Journal Description
Journal of Fungi
Journal of Fungi
is an international, peer-reviewed, open access journal of mycology published monthly online by MDPI. The Medical Mycological Society of the Americas (MMSA) and the Spanish Phytopathological Society (SEF) are affiliated with the Journal of Fungi, and their members receive a discount on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, CAPlus / SciFinder, AGRIS, and other databases.
- Journal Rank: JCR - Q2 (Mycology) / CiteScore - Q1 (Ecology, Evolution, Behavior and Systematics)
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 18.4 days after submission; acceptance to publication is undertaken in 2.8 days (median values for papers published in this journal in the second half of 2023).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
4.7 (2022);
5-Year Impact Factor:
5.2 (2022)
Latest Articles
Synthesis of Extracellular L-lysine-α-oxidase along with Degrading Enzymes by Trichoderma cf. aureoviride Rifai VKM F-4268D: Role in Biocontrol and Systemic Plant Resistance
J. Fungi 2024, 10(5), 323; https://doi.org/10.3390/jof10050323 (registering DOI) - 28 Apr 2024
Abstract
When cultivating on wheat bran or deactivated fungal mycelium as a model of “natural growth”, the ability of Trichoderma to synthesize extracellular L-lysine-α-oxidase (LysO) simultaneously with cell-wall-degrading enzymes (proteases, xylanase, glucanases, chitinases, etc.), responsible for mycoparasitism, was shown. LysO, in turn, causes the
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When cultivating on wheat bran or deactivated fungal mycelium as a model of “natural growth”, the ability of Trichoderma to synthesize extracellular L-lysine-α-oxidase (LysO) simultaneously with cell-wall-degrading enzymes (proteases, xylanase, glucanases, chitinases, etc.), responsible for mycoparasitism, was shown. LysO, in turn, causes the formation of H2O2 and pipecolic acid. These compounds are known to be signaling molecules and play an important role in the induction and development of systemic acquired resistance in plants. Antagonistic effects of LysO have been demonstrated against phytopathogenic fungi and Gram-positive or Gram-negative bacteria with dose-dependent cell death. The antimicrobial effect of LysO decreased in the presence of catalase. The generating intracellular ROS in the presence of LysO was also shown in both bacteria and fungi, which led to a decrease in viable cells. These results suggest that the antimicrobial activity of LysO is due to two factors: the formation of exogenous hydrogen peroxide as a product of the enzymatic oxidative deamination of L-lysine and the direct interaction of LysO with the cell wall of the micro-organisms. Thus, LysO on its own enhances the potential of the producer in the environment; namely, the enzyme complements the strategy of the fungus in biocontrol and indirectly participates in inducing SAR and regulating the relationship between pathogens and plants.
Full article
(This article belongs to the Special Issue The Role of Fungi in Plant Defense Mechanisms 2.0)
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Evaluation of the Analytical Performance of a Lateral Flow Assay for the Detection of Anti-Coccidioides Antibodies in Human Sera—Argentina
by
Mariana N. Viale, Diego H. Caceres, Patricia E. Mansilla, María C. Lopez-Joffre, Flavia G. Vivot, Andrea N. Motter, Adriana I. Toranzo and Cristina E. Canteros
J. Fungi 2024, 10(5), 322; https://doi.org/10.3390/jof10050322 (registering DOI) - 28 Apr 2024
Abstract
Coccidiomycosis is a potentially life-threatening fungal infection endemic to certain regions of Argentina. The infection is caused by Coccidioides spp. and is primarily diagnosed by Coccidioides antibody (Ab) detection. Access to rapid, highly accurate diagnostic testing is critical to ensure prompt antifungal therapy.
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Coccidiomycosis is a potentially life-threatening fungal infection endemic to certain regions of Argentina. The infection is caused by Coccidioides spp. and is primarily diagnosed by Coccidioides antibody (Ab) detection. Access to rapid, highly accurate diagnostic testing is critical to ensure prompt antifungal therapy. The sōna Coccidioides Ab Lateral Flow Assay (LFA) performs faster and requires less laboratory infrastructure and equipment compared with other Ab detection assays, potentially providing a substantial improvement for rapid case screening in coccidioidomycosis-endemic regions; however, validation of this test is needed. Thus, we aimed to evaluate the analytical performance of the sōna Coccidioides Ab (LFA) and compare agreement with anti-Coccidioides Ab detection assays. A total of 103 human sera specimens were tested, including 25 specimens from patients with coccidioidomycosis and 78 from patients without coccidioidomycosis. The sōna Coccidioides Ab Lateral Flow Assay (LFA) was performed with a sensitivity of 88%, and specificity and accuracy of 87%. Furthermore, the Coccidioides Ab LFA had good agreement with other anti-Coccidioides Ab detection assays. Our findings suggest the sōna Coccidioides Ab LFA has satisfactory performance and may be useful for diagnosing coccidioidomycosis in endemic regions.
Full article
(This article belongs to the Special Issue Coccidioides and Coccidioidomycosis, 2nd Edition)
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Open AccessArticle
An Enzymatic and Proteomic Analysis of Panus lecomtei during Biodegradation of Gossypol in Cottonseed
by
Clemente Batista Soares Neto, Taísa Godoy Gomes, Edivaldo Ximenes Ferreira Filho, Wagner Fontes, Carlos André Ornelas Ricart, João Ricardo Moreira de Almeida, Félix Gonçalves de Siqueira and Robert Neil Gerard Miller
J. Fungi 2024, 10(5), 321; https://doi.org/10.3390/jof10050321 (registering DOI) - 27 Apr 2024
Abstract
Cotton is an important plant-based protein. Cottonseed cake, a byproduct of the biodiesel industry, offers potential in animal supplementation, although the presence of the antinutritional sesquiterpenoid gossypol limits utilization. The macrofungus Panus lecomtei offers potential in detoxification of antinutritional factors. Through an enzymatic
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Cotton is an important plant-based protein. Cottonseed cake, a byproduct of the biodiesel industry, offers potential in animal supplementation, although the presence of the antinutritional sesquiterpenoid gossypol limits utilization. The macrofungus Panus lecomtei offers potential in detoxification of antinutritional factors. Through an enzymatic and proteomic analysis of P. lecomtei strain BRM044603, grown on crushed whole cottonseed contrasting in the presence of free gossypol (FG), this study investigated FG biodegradation over a 15-day cultivation period. Fungal growth reduced FG to levels at 100 μg/g, with a complex adaptive response observed, involving primary metabolism and activation of oxidative enzymes for metabolism of xenobiotics. Increasing activity of secreted laccases correlated with a reduction in FG, with enzyme fractions degrading synthetic gossypol to trace levels. A total of 143 and 49 differentially abundant proteins were observed across the two contrasting growth conditions after 6 and 12 days of cultivation, respectively, revealing a dynamic protein profile during FG degradation, initially related to constitutive metabolism, then later associated with responses to oxidative stress. The findings advance our understanding of the mechanisms involved in gossypol degradation and highlight the potential of P. lecomtei BRM044603 in cotton waste biotreatment, relevant for animal supplementation, sustainable resource utilization, and bioremediation.
Full article
(This article belongs to the Special Issue Fungal-Related Proteomics in Biotechnology and Health)
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Open AccessArticle
Integrated Transcriptomics and Metabolomics Analysis Reveal the Regulatory Mechanisms Underlying Sodium Butyrate-Induced Carotenoid Biosynthesis in Rhodotorula glutinis
by
Xingyu Huang, Jingdie Fan, Caina Guo, Yuan Chen, Jingwen Qiu and Qi Zhang
J. Fungi 2024, 10(5), 320; https://doi.org/10.3390/jof10050320 (registering DOI) - 27 Apr 2024
Abstract
Sodium butyrate (SB) is a histone deacetylase inhibitor that can induce changes in gene expression and secondary metabolite titers by inhibiting histone deacetylation. Our preliminary analysis also indicated that SB significantly enhanced the biosynthesis of carotenoids in the Rhodotorula glutinis strain YM25079, although
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Sodium butyrate (SB) is a histone deacetylase inhibitor that can induce changes in gene expression and secondary metabolite titers by inhibiting histone deacetylation. Our preliminary analysis also indicated that SB significantly enhanced the biosynthesis of carotenoids in the Rhodotorula glutinis strain YM25079, although the underlying regulatory mechanisms remained unclear. Based on an integrated analysis of transcriptomics and metabolomics, this study revealed changes in cell membrane stability, DNA and protein methylation levels, amino acid metabolism, and oxidative stress in the strain YM25079 under SB exposure. Among them, the upregulation of oxidative stress may be a contributing factor for the increase in carotenoid biosynthesis, subsequently enhancing the strain resistance to oxidative stress and maintaining the membrane fluidity and function for normal cell growth. To summarize, our results showed that SB promoted carotenoid synthesis in the Rhodotorula glutinis strain YM25079 and increased the levels of the key metabolites and regulators involved in the stress response of yeast cells. Additionally, epigenetic modifiers were applied to produce fungal carotenoid, providing a novel and promising strategy for the biosynthesis of yeast-based carotenoids.
Full article
(This article belongs to the Special Issue New Trends in Yeast Metabolic Engineering)
Open AccessArticle
New Insights into Tetraplosphaeriaceae Based on Taxonomic Investigations of Bambusicolous Fungi and Freshwater Fungi
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Hai-Jun Zhao, Mingkwan Doilom, Ausana Mapook, Gennuo Wang, Kevin D. Hyde and Wei Dong
J. Fungi 2024, 10(5), 319; https://doi.org/10.3390/jof10050319 (registering DOI) - 27 Apr 2024
Abstract
Species within Tetraplosphaeriaceae have been frequently documented in recent years with the extensive investigations of microfungi along a latitudinal gradient from north to south in the Asian/Australian region. Both bamboo substrates and freshwater habitats serve as extensive reservoirs, hosting a rich diversity of
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Species within Tetraplosphaeriaceae have been frequently documented in recent years with the extensive investigations of microfungi along a latitudinal gradient from north to south in the Asian/Australian region. Both bamboo substrates and freshwater habitats serve as extensive reservoirs, hosting a rich diversity of fungi that exhibit broad geographical distributions. The most common fungi in these two environments are generally distributed in distinct families. However, our statistics have revealed an intriguingly distinct preference of Tetraplosphaeriaceae species for inhabiting both bamboo substrates and freshwater habitats. The genera Pseudotetraploa (100%) and Triplosphaeria (100%) exhibit a strong preference, followed by Shrungabeeja (71%) and Quadricrura (67%). Our taxonomic and phylogenetic study of microfungi in southern China have identified four additional novel species, viz., Aquatisphaeria bambusae sp. nov., Pseudotetraploa phyllostachydis sp. nov., Pseudotetraploa yangjiangensis sp. nov., and Tetraploa submersa sp. nov. from bamboo substrates and freshwater habitats. In addition, Aquatisphaeria thailandica has previously been documented from freshwater habitats in Thailand; however, we have once again isolated this species from decaying bamboo substrates in Guangdong, China. The new findings substantiate our hypothesis that the preference of Tetraplosphaeriaceae species for colonizing bamboo substrates and freshwater habitats will be more evident through more extensive investigations conducted in such environments.
Full article
(This article belongs to the Special Issue Freshwater Fungal Diversity)
Open AccessArticle
Phytophthora sojae Effector PsAvh113 Targets Transcription Factors in Nicotiana benthamiana
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Shuai Wu, Jinxia Shi, Qi Zheng, Yuqin Ma, Wenjun Zhou, Chengjie Mao, Chengjie Chen, Zhengwu Fang, Rui Xia and Yongli Qiao
J. Fungi 2024, 10(5), 318; https://doi.org/10.3390/jof10050318 (registering DOI) - 27 Apr 2024
Abstract
Phytophthora sojae is a type of pathogenic oomycete that causes Phytophthora root stem rot (PRSR), which can seriously affect the soybean yield and quality. To subvert immunity, P. sojae secretes a large quantity of effectors. However, the molecular mechanisms regulated by most P.
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Phytophthora sojae is a type of pathogenic oomycete that causes Phytophthora root stem rot (PRSR), which can seriously affect the soybean yield and quality. To subvert immunity, P. sojae secretes a large quantity of effectors. However, the molecular mechanisms regulated by most P. sojae effectors, and their host targets remain unexplored. Previous studies have shown that the expression of PsAvh113, an effector secreted by Phytophthora sojae, enhances viral RNA accumulations and symptoms in Nicotiana benthamiana via VIVE assay. In this study, we analyzed RNA-sequencing data based on disease symptoms in N. benthamiana leaves that were either mocked or infiltrated with PVX carrying the empty vector (EV) and PsAvh113. We identified 1769 differentially expressed genes (DEGs) dependent on PsAvh113. Using stricter criteria screening and Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analysis of DEGs, we found that 38 genes were closely enriched in response to PsAvh113 expression. We selected three genes of N. benthamiana (NbNAC86, NbMyb4, and NbERF114) and found their transcriptional levels significantly upregulated in N. benthamiana infected with PVX carrying PsAvh113. Furthermore, individual silencing of these three genes promoted P. capsici infection, while their overexpression increased resistance to P. capsici in N. benthamiana. Our results show that PsAvh113 interacts with transcription factors NbMyb4 and NbERF114 in vivo. Collectively, these data may help us understand the pathogenic mechanism of effectors and manage PRSR in soybeans.
Full article
(This article belongs to the Special Issue Genetic, Genomics and Big Data Analysis of the Interaction between Pathogenic Fungi and Plants)
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Open AccessArticle
Analysis and Interpretation of Automated Blood Count in the Treatment of Chronic Paracoccidioidomycosis
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Eliana da Costa Alvarenga de Brito, Adriana de Oliveira França, Igor Valadares Siqueira, Vinícius Lopes Teodoro Félix, Amanda Alves Rezende, Bárbara Casella Amorim, Suzane Eberhart Ribeiro da Silva, Rinaldo Poncio Mendes, Simone Schneider Weber and Anamaria Mello Miranda Paniago
J. Fungi 2024, 10(5), 317; https://doi.org/10.3390/jof10050317 (registering DOI) - 27 Apr 2024
Abstract
Blood count is crucial for assessing bone marrow’s cell production and differentiation during infections, gaging disease severity, and monitoring therapeutic responses. The profile of blood count in chronic forms of paracoccidioidomycosis (PCM) has been insufficiently explored. To better understand the changes in hematological
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Blood count is crucial for assessing bone marrow’s cell production and differentiation during infections, gaging disease severity, and monitoring therapeutic responses. The profile of blood count in chronic forms of paracoccidioidomycosis (PCM) has been insufficiently explored. To better understand the changes in hematological cells in different stages of the PCM chronic form, we evaluated the blood count, including immature blood cells in automated equipment, before and during the treatment follow-up of 62 chronic PCM patients. Predominantly male (96.8%) with an average age of 54.3 (standard deviation SD 6.9) years, participants exhibited pre-treatment conditions such as anemia (45.2%), monocytosis (38.7%), and leukocytosis (17.7%), which became less frequent after clinical cure. Anemia was more prevalent in severe cases. Notably, hemoglobin and reticulocyte hemoglobin content increased, while leukocytes, monocytes, neutrophils, immature granulocytes, and platelets decreased. Chronic PCM induced manageable hematological abnormalities, mainly in the red blood series. Monocytosis, indicating monocytes’ role in PCM’s immune response, was frequent. Post-treatment, especially after achieving clinical cure, significant improvements were observed in various hematological indices, including immature granulocytes and reticulocyte hemoglobin content, underscoring the impact of infection on these parameters.
Full article
(This article belongs to the Special Issue New Insights into Paracoccidioides and Paracoccidioidomycosis)
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Open AccessArticle
The Putative Cytochrome b5 Domain-Containing Protein CaDap1 Homologue Is Involved in Antifungal Drug Tolerance, Cell Wall Chitin Maintenance, and Virulence in Candida albicans
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Dayong Xu, Manman Wang, Xing Zhang, Hongchen Mao, Haitao Xu, Biao Zhang, Xin Zeng and Feng Li
J. Fungi 2024, 10(5), 316; https://doi.org/10.3390/jof10050316 - 26 Apr 2024
Abstract
Candida albicans (Ca), a prominent opportunistic fungal pathogen in humans, has garnered considerable attention due to its infectious properties. Herein, we have identified and characterized CaCDAP1 (Ca orf19.1034), a homolog of ScDAP1 found in Saccharomyces cerevisiae.
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Candida albicans (Ca), a prominent opportunistic fungal pathogen in humans, has garnered considerable attention due to its infectious properties. Herein, we have identified and characterized CaCDAP1 (Ca orf19.1034), a homolog of ScDAP1 found in Saccharomyces cerevisiae. CaCDAP1 encodes a 183-amino acid protein with a conserved cytochrome b5-like heme-binding domain. The deletion of CaDAP1 renders Ca cells susceptible to caspofungin and terbinafine. CaDAP1 deletion confers resistance to Congo Red and Calcofluor White, and sensitivity to sodium dodecyl sulfate. The deletion of CaDAP1 results in a 50% reduction in chitin content within the cell wall, the downregulation of phosphorylation levels in CaMkc1, and the upregulation of phosphorylation levels in CaCek1. Notably, CaDAP1 deletion results in the abnormal hyphal development of Ca cells and diminishes virulence in a mouse systemic infection model. Thus, CaDAP1 emerges as a critical regulator governing cellular responses to antifungal drugs, the synthesis of cell wall chitin, and virulence in Ca.
Full article
(This article belongs to the Section Fungal Pathogenesis and Disease Control)
Open AccessArticle
A Lateral Flow-Recombinase Polymerase Amplification Method for Colletotrichum gloeosporioides Detection
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Wei-Teng Xu, Xin-Yu Lu, Yue Wang, Ming-Han Li, Ke Hu, Zi-Jie Shen, Xiao-Qin Sun and Yan-Mei Zhang
J. Fungi 2024, 10(5), 315; https://doi.org/10.3390/jof10050315 - 26 Apr 2024
Abstract
The greater yam (Dioscorea alata), a widely cultivated and nutritious food crop, suffers from widespread yield reduction due to anthracnose caused by Colletotrichum gloeosporioides. Latent infection often occurs before anthracnose phenotypes can be detected, making early prevention difficult and causing
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The greater yam (Dioscorea alata), a widely cultivated and nutritious food crop, suffers from widespread yield reduction due to anthracnose caused by Colletotrichum gloeosporioides. Latent infection often occurs before anthracnose phenotypes can be detected, making early prevention difficult and causing significant harm to agricultural production. Through comparative genomic analysis of 60 genomes of 38 species from the Colletotrichum genus, this study identified 17 orthologous gene groups (orthogroups) that were shared by all investigated C. gloeosporioides strains but absent from all other Colletotrichum species. Four of the 17 C. gloeosporioides-specific orthogroups were used as molecular markers for PCR primer designation and C. gloeosporioides detection. All of them can specifically detect C. gloeosporioides out of microbes within and beyond the Colletotrichum genus with different sensitivities. To establish a rapid, portable, and operable anthracnose diagnostic method suitable for field use, specific recombinase polymerase amplification (RPA) primer probe combinations were designed, and a lateral flow (LF)-RPA detection kit for C. gloeosporioides was developed, with the sensitivity reaching the picogram (pg) level. In conclusion, this study identified C. gloeosporioides-specific molecular markers and developed an efficient method for C. gloeosporioides detection, which can be applied to the prevention and control of yam anthracnose as well as anthracnose caused by C. gloeosporioides in other crops. The strategy adopted by this study also serves as a reference for the identification of molecular markers and diagnosis of other plant pathogens.
Full article
(This article belongs to the Collection Advances in Plant Pathogenic Fungi: Diagnosis, Biological Control, and Eco-Sustainable Formulations)
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Open AccessArticle
Proteome and Dihydrorhodamine Profiling of Bronchoalveolar Lavage in Patients with Chronic Pulmonary Aspergillosis
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Kristian Assing, Christian B. Laursen, Amanda Jessica Campbell, Hans Christian Beck and Jesper Rømhild Davidsen
J. Fungi 2024, 10(5), 314; https://doi.org/10.3390/jof10050314 - 25 Apr 2024
Abstract
Neutrophil and (alveolar) macrophage immunity is considered crucial for eliminating Aspergillus fumigatus. Data derived from bronchoalveloar lavage (BAL) characterizing the human immuno-pulmonary response to Aspergillus fumigatus are non-existent. To obtain a comprehensive picture of the immune pathways involved in chronic pulmonary aspergillosis
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Neutrophil and (alveolar) macrophage immunity is considered crucial for eliminating Aspergillus fumigatus. Data derived from bronchoalveloar lavage (BAL) characterizing the human immuno-pulmonary response to Aspergillus fumigatus are non-existent. To obtain a comprehensive picture of the immune pathways involved in chronic pulmonary aspergillosis (CPA), we performed proteome analysis on AL of 9 CPA patients and 17 patients with interstitial lung disease (ILD). The dihydrorhodamine (DHR) test was also performed on BAL and blood neutrophils from CPA patients and compared to blood neutrophils from healthy controls (HCs). BAL from CPA patients primarily contained neutrophils, while ILD BAL was also characterized by a large fraction of lymphocytes; these differences likely reflecting the different immunological etiologies underlying the two disorders. BAL and blood neutrophils from CPA patients displayed the same oxidative burst capacity as HC blood neutrophils. Hence, immune evasion by Aspergillus involves other mechanisms than impaired neutrophil oxidative burst capacity per se. CPA BAL was enriched by proteins associated with innate immunity, as well as, more specifically, with neutrophil degranulation, Toll-like receptor 4 signaling, and neutrophil-mediated iron chelation. Our data provide the first comprehensive target organ-derived immune data on the human pulmonary immune response to Aspergillus fumigatus.
Full article
(This article belongs to the Special Issue Chronic Pulmonary Aspergillosis 2.0)
Open AccessArticle
Transcriptome Analysis of Picea crassifolia in Response to Rust Infestation
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Hailan Li and Luchao Bai
J. Fungi 2024, 10(5), 313; https://doi.org/10.3390/jof10050313 - 25 Apr 2024
Abstract
This study examines the relationship between needle age and rust resistance in Picea crassifolia, focusing on the needle morphology, including size, shape, and physiological traits. One-year-old spruce needles are more susceptible to rust, while two-year-old needles show effective resistance. Using RNA-seq on
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This study examines the relationship between needle age and rust resistance in Picea crassifolia, focusing on the needle morphology, including size, shape, and physiological traits. One-year-old spruce needles are more susceptible to rust, while two-year-old needles show effective resistance. Using RNA-seq on the Illumina HiSeq500 platform, we analyzed both healthy and diseased one-year-old needles (N and B), as well as healthy one-year-old and two-year-old needles (N and L). We applied a fold change (FC) threshold of ≥2 and a false discovery rate (FDR) of <0.01, alongside GO annotation and KEGG pathway enrichment, to identify differentially expressed genes (DEGs). In N vs. B, DEGs were significantly enriched in processes such as metabolism, cellular function, catalysis, binding, ribosomal function, plant-pathogen interactions, endoplasmic reticulum protein processing, and signal transduction, revealing a polygenic network regulating the rust response. Similarly, in N vs. L, electron microscopy highlighted morphological differences in the wax layers of needles, with subsequent transcriptome sequencing uncovering genes involved in the development of one-year-old and two-year-old needles. DEGs were primarily found in pathways related to cutin, suberin, wax biosynthesis, fatty acid metabolism, photosynthesis, and phenylalanine synthesis. Two-year-old needles displayed reduced stomatal density, higher lignin content, and a thicker wax layer compared to one-year-old needles. Validation of the RNA-seq data through RT-qPCR on 10 DEGs confirmed the consistency of gene expression trends, enhancing our understanding of Picea crassifolia’s genetic response to rust and supporting future research into its disease resistance.
Full article
(This article belongs to the Special Issue Rust Fungi)
Open AccessReview
Strategies for the Enhancement of Secondary Metabolite Production via Biosynthesis Gene Cluster Regulation in Aspergillus oryzae
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Xiao Jia, Jiayi Song, Yijian Wu, Sai Feng, Zeao Sun, Yan Hu, Mengxue Yu, Rui Han and Bin Zeng
J. Fungi 2024, 10(5), 312; https://doi.org/10.3390/jof10050312 - 25 Apr 2024
Abstract
The filamentous fungus Aspergillus oryzae (A. oryzae) has been extensively used for the biosynthesis of numerous secondary metabolites with significant applications in agriculture and food and medical industries, among others. However, the identification and functional prediction of metabolites through genome mining
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The filamentous fungus Aspergillus oryzae (A. oryzae) has been extensively used for the biosynthesis of numerous secondary metabolites with significant applications in agriculture and food and medical industries, among others. However, the identification and functional prediction of metabolites through genome mining in A. oryzae are hindered by the complex regulatory mechanisms of secondary metabolite biosynthesis and the inactivity of most of the biosynthetic gene clusters involved. The global regulatory factors, pathway-specific regulatory factors, epigenetics, and environmental signals significantly impact the production of secondary metabolites, indicating that appropriate gene-level modulations are expected to promote the biosynthesis of secondary metabolites in A. oryzae. This review mainly focuses on illuminating the molecular regulatory mechanisms for the activation of potentially unexpressed pathways, possibly revealing the effects of transcriptional, epigenetic, and environmental signal regulation. By gaining a comprehensive understanding of the regulatory mechanisms of secondary metabolite biosynthesis, strategies can be developed to enhance the production and utilization of these metabolites, and potential functions can be fully exploited.
Full article
(This article belongs to the Special Issue Fungal Metabolism in Filamentous Fungi: 2nd Edition)
Open AccessReview
Current Advances in the Functional Genes of Edible and Medicinal Fungi: Research Techniques, Functional Analysis, and Prospects
by
Wenyun Li, Gen Zou, Dapeng Bao and Yingying Wu
J. Fungi 2024, 10(5), 311; https://doi.org/10.3390/jof10050311 - 25 Apr 2024
Abstract
Functional genes encode various biological functions required for the life activities of organisms. By analyzing the functional genes of edible and medicinal fungi, varieties of edible and medicinal fungi can be improved to enhance their agronomic traits, growth rates, and ability to withstand
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Functional genes encode various biological functions required for the life activities of organisms. By analyzing the functional genes of edible and medicinal fungi, varieties of edible and medicinal fungi can be improved to enhance their agronomic traits, growth rates, and ability to withstand adversity, thereby increasing yield and quality and promoting industrial development. With the rapid development of functional gene research technology and the publication of many whole-genome sequences of edible and medicinal fungi, genes related to important biological traits have been mined, located, and functionally analyzed. This paper summarizes the advantages and disadvantages of different functional gene research techniques and application examples for edible and medicinal fungi; systematically reviews the research progress of functional genes of edible and medicinal fungi in biological processes such as mating type, mycelium and fruit growth and development, substrate utilization and nutrient transport, environmental response, and the synthesis and regulation of important active substances; and proposes future research directions for functional gene research for edible and medicinal fungi. The overall aim of this study was to provide a valuable reference for further promoting the molecular breeding of edible and medicinal fungi with high yield and quality and to promote the wide application of edible and medicinal fungi products in food, medicine, and industry.
Full article
(This article belongs to the Section Fungal Genomics, Genetics and Molecular Biology)
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Open AccessArticle
Age-Related Conservation in Plant–Soil Feedback Accompanied by Ectomycorrhizal Domination in Temperate Forests in Northeast China
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Zhen Bai, Ji Ye, Shu-Fang Liu, Hai-Hong Sun, Zuo-Qiang Yuan, Zi-Kun Mao, Shuai Fang, Shao-Fen Long and Xu-Gao Wang
J. Fungi 2024, 10(5), 310; https://doi.org/10.3390/jof10050310 - 24 Apr 2024
Abstract
This study investigates the effects of forest aging on ectomycorrhizal (EcM) fungal community and foraging behavior and their interactions with plant–soil attributes. We explored EcM fungal communities and hyphal exploration types via rDNA sequencing and investigated their associations with plant–soil traits by comparing
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This study investigates the effects of forest aging on ectomycorrhizal (EcM) fungal community and foraging behavior and their interactions with plant–soil attributes. We explored EcM fungal communities and hyphal exploration types via rDNA sequencing and investigated their associations with plant–soil traits by comparing younger (~120 years) and older (~250 years) temperate forest stands in Northeast China. The results revealed increases in the EcM fungal richness and abundance with forest aging, paralleled by plant–soil feedback shifting from explorative to conservative nutrient use strategies. In the younger stands, Tomentella species were prevalent and showed positive correlations with nutrient availability in both the soil and leaves, alongside rapid increases in woody productivity. However, the older stands were marked by the dominance of the genera Inocybe, Hymenogaster, and Otidea which were significantly and positively correlated with soil nutrient contents and plant structural attributes such as the community-weighted mean height and standing biomass. Notably, the ratios of longer-to-shorter distance EcM fungal exploration types tended to decrease along with forest aging. Our findings underscore the integral role of EcM fungi in the aging processes of temperate forests, highlighting the EcM symbiont-mediated mechanisms adapting to nutrient scarcity and promoting sustainability in plant–soil consortia.
Full article
(This article belongs to the Special Issue Soil Fungi and Their Role in Plant Growth)
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Open AccessArticle
The Response of Naturally Based Coatings and Citrus Fungicides to the Development of Four Postharvest Fungi
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Lizette Serrano-Molina, Mónica Hernández-López, Dolores Azucena Salazar-Piña, Silvia Bautista-Baños and Margarita de Lorena Ramos-García
J. Fungi 2024, 10(5), 309; https://doi.org/10.3390/jof10050309 - 24 Apr 2024
Abstract
The tomato (Licopersicon esculentum Mill.) is considered to be one of the products with the highest demand due to its nutritional value; however, it is susceptible to infection by fungi during its pre- and postharvest stages. In this research, three commercial products
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The tomato (Licopersicon esculentum Mill.) is considered to be one of the products with the highest demand due to its nutritional value; however, it is susceptible to infection by fungi during its pre- and postharvest stages. In this research, three commercial products (1% Citrocover, 1% Citro 80, and 0.002% Microdyn) and two coatings based on 1.0% chitosan/0.1% lime or 0.1% orange essential oils were evaluated in vitro and on Saladette tomatoes that were previously inoculated with four postharvest fungi. The application of the commercial citrus-based product Citrocover was highly effective in reducing the in vitro development of Aspergillus flavus, Fusarium oxysporum, and Colletotrichum gloeosporioides, but not Rhizopus stolonifer. The sanitizer Microdyn promoted infections with most fungi. Citrus-based products were effective in reducing infections with A. flavus in the tomatoes during storage. Overall, mycotoxin production was very low for all treatments. The use of commercial citrus-based products and coatings did not alter the weight loss, firmness, or total soluble solid contents of the treated tomatoes. The changes observed were, rather, associated with the normal ripening process of Saladette tomatoes. The commercial citrus-based products satisfactorily controlled the in vitro growth of the fungi Aspergillus flavus, Fusarium oxysporum, and Colletotrichum gloeosporioides.
Full article
(This article belongs to the Special Issue Toxigenic Fungi and Mycotoxins)
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Open AccessArticle
Impact of Nitric Oxide-Release Kinetics on Antifungal Activity
by
Quincy E. Grayton, Ivie L. Conlon, Christopher A. Broberg and Mark H. Schoenfisch
J. Fungi 2024, 10(5), 308; https://doi.org/10.3390/jof10050308 - 24 Apr 2024
Abstract
Pathogenic fungi are an increasing health threat due to the rise in drug resistance. The limited number of antifungals currently available and growing incidence of multi-drug-resistant fungi has caused rising healthcare costs and a decreased quality of life for patients with fungal infections.
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Pathogenic fungi are an increasing health threat due to the rise in drug resistance. The limited number of antifungals currently available and growing incidence of multi-drug-resistant fungi has caused rising healthcare costs and a decreased quality of life for patients with fungal infections. Nitric oxide (NO) has previously been shown to act as an antimicrobial agent, albeit with a limited understanding of the effects of the NO-release kinetics against pathogenic fungi. Herein, the antifungal effects of four nitric oxide-releasing small molecules were studied against the pathogenic fungi Candida albicans, Candida auris, Cryptococcus neoformans, and Aspergillus fumigatus, to demonstrate the broad-spectrum antifungal activity of NO. A bolus dose of NO was found to eradicate fungi after 24 h, where nitric oxide donors with shorter half-lives achieved antifungal activity at lower concentrations and thus had wider selectivity indexes. Each NO donor was found to cause a severe surface destruction of fungi, and all NO donors exhibited compatibility with currently prescribed antifungals against several different fungi species.
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(This article belongs to the Special Issue Multidrug-Resistant Fungi: New Strategies for Diagnosis and Treatment)
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Open AccessCommunication
Discovery of a Unique Set of Dog-Seroreactive Coccidioides Proteins Using Nucleic Acid Programmable Protein Array
by
Megan A. Koehler, Lusheng Song, Francisca J. Grill, Lisa F. Shubitz, Daniel A. Powell, John N. Galgiani, Marc J. Orbach, Edward J. Robb, Yunro Chung, Stacy A. Williams, Vel Murugan, Jin-gyoon Park, Joshua LaBaer, Douglas F. Lake and D. Mitchell Magee
J. Fungi 2024, 10(5), 307; https://doi.org/10.3390/jof10050307 - 24 Apr 2024
Abstract
Valley Fever (VF), caused by fungi in the genus Coccidioides, is a prevalent disease in southwestern and western parts of the United States that affects both humans and animals, such as dogs. Although the immune responses to infection with Coccidioides spp. are
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Valley Fever (VF), caused by fungi in the genus Coccidioides, is a prevalent disease in southwestern and western parts of the United States that affects both humans and animals, such as dogs. Although the immune responses to infection with Coccidioides spp. are not fully characterized, antibody-detection assays are used in conjunction with clinical presentation and radiologic findings to aid in the diagnosis of VF. These assays often use Complement Fixation (CF) and Tube Precipitin (TP) antigens as the main targets of IgG and IgM reactivity, respectively. Our group previously reported evidence of over 800 genes expressed at the protein level in C. posadasii. However, antibody reactivity to the majority of these proteins has never been explored. Using a new, high-throughput screening technology, the Nucleic Acid Programmable Protein Array (NAPPA), we screened serum specimens from dogs against 708 of these previously identified proteins for IgG reactivity. Serum from three separate groups of dogs was analyzed and revealed a small panel of proteins to be further characterized for immuno-reactivity. In addition to CF/CTS1 antigen, sera from most infected dogs showed antibody reactivity to endo-1,3-betaglucanase, peroxisomal matrix protein, and another novel reactive protein, CPSG_05795. These antigens may provide additional targets to aid in antibody-based diagnostics.
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(This article belongs to the Special Issue Coccidioides and Coccidioidomycosis, 2nd Edition)
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Open AccessArticle
The Diversity and Community Composition of Three Plants’ Rhizosphere Fungi in Kaolin Mining Areas
by
Wenqi Xiao, Yunfeng Zhang, Xiaodie Chen, Ajia Sha, Zhuang Xiong, Yingyong Luo, Lianxin Peng, Liang Zou, Changsong Zhao and Qiang Li
J. Fungi 2024, 10(5), 306; https://doi.org/10.3390/jof10050306 - 24 Apr 2024
Abstract
Mining activities in the kaolin mining area have led to the disruption of the ecological health of the mining area and nearby soils, but the effects on the fungal communities in the rhizosphere soils of the plants are not clear. Three common plants
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Mining activities in the kaolin mining area have led to the disruption of the ecological health of the mining area and nearby soils, but the effects on the fungal communities in the rhizosphere soils of the plants are not clear. Three common plants (Conyza bonariensis, Artemisia annua, and Dodonaea viscosa) in kaolin mining areas were selected and analyzed their rhizosphere soil fungal communities using ITS sequencing. The alpha diversity indices (Chao1, Shannon, Simpson, observed-species, pielou-e) of the fungal communities decreased to different extents in different plants compared to the non-kauri mining area. The β-diversity (PCoA, NMDS) analysis showed that the rhizosphere soil fungal communities of the three plants in the kaolin mine area were significantly differentiated from those of the control plants grown in the non-kaolin mine area, and the extent of this differentiation varied among the plants. The analysis of fungal community composition showed that the dominant fungi in the rhizosphere fungi of C. bonariensis and A. annua changed, with an increase in the proportion of Mycosphaerella (genus) by about 20% in C. bonariensis and A. annua. An increase in the proportion of Didymella (genus) by 40% in D. viscosa was observed. At the same time, three plant rhizosphere soils were affected by kaolin mining activities with the appearance of new fungal genera Ochrocladosporium and Plenodomus. Predictive functional potential analysis of the samples revealed that a significant decrease in the potential of functions such as biosynthesis and glycolysis occurred in the rhizosphere fungal communities of kaolin-mined plants compared to non-kaolin-mined areas. The results show that heavy metals and plant species are the key factors influencing these changes, which suggests that selecting plants that can bring more abundant fungi can adapt to heavy metal contamination to restore soil ecology in the kaolin mining area.
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(This article belongs to the Special Issue Diversity and Biotechnology of Soil Fungi and Rhizosphere Fungi)
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Open AccessArticle
Corona-Associated Mucormycosis: Case Series Reports and Review of the Literature
by
Andreea Fitero, Nicoleta Negrut, Harrie Toms John, Anca Ferician and Paula Marian
J. Fungi 2024, 10(5), 305; https://doi.org/10.3390/jof10050305 - 24 Apr 2024
Abstract
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During the COVID-19 pandemic, a significant increase in cases of mucormycosis was observed in COVID-19 patients, especially in India, but not exclusively. The presented cases highlight the heterogeneous nature of mucormycosis, emphasizing the importance of recognizing predisposing factors, such as immunosuppression, due to
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During the COVID-19 pandemic, a significant increase in cases of mucormycosis was observed in COVID-19 patients, especially in India, but not exclusively. The presented cases highlight the heterogeneous nature of mucormycosis, emphasizing the importance of recognizing predisposing factors, such as immunosuppression, due to comorbidities or medication. Diagnosing mucormycosis poses a challenge due to nonspecific clinical manifestations, requiring a multidisciplinary approach for accurate diagnosis. Treatment involves a multi-pronged approach centered around the early initiation of antifungal therapy alongside surgical intervention and the management of underlying conditions, with an emphasis on controlling immunosuppression. Understanding the relationship between COVID-19 and predisposing factors for mucormycosis is fundamental for developing prevention and treatment strategies.
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Open AccessArticle
Prevalence and Species Distribution of Candida Clinical Isolates in a Tertiary Care Hospital in Ecuador Tested from January 2019 to February 2020
by
Yessenia Acosta-Mosquera, Juan Carlos Tapia, Rubén Armas-González, María José Cáceres-Valdiviezo, Juan Carlos Fernández-Cadena and Derly Andrade-Molina
J. Fungi 2024, 10(5), 304; https://doi.org/10.3390/jof10050304 - 24 Apr 2024
Abstract
The incidence of candidemia in healthcare centers is associated with high morbidity and mortality. Frequency varies significantly among regions, with some species being more prevalent than others in Latin America. In this study, 191 clinical Candida isolates were collected from a major hospital
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The incidence of candidemia in healthcare centers is associated with high morbidity and mortality. Frequency varies significantly among regions, with some species being more prevalent than others in Latin America. In this study, 191 clinical Candida isolates were collected from a major hospital in Ecuador from January 2019 to February 2020 aiming to assess their prevalence and distribution. After data processing, 168 isolates characterized by the VITEK 2 system were subsequently identified by ITS sequencing. Results showed diverse Candida species distributions, with C. albicans and C. tropicalis being the most prevalent across different clinical sources. In hospitalized individuals, C. tropicalis (38%) and C. albicans (37%) were the most prevalent, followed by, C. parapsilosis (16%), C. glabrata (5%), and other non-Candida albicans (NCA) species (6%). Conversely, C. parapsilosis (48%), C. albicans (20%), and C. glabrata (14%), associated with candidemia, were the most common in blood and CSF. Additionally, uncommon NCA species such as C. haemulonii, C. kefyr, and C. pelliculosa were identified in Ecuador for the first time. Discrepancies in species identification were observed between the VITEK 2 system and ITS sequencing, coinciding at 85%. This highlights the need for ongoing surveillance and identification efforts in Ecuador’s clinical and epidemiological settings.
Full article
(This article belongs to the Special Issue New Perspectives for Candidiasis 2.0)
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