for recognizing fungal involvement in the biodegradation of synthetic polymers. It will ultimately advance fungal biotechnology efforts to address the global issue of plastic accumulation in natural environments. Full article

(This article belongs to the Special Issue Fungi Activity on Remediation of Polluted Environments, 2nd Edition)

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14 pages, 1149 KiB

Open AccessArticle

Retrospective Analysis of Fungal Isolations in Patients on Veno-Venous Extracorporeal Membrane Oxygenation: The Multicenter RANGER STUDY 2.0

by Annalisa Boscolo, Andrea Bruni, Marco Giani, Eugenio Garofalo, Nicolò Sella, Tommaso Pettenuzzo, Arianna Peralta, Michela Bombino, Matteo Palcani, Emanuele Rezoagli, Matteo Pozzi, Elena Falcioni, Eugenio Biamonte, Francesco Murgolo, Leonardo Gottin, Federico Longhini, Salvatore Grasso, Paolo Navalesi and Giuseppe Foti

J. Fungi 2025, 11(5), 377; https://doi.org/10.3390/jof11050377 - 15 May 2025

Viewed by 78

Abstract

Background: Veno-venous extracorporeal membrane oxygenation (V-V ECMO) represents a progressively adopted life-sustaining intervention worldwide, particularly in the management of acute respiratory distress syndrome. Nevertheless, data concerning the prognostic significance of fungal isolation in this setting remain unclear. This study aims (i) to assess [...] Read more.

Background: Veno-venous extracorporeal membrane oxygenation (V-V ECMO) represents a progressively adopted life-sustaining intervention worldwide, particularly in the management of acute respiratory distress syndrome. Nevertheless, data concerning the prognostic significance of fungal isolation in this setting remain unclear. This study aims (i) to assess the incidence of fungal infection and colonization in a homogeneous cohort of V-V ECMO patients, and (ii) to evaluate the association between fungal infection or colonization and 1-year mortality, with a focus on the impact of specific fungal species. Methods: All consecutive adults admitted to the Intensive Care Units of five Italian university-affiliated hospitals and requiring V-V ECMO were screened. Exclusion criteria were age < 18 years, pregnancy, veno-arterial or mixed ECMO-configuration, incomplete records and survival < 24 h after V-V ECMO placement. A standard protocol of microbiological surveillance was applied and the distinction between different fungal species were made through in vivo and vitro tests. Cox-proportional hazards models, Kaplan–Meier curves and linear logistic regressions were applied for investigating mortality. Results: Two-hundred and seventy-nine V-V ECMO patients (72% male) were enrolled. The overall fungal isolation was 41% (n. 114): 23% infections and 18% colonizations. The overall 1-year mortality, among fungal isolations, was 40%, with no different risk in case of fungal infection (26 out of 63, 41%) (aHR 0.85, 95% CI [0.53–1.37], p-value 0.505) and colonization (20 out of 51, 39%) (aHR 0.86, 95%CI [0.51–1.43], p-value 0.556), as compared to patients never detecting fungi (68 out of 165, 41%, reference). According to the isolated mycotic species, as compared to Candida sp. group (reference), the risk of death was greater when different fungal species (e.g., Aspergillus sp. and Candida sp.) were concomitantly isolated in the same patient (OR 1.17, 95%CI [1.12–11.07], p-value 0.031. Conclusions: In the overall population, 23% V-V ECMO patients recorded ‘late’ fungal infections and 18% fungal colonizations, with a similar risk of death as compared to patients never experiencing fungi during the V-V ECMO course. The detection of concomitant different fungal species was an independent risk factor for 1-year mortality. Full article

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15 pages, 4782 KiB

Open AccessArticle

Alternaria alternata botybirnavirus 1 (AaBRV1) Infection Affects the Biological Characteristics of Its Host Fungus Alternaria alternata

by Xinyi Zhang, Qiqi Zhu, Ziyuan Chen, Ju Chen, Zhijun Liu and Xuehong Wu

J. Fungi 2025, 11(5), 376; https://doi.org/10.3390/jof11050376 - 15 May 2025

Viewed by 122

Abstract

A botybirnavirus, Alternaria alternata botybirnavirus 1 (AaBRV1), had been identified from Alternaria alternata strain SD-BZF-19 isolated from diseased watermelon leaves in our previous study. In the current study, AaBRV1 was eliminated from its host fungus strain SD-BZF-19 using single hyphal tip culture method [...] Read more.

A botybirnavirus, Alternaria alternata botybirnavirus 1 (AaBRV1), had been identified from Alternaria alternata strain SD-BZF-19 isolated from diseased watermelon leaves in our previous study. In the current study, AaBRV1 was eliminated from its host fungus strain SD-BZF-19 using single hyphal tip culture method combined with high-temperature treatment to obtain the AaBRV1-free strain, which was named SD-BZF-19-G14. Compared with strain SD-BZF-19-G14, following AaBRV1 infection, colony color of strain SD-BZF-19 changed, and colony growth rate, dry weight of mycelial biomass, and sensitivity to difenoconazole, fludioxonil, and tebuconazole of strain SD-BZF-19 all decreased. However, the virulence of strain SD-BZF-19 was not significantly different from strain SD-BZF-19-G14, with disease index of watermelon leaves inoculated with SD-BZF-19 and SD-BZF-19-G14 being 90.83 and 81.67, respectively. A total of 1244 differentially expressed genes (DEGs) were identified in a comparative transcriptome analysis between the two strains, SD-BZF-19 and SD-BZF-19-G14. Relative to strain SD-BZF-19, the number of upregulated and downregulated DEGs in strain SD-BZF-19-G14 was 660 and 584, respectively. Notably, Pfam database annotated that the number of DEGs related to Major Facilitator Superfamily (MFS) and Cytochrome P450 (CYP450) was 36 and 28, respectively. To our knowledge, this is the first documentation of biological characteristics induced by AaBRV1 infection in A. alternata. Full article

(This article belongs to the Special Issue Fusarium, Alternaria and Rhizoctonia: A Spotlight on Fungal Pathogens, 2nd Edition)

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28 pages, 4104 KiB

Open AccessArticle

Transcriptome Analysis Reveals the Molecular Mechanisms for Mycorrhiza-Enhanced Drought Tolerance in Maize by Regulating the Ca²⁺ Signaling Pathway

by Qiaoming Zhang, Wenjing Yang, Miaomiao Wang, Junwei Chen, Zhaoran Zhang, Yanan Wei, Qingshan Chang and Minggui Gong

J. Fungi 2025, 11(5), 375; https://doi.org/10.3390/jof11050375 - 14 May 2025

Viewed by 172

Abstract

With the continuous change of climate, drought stress has emerged as the primary constraint on crop growth, posing a significant threat to the stability of global grain reserves. Arbuscular mycorrhizal fungi (AMF), as a kind of widely distributed root endophytes, enhance the drought [...] Read more.

With the continuous change of climate, drought stress has emerged as the primary constraint on crop growth, posing a significant threat to the stability of global grain reserves. Arbuscular mycorrhizal fungi (AMF), as a kind of widely distributed root endophytes, enhance the drought tolerance of maize (Zea mays L.) through regulating the physiological and molecular responses. However, comprehensive transcriptome analysis to reveal the molecular mechanism of drought tolerance in the symbiotic process between AMF and maize is still limited. In the potted plant experiment, maizes inoculated with and without arbuscular mycorrhizal fungus Funneliformis mosseae were grown under well-watered (WW) or drought-stressed (DS) conditions. By using RNA-Seq and transcriptome analysis on maize roots and leaves, this work aimed to investigate the differential expressed genes (DEGs) related to the Ca²⁺ signaling pathway induced by AMF symbiosis under drought stress. Our findings indicated that F. mosseae inoculation resulted in a decrease in the net fluxes of Ca²⁺, while simultaneously elevating Ca²⁺ contents in the maize roots and leaves under well-watered or drought-stressed conditions. Notably, 189 DEGs were regulated not only by AMF symbiosis and drought stress, but also exhibited preferential expression in either leaves or roots. The annotation and enrichment of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that most of the DEGs were significantly enriched in Ca²⁺ signaling pathway genes, related to signal transduction, cellular process, and defense response. A high number of DEGs with this function (including calcineurin B-like protein (CBL), CBL-interacting protein kinase (CIPK), mitogen-activated protein kinase (MAPK), and calcium-dependent protein kinase (CDPK) receptor kinases) were upregulated-DEGs or downregulated-DEGs in F. mosseae-inoculated maizes under drought stress. Furthermore, some DEGs belong to transcription factor (TF) families, including bHLH ERF, and, MYB, were speculated to play key roles in improving the drought tolerance of maize. Based on the expression data and co-expression analysis between TF and Ca²⁺ signaling pathway genes, Whirly1 with CBL11, and BRI1-EMS-SUPPRESSOR 1 (BES1) with CBL10, CIPK24, CDPK1, CDPK14, CDPK19, and MAPK9 genes showed significant positive correlations, while B3 domain-containing transcription factors (B3 TFs) with MAPK1 and both CBL9 genes showed significant negative correlations in response to both F. mosseae inoculation and drought stress. The regulation of Ca²⁺ signaling pathways by AMF symbiosis was an important response mechanism of maize to improve their drought resistance. This study provides insightful perspectives on how AMF-induced modulation of gene expression within the Ca²⁺ signaling pathway can enhance the drought tolerance of mycorrhizal maize in the future. Full article

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21 pages, 4901 KiB

Open AccessArticle

Arsenic Stress Resistance in the Endophytic Fungus Cladosporium cladosporioides: Physiological and Transcriptomic Insights into Heavy Metal Detoxification

by Xiao-Xu You, Xiao-Gang Li, Xing-Kai Zhang, Wen Gu, Di Chen, Sen He and Guan-Hua Cao

J. Fungi 2025, 11(5), 374; https://doi.org/10.3390/jof11050374 - 14 May 2025

Viewed by 93

Abstract

This study aims to evaluate the tolerance of an endophytic fungus isolated from the fibrous roots of Gentiana yunnanensis Franch. to arsenic (As) and elucidate the underlying physiological and molecular mechanisms. The filamentous fungus is identified as Cladosporium cladosporioides based on morphological characteristics [...] Read more.

This study aims to evaluate the tolerance of an endophytic fungus isolated from the fibrous roots of Gentiana yunnanensis Franch. to arsenic (As) and elucidate the underlying physiological and molecular mechanisms. The filamentous fungus is identified as Cladosporium cladosporioides based on morphological characteristics and phylogenetic tree analysis, belonging to the family Moniliaceae and Phyla Hyphomycetes. The tolerance of C. cladosporioides to As(V) was assessed by measuring its biomass under varying concentrations of As(V). The fungus exhibited remarkable As(V) tolerance, with an EC₅₀ value of 2051.94 mg/L, and accumulated high concentrations of As in its mycelium. Subcellular distribution analysis revealed that As was predominantly localized in the cell wall fraction, with levels 4.06 times higher than those in the non-cell wall fraction. Notably, the concentrations of total organic As and As(III) in the mycelium were 852.75 μg/g and 24.94 μg/g, respectively, with conversion ratios of 76.64% and 2.24%. The organic As levels significantly surpassed both As(V) and As(III) concentrations in all cellular fractions (cell wall and non-cell wall components), demonstrating particularly efficient As transformation in C. cladosporioides. Under As(V) stress, the membrane antioxidant system, including superoxide dismutase (SOD), metallothionein (MT), glutathione (GSH), and melanin, was activated and significantly enhanced to mitigate oxidative damage. Transcriptomic analysis identified 4771 differentially expressed genes (DEGs; 2527 upregulated), including highly expressed As-responsive genes (CcArsH_1, CcARR_1, CcARR_3, CcGST_1, and CcGST_3). Strong correlations emerged between As speciation (total/organic/As(V)/As(III)), antioxidant levels, and DEG expression patterns. Taken together, these findings demonstrate that C. cladosporioides employs a multi-faceted As detoxification strategy involving subcellular distribution and reductive transformation (As(V) to As(III)/organic As), antioxidant system enhancement, transcriptomic adaptations, and integrated defense strategy. This work highlights C. cladosporioides potential for As bioremediation and elucidates As accumulation mechanisms in G. yunnanensis. Full article

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12 pages, 4153 KiB

Open AccessArticle

Molecular Identification of Fusarium Isolates from Bozcaada Çavuş and Karalahna Grapes in Türkiye

by Gülçin Özcan Ateş

J. Fungi 2025, 11(5), 373; https://doi.org/10.3390/jof11050373 - 14 May 2025

Viewed by 162

Abstract

Contamination of agricultural products by Fusarium species is a significant concern and is commonly found in various agricultural products. They cause severe economic losses in the products, and contaminate and threaten human and animal health due to the toxins they produce. Therefore, determining [...] Read more.

Contamination of agricultural products by Fusarium species is a significant concern and is commonly found in various agricultural products. They cause severe economic losses in the products, and contaminate and threaten human and animal health due to the toxins they produce. Therefore, determining species diversity in various agricultural products is crucial. Bozcaada is well suited for cultivating the highest quality Çavuş grape due to its unique location and climate. Therefore, in this study, the sequencing of the tef1 and tub2 genes in Fusarium isolates from table Çavuş and wine grapes Karalahna, which are specific to Bozcaada, was performed, and their phylogenetic relationships were examined. As a result, it was determined that 11 of the 17 isolates were Fusarium annulatum from the Fusarium fujikuroi species complex (FFSC), 2 were Fusarium nirenbergiae from the Fusarium oxysporum species complex (FOSC), 2 were Fusarium fabacearum from the FOSC, and the last 2 isolates were Fusarium makinsoniae and Fusarium clavus (as ‘clavum’) from the F. incarnatum-equiseti species complex (FIESC). The F. makinsoniae and F. fabacearum species obtained in the study are the first recorded for Türkiye. This research highlights the variety of Fusarium species identified in Bozcaada vineyards in Türkiye. Full article

(This article belongs to the Special Issue Morphology, Phylogeny and Pathogenicity of Fusarium)

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21 pages, 3388 KiB

Open AccessArticle

Pseudogymnoascus destructans Transcriptional Response to Chronic Copper Stress

by Saika Anne, Maranda R. McDonald, Yuan Lu and Ryan L. Peterson

J. Fungi 2025, 11(5), 372; https://doi.org/10.3390/jof11050372 - 13 May 2025

Viewed by 206

Abstract

Copper (Cu) is an essential metal micronutrient, and a fungal pathogen’s ability to thrive in diverse niches across a broad range of bioavailable copper levels is vital for host colonization and fungal propagation. Recent transcriptomic studies have implied that trace metal acquisition is [...] Read more.

Copper (Cu) is an essential metal micronutrient, and a fungal pathogen’s ability to thrive in diverse niches across a broad range of bioavailable copper levels is vital for host colonization and fungal propagation. Recent transcriptomic studies have implied that trace metal acquisition is important for the propagation of the white nose syndrome (WNS) causing fungus, Pseudogymnoascus destructans, on bat hosts. This report characterizes the P. destructans transcriptional response to Cu-withholding and Cu-overload stress. We identify 583 differently expressed genes (DEGs) that respond to Cu-withholding stress and 667 DEGs that respond to Cu-overload stress. We find that the P. destructans Cu-transporter genes CTR1a and CTR1b, as well as two homologs to Cryptococcus neoformans Cbi1/BIM1 VC83_03095 (BLP2) and VC83_07867 (BLP3), are highly regulated by Cu-withholding stress. We identify a cluster of genes, VC83_01834 – VC83_01838, that are regulated by copper bioavailability, which we identify as the Cu-Responsive gene Cluster (CRC). We find that chronic exposure to elevated copper levels leads to an increase in genes associated with DNA repair and DNA replication fidelity. A comparison of our transcriptomic datasets with P. destructans at WNS fungal infection sites reveals several putative fungal virulence factors that respond to environmental copper stress. Full article

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

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9 pages, 12984 KiB

Open AccessArticle

Multiple Analyses Reveal Evidence for Three New Species of Collybia (Clitocybaceae, Basidiomycete) from China

by Yue Qi, Aiguo Xu, Liu Yang, Hongbo Guo, Yaobin Guo, Fashuang Wan, Ruiheng Yang, Ying Pei and Xiaodan Yu

J. Fungi 2025, 11(5), 371; https://doi.org/10.3390/jof11050371 - 13 May 2025

Viewed by 202

Abstract

Three new species of Collybia in China, Collybia clavipes, C. carnea and C. violea, are originally reported and described based on morphological characteristics and molecular data. This study provides detailed morphological descriptions of these three new species of Collybia, which [...] Read more.

Three new species of Collybia in China, Collybia clavipes, C. carnea and C. violea, are originally reported and described based on morphological characteristics and molecular data. This study provides detailed morphological descriptions of these three new species of Collybia, which can be accurately distinguished from other species within the genus Collybia. Phylogenetic relationships of Clitocybaceae were analyzed using a four-loci combined dataset (ITS-nrLSU-rpb2-tef1-α), and the results show that the three newly discovered species of Collybia form three distinct lineages, respectively. Based on the combination of morphological and molecular methods, these three newly collected species of Collybia are confirmed as new to science. A theoretical basis is provided for the species diversity of Collybia. Full article

(This article belongs to the Special Issue Diversity, Phylogeny and Ecology of Forest Fungi)

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28 pages, 5232 KiB

Open AccessArticle

Evaluation of the Synergistic Activity of Antimicrobial Peptidomimetics or Colistin Sulphate with Conventional Antifungals Against Yeasts of Medical Importance

by Shyam Kumar Mishra, Rajesh Kuppusamy, Christina Nguyen, Jennifer Doeur, Harleen Atwal, Samuel Attard, Kristian Sørensen, Jennifer S. Lin, Edgar H. H. Wong, Alex Hui, Annelise E. Barron, Naresh Kumar and Mark Willcox

J. Fungi 2025, 11(5), 370; https://doi.org/10.3390/jof11050370 - 12 May 2025

Viewed by 549

Abstract

With rising multidrug-resistant yeast pathogens, conventional antifungals are becoming less effective, urging the need for adjuvants that enhance their activity at lower doses. This study evaluated the synergistic activity of antimicrobial peptidomimetics (TM8 and RK758) or colistin sulphate in combination with conventional antifungals [...] Read more.

With rising multidrug-resistant yeast pathogens, conventional antifungals are becoming less effective, urging the need for adjuvants that enhance their activity at lower doses. This study evaluated the synergistic activity of antimicrobial peptidomimetics (TM8 and RK758) or colistin sulphate in combination with conventional antifungals against Candida albicans, C. tropicalis, C. parapsilosis, Meyerozyma guilliermondii, Nakaseomyces glabratus, Pichia kudriavzevii and Kluyveromyces marxianus, and Candidozyma auris using the checkerboard microdilution test. RK758 was synergistic with fluconazole in 78% of isolates, with the remaining 22% of isolates still showing partial synergy; it showed synergy with amphotericin B in 56% of isolates, and with caspofungin, 78% of isolates exhibited either synergy or partial synergy. TM8 showed synergy with fluconazole in 44% (with partial synergy in another 44%) of isolates, with amphotericin B in 67% of isolates, and with caspofungin in 44% (with partial synergy in another 44%) of isolates. Colistin with fluconazole or caspofungin exhibited synergy or partial synergy in 56% of the isolates. No antagonism was observed in any of the combinations. Additionally, a time-kill assay further demonstrated synergistic activity between fluconazole and TM8 or RK758. The effects of these peptidomimetics on cell membrane integrity were demonstrated in an ergosterol binding assay, supported by SYTOX Green and cellular leakage assays, both indicating a lytic effect. These results suggest that peptidomimetics can synergise with conventional antifungals, offering a potential strategy for combination therapy against yeast infections. The membrane lytic activity of the peptidomimetics likely plays a role in their synergistic interaction with antifungals, thereby enhancing the antimicrobial activities of both compounds at sub-MIC levels. Full article

(This article belongs to the Special Issue Alternative Therapeutic Approaches of Candida Infections, 4th Edition)

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31 pages, 2867 KiB

Open AccessReview

A Comprehensive Review on Chemical Structures and Bioactivities of Ostropomycetidae Lichens

by Yunhui Wang, Chengyue Hao, Shuhao Jiang, Yanhu Ju, Wei Li and Zefeng Jia

J. Fungi 2025, 11(5), 369; https://doi.org/10.3390/jof11050369 - 9 May 2025

Viewed by 378

Abstract

Lichenized fungi, recognized as an ecologically vital and pharmaceutically promising resource, hold substantial value in both environmental conservation and medicinal applications. As the second largest subclass within the lichen-forming fungi of Lecanoromycetes, Ostropomycetidae emerged as a critical reservoir of bioactive secondary metabolites. Current [...] Read more.

Lichenized fungi, recognized as an ecologically vital and pharmaceutically promising resource, hold substantial value in both environmental conservation and medicinal applications. As the second largest subclass within the lichen-forming fungi of Lecanoromycetes, Ostropomycetidae emerged as a critical reservoir of bioactive secondary metabolites. Current research has revealed that these secondary metabolites demonstrate remarkable bioactivities, positioning them as potential sources for novel pharmaceutical compounds. Despite considerable progress in characterizing chemical constituents and evaluating bioactivities within this subclass, a systematic summary of these discoveries remains absent. This review synthesizes the lichenochemical research progress, providing critical evaluations of 202 structurally characterized compounds from Ostropomycetidae lichen species over recent decades. These Ostropomycetidae-derived compounds cover the phenols, polyketides, fatty acids, terpenoids, steroids, and non-ribosomal peptides, and exhibit diverse bioactivities including antitumor, anti-inflammatory, antibacterial, antifungal, antiviral, antioxidant, anti-angiogenic, anti-neurodegenerative diseases, antitubercular, anti-herbivore, and antitrypanosomal, and so on. The aim of this review is to establish a robust chemodiversity framework and to offer strategic guidance for targeted exploration of lichen-derived drug candidates in the biological resources of Ostropomycetidae lichens. Full article

(This article belongs to the Special Issue Bioactive Secondary Metabolites from Fungi)

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13 pages, 1119 KiB

Open AccessSystematic Review

Mucormycosis Caused by Apophysomyces elegans—A Case Report and Systematic Review of the Literature of Rhino-Orbito-Cerebral Cases of the Genus Apophysomyces

by Vincent Landré, Felix Karl-Ludwig Klingebiel, Christiaan Hendrik Bas van Niftrik, Elisabeth Goetze, Roberto F. Speck, Christian Thomas Hübner, Hans-Christoph Pape and Frank Peter Schäfer

J. Fungi 2025, 11(5), 368; https://doi.org/10.3390/jof11050368 - 9 May 2025

Viewed by 251

Abstract

Introduction: Orbitocerebral mucormycosis, caused by Apophysomyces, is a rare infection, usually occurring in tropical and subtropical climates, with a high mortality rate. We report a case of orbitocerebral mucormycosis caused by A. elegans in a person living with HIV (PLWHIV) from Africa [...] Read more.

Introduction: Orbitocerebral mucormycosis, caused by Apophysomyces, is a rare infection, usually occurring in tropical and subtropical climates, with a high mortality rate. We report a case of orbitocerebral mucormycosis caused by A. elegans in a person living with HIV (PLWHIV) from Africa alongside a systematic literature review updating current diagnostic and treatment strategies for orbitocerebral mucormycosis caused by Apophysomyces. Methods: The presented case was treated in our hospital for polytrauma following a motor vehicle accident (MVA) with aggressive surgical debridement and therapy with liposomal Amphotericin B (AMB). We evaluated clinical presentation, imaging, surgery, and postoperative outcomes. A systematic review of English or German language articles (published between 1985 and 2025) was performed according to PRISMA guidelines. Articles describing patients with mucormycosis due to Apophysomyces were summarized. Quantitative values for relevant parameters that indicated a reduction in mortality and morbidity were obtained. Results: The systematic search initially identified 452 publications, from which 79 studies were retrieved. Seventeen publications comprising 21 cases were included, along with one additional case from our institution, for a total of 22 rhino-orbito-cerebral infections caused by the genus Apophysomyces. Apophysomyces elegans (A. elegans) was the most frequently isolated species (n = 17), followed by A. variabilis (n = 4) and A. ossiformis (n = 1); A. trapeziformis was not reported. The majority of patients were male (72.7%), with a mean age of 40.7 ± 15.9 years. Trauma (27.3%) and diabetes mellitus (18.2%) were the most common underlying risk factors, with SARS-CoV-2 infection identified in 13.6% of cases. Conclusion: Mucormycosis due to Apophysomyces is a rare but potentially devastating condition. Based on our experience and the literature, we suggest that the early diagnosis of Apophysomyces treated with liposomal AMB and aggressive surgical debridement is essential to reduce morbidity and mortality. Full article

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

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13 pages, 3064 KiB

Open AccessArticle

Isolation and Identification of Spoilage Fungi in Potato Fresh Wet Vermicelli and Inhibition Effect of Different Fungicides on Spoilage Fungi

by Feng Zhang, Mei Li, Jiachun Tian, Xia Ge, Shouqiang Li, Jianxin Chen, Yumei Li and Yaqian Zhang

J. Fungi 2025, 11(5), 367; https://doi.org/10.3390/jof11050367 - 8 May 2025

Viewed by 271

Abstract

Fresh wet vermicelli is highly susceptible to microbial contamination during storage as a result of its high moisture content and rich nutrients, which leads to spoilage and deterioration. In addition to exerting a great impact on the quality of the product, this results [...] Read more.

Fresh wet vermicelli is highly susceptible to microbial contamination during storage as a result of its high moisture content and rich nutrients, which leads to spoilage and deterioration. In addition to exerting a great impact on the quality of the product, this results in significant economic losses and potential food safety risks. This work aimed to identify spoilage microorganisms via traditional culturing methods and molecular biology techniques. The effects of environmental factors such as temperature and pH on the growth and development of the dominant spoilage fungi were investigated, and the inhibitory effects of both chemical (potassium sorbate) and natural antimicrobial agents (chitooligosaccharides, chitosan, tea polyphenols, citric acid, and ε-polylysine hydrochloride) were evaluated. The results indicated that Penicillium crustosum was the major spoilage microorganism in fresh wet vermicelli, whose optimal growth temperature and pH was 28 °C and 7, respectively. While conidial germination began at 7 h, hyphal formation was only observed after 12 h. Moreover, the findings suggest that both natural and chemical antimicrobial agents can effectively inhibit the growth of P. crustosum, with ε-polylysine hydrochloride being the strongest antimicrobial agent. Overall, the findings of this study provide a scientific foundation for improving the preservation of fresh wet vermicelli, which is of great significance for extending its shelf life and enhancing food safety. Full article

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

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19 pages, 4426 KiB

Open AccessArticle

Exploration of Mangrove Endophytes as Novel Sources of Tannase Producing Fungi

by Vinodkumar Kushwaha, Jitendra R. Patil, Ganesh Chandrakant Nikalje and Lal Sahab Yadav

J. Fungi 2025, 11(5), 366; https://doi.org/10.3390/jof11050366 - 8 May 2025

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Abstract

Tannase, a highly adaptive biocatalyst, plays a pivotal role in diverse bioconversion reactions in nature. This enzyme exhibits numerous applications across various industrial sectors, including food, pharmaceuticals, chemicals, and beverages. This study aimed to screen and characterize fungal endophytes isolated from mangrove plants [...] Read more.

Tannase, a highly adaptive biocatalyst, plays a pivotal role in diverse bioconversion reactions in nature. This enzyme exhibits numerous applications across various industrial sectors, including food, pharmaceuticals, chemicals, and beverages. This study aimed to screen and characterize fungal endophytes isolated from mangrove plants for their enzyme tannase-producing ability. Eighty-five filamentous endophytic fungi were isolated from different mangrove samples and subsequently identified. These fungal strains were initially screened using the tannic acid agar plate method. Out of the screened strains, 13 fungal isolates demonstrated tannase production ability. The quantitative estimation of extracellular tannase was performed using the submerged fermentation technique. Among the studied endophytes, eight isolates, namely LV_084 (21.21 IU/mL), LV_074 (15.41 IU/mL), LV_078 (6.98 IU/mL), LV_038 (6.97 IU/mL), LV_077 (6.32 IU/mL), LV_016 and LV_066 (6.37 IU/mL), and LV_060 (6.18 IU/mL) exhibited excellent tannase activity. Among these isolates, LV_084 Phyllosticta capitalensis and LV_074 Aspergillus chevalieri showed the highest enzyme-producing ability. These isolates were authenticated using ITS rDNA sequencing, followed by BLAST search and phylogenetic analysis. Furthermore, the physical and chemical conditions for the maximum enzyme production were optimized. This is the first report of enzyme tannase production by Phyllosticta capitalensis and Aspergillus chevalieri. Full article

(This article belongs to the Special Issue Fungal Wonders: Investigating the Diverse Biological Activities of Fungal-Derived Compounds)

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17 pages, 4468 KiB

Open AccessArticle

Integrated Amino Acid Profiling and 4D-DIA Proteomics Reveal Protein Quality Divergence and Metabolic Adaptation in Cordyceps Species

by Chuyu Tang, Yuejun Fan, Tao Wang, Jie Wang, Mengjun Xiao, Min He, Xiyun Chang, Yuling Li and Xiuzhang Li

J. Fungi 2025, 11(5), 365; https://doi.org/10.3390/jof11050365 - 8 May 2025

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Abstract

To explore the differences in protein quality among classic medicinal entomopathogenic fungi and to evaluate their metabolic adaptability, we analyzed the amino acid composition and proteomic characteristics of Cordyceps sinensis (CS), Cordyceps militaris (CM), and Cordyceps cicadae (CC). Quantitative analysis showed CM contained [...] Read more.

To explore the differences in protein quality among classic medicinal entomopathogenic fungi and to evaluate their metabolic adaptability, we analyzed the amino acid composition and proteomic characteristics of Cordyceps sinensis (CS), Cordyceps militaris (CM), and Cordyceps cicadae (CC). Quantitative analysis showed CM contained the highest crude protein and lysine, methionine, threonine, and valine. CS adapted to high-altitude hypoxia and exhibited lower protein but elevated leucine, isoleucine, and histidine contents, which may contribute to membrane stabilization and oxidative stress resistance. CC displayed higher non-essential amino acids such as arginine, proline, and tyrosine, reflecting active nitrogen metabolism. Four-dimensional data-independent acquisition (4D-DIA) proteomics identified 495 differentially expressed proteins (DEPs). Compared with CS, CM and CC displayed upregulated glutamate oxaloacetate transaminases 2 (GOT2), glutamate dehydrogenase (GDH), and argininosuccinate synthase 1 (ASS1) coordinately regulate nitrogen flux through the alanine-aspartate-glutamate metabolic network and urea cycle, supporting metabolic intermediate replenishment for energy metabolism. The upregulation of branched-chain keto acid dehydrogenase E1 subunit alpha (BCKDHA) and acyl-CoA dehydrogenase short/branched chain (ACADSB) in CM and CC facilitated the integration of branched-chain amino acid catabolism with the TCA cycle, explaining species-specific differences in protein content. This study presents the first application of 4D-DIA proteomics to compare CS, CM, and CC, providing insights into quality divergence mechanisms in medicinal fungi. Full article

(This article belongs to the Special Issue Fungal Metabolomics and Genomics)

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14 pages, 7554 KiB

Open AccessArticle

High-Throughput Sequencing Uncovers Fungal Community Succession During Morchella sextelata Development

by Qi Yan, Peng Wang, Zhushan Liu, Ya Yu, Xiao Tan, Xiao Huang, Jiawei Wen and Weidong Zhang

J. Fungi 2025, 11(5), 364; https://doi.org/10.3390/jof11050364 - 7 May 2025

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Abstract

To investigate the correlation between soil fungal communities and the growth and development of Morchella sextelata, this study utilized high-throughput sequencing technology to analyze the structure and diversity of soil fungal communities at various growth stages of Morchella sextelata. The results [...] Read more.

To investigate the correlation between soil fungal communities and the growth and development of Morchella sextelata, this study utilized high-throughput sequencing technology to analyze the structure and diversity of soil fungal communities at various growth stages of Morchella sextelata. The results revealed significant variations in the diversity, composition, and relative abundance of soil fungal communities across different growth stages of Morchella sextelata, demonstrating stage-specific characteristics. Alpha diversity analysis indicated that the Shannon index was highest during the CK stage, significantly decreased in the LS stage (p < 0.01), increased again in the LY stage, and then declined once more in the LC stage. Beta diversity analysis (Principal Coordinates Analysis, PCoA) demonstrated significant differences in fungal community structure across various stages (R = 0.9567, p = 0.001). At the phylum level, Ascomycota remained dominant throughout all growth stages of Morchella sextelata, but its relative abundance exhibited significant dynamic changes. At the fungal genus level, Paecilomyces dominated in the primordium stage (27.12%), whereas Morchella dominated in the conidial stage (LS) and fruiting body stage (LC), accounting for 43.48% and 41.61%, respectively. Additionally, in the LC stage, the plant pathogenic genus Fusarium significantly increased (3.49%), indicating an elevated risk of disease. Functional prediction results revealed that saprotrophic fungi were predominant at all stages, but the relative abundance of pathogenic fungi gradually increased, rising from 0.06% in the LS stage to 41.41% in the LC stage, a substantial increase of 40.81% compared to the LS stage. This suggests a higher potential risk of disease occurrence during the fruiting body stage. Our study provides an overview of the dynamics of soil fungal communities during the cultivation of Morchella sextelata. These findings offer scientific insights for optimizing the artificial cultivation technology of Morchella sextelata and provide a reference for disease prevention and control. Full article

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J. Fungi, Volume 11, Issue 5 (May 2025) – 65 articles

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