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Microorganisms
Special Issues
Fungal Biology and Interactions—3rd Edition
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Fungal Biology and Interactions—3rd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: 31 January 2026 | Viewed by 987

Special Issue Editors

Prof. Dr. Renato Graciano de Paula

E-Mail Website
Guest Editor
1. Department of Physiological Sciences, Health Sciences Centre, Federal University of Espirito Santo, Vitoria 29047-105, ES, Brazil
2. National Institute of Science and Technology in Human Pathogenic Fungi (INCT-FUNVIR), São Paulo, Brazil
Interests: functional genomics; cellular signaling; biotechnology; secondary metabolism; filamentous fungi
Special Issues, Collections and Topics in MDPI journals
Dr. Roberto Nascimento Silva

E-Mail Website
Guest Editor
1. Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
2. National Institute of Science and Technology in Human Pathogenic Fungi, Brazil
Interests: molecular biology of fungi; genomics and proteomics; biomass degradation; bioethanol
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our previous Special Issues, ”Fungal Biology and Interactions" and “Fungal Biology and Interactions—2nd Edition”.

Interactions involving fungi are of fundamental importance to human life and in biotechnological processes. Thus, in this Special Issue on “Fungal Biology and Interactions—3rd Edition", we aim to present new research and trends regarding fungi–fungi, fungi–plants, fungi–environment, and fungi–microbial community interactions. Articles to be submitted should address basic biology, molecular interactions, cell signaling, pathogen–host relationships, climate change, biofuels and biomaterials, and sustainable agriculture.

Reviews, original research, and communications are welcome.

Prof. Dr. Renato Graciano de Paula
Dr. Roberto Nascimento Silva
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • fungi
  • molecular biology
  • filamentous fungi

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Published Papers (3 papers)

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Research

15 pages, 5000 KiB  
Article
High-Resolution Core Gene-Associated Multiple Nucleotide Polymorphism (cgMNP) Markers for Strain Identification in the Wine Cap Mushroom Stropharia rugosoannulata
by Fei Liu, Bin Cao, Hongmei Dai, Guojie Li, Shoumian Li, Wei Gao and Ruilin Zhao
Microorganisms 2025, 13(7), 1685; https://doi.org/10.3390/microorganisms13071685 - 17 Jul 2025
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Abstract
Stropharia rugosoannulata, an ecologically valuable and economically important edible mushroom, faces challenges in strain-level identification and breeding due to limited genomic resources and the lack of high-resolution molecular markers. In this study, we generated high-quality genomic data for 105 S. rugosoannulata strains [...] Read more.
Stropharia rugosoannulata, an ecologically valuable and economically important edible mushroom, faces challenges in strain-level identification and breeding due to limited genomic resources and the lack of high-resolution molecular markers. In this study, we generated high-quality genomic data for 105 S. rugosoannulata strains and identified over 2.7 million SNPs, unveiling substantial genetic diversity within the species. Using core gene-associated multiple nucleotide polymorphism (cgMNP) markers, we developed an efficient and transferable framework for strain discrimination. The analysis revealed pronounced genetic differentiation among cultivars, clustering them into two distinct phylogenetic groups. Nucleotide diversity (π) across 83 core genes varied significantly, highlighting both highly conserved loci under purifying selection and highly variable loci potentially associated with adaptive evolution. Phylogenetic analysis of the most variable gene, Phosphatidate cytidylyltransferase mitochondrial, identified 865 SNPs, enabling precise differentiation of all 85 cultivars. Our findings underscore the utility of cgMNP markers in addressing challenges posed by horizontal gene transfer and phylogenetic noise, demonstrating their robustness in cross-species applications. By providing insights into genetic diversity, evolutionary dynamics, and marker utility, this study establishes a foundation for advancing breeding programs, conservation strategies, and functional genomics in S. rugosoannulata. Furthermore, the adaptability of cgMNP markers offers a universal tool for high-resolution strain identification across diverse fungal taxa, contributing to broader fungal phylogenomics and applied mycology. Full article
(This article belongs to the Special Issue Fungal Biology and Interactions—3rd Edition)
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15 pages, 9151 KiB  
Article
Study of the Herbicidal Potential and Infestation Mechanism of Fusarium oxysporum JZ-5 on Six Broadleaved Weeds
by Suifang Zhang, Haixia Zhu, Yongqiang Ma and Liang Cheng
Microorganisms 2025, 13(7), 1541; https://doi.org/10.3390/microorganisms13071541 - 30 Jun 2025
Viewed by 207
Abstract
Weeds compete with crops for resources, posing multiple negative impacts for agricultural production systems and triggering degradation of ecosystem services (e.g., alterations in the soil microbial community structure). Under the guidance of green plant protection, the development of efficient biocontrol strains with environmentally [...] Read more.
Weeds compete with crops for resources, posing multiple negative impacts for agricultural production systems and triggering degradation of ecosystem services (e.g., alterations in the soil microbial community structure). Under the guidance of green plant protection, the development of efficient biocontrol strains with environmentally friendly characteristics has become a crucial research direction for sustainable agriculture. This study aimed to develop a fungal bioherbicide by isolating and purifying a pathogenic fungal strain (JZ-5) from infected redroot pigweed (Amaranthus retroflexus L.). The strain exhibited pathogenicity rates ranging from 23.46% to 86.25% against six weed species, with the most pronounced control efficacy observed against henbit deadnettle (Lamium amplexicaule L.), achieving a pathogenicity rate of 86.25%. Through comprehensive characterization of cultural features, morphological observations, and molecular biological identification, the strain was taxonomically classified as Fusarium oxysporum. Scanning electron microscopy revealed that seven days post-inoculation, F. oxysporum JZ-5 formed dense mycelial networks on the leaf surfaces of cluster mallow (Malva verticillata L.), causing severe tissue damage. Safety assessments demonstrated that the spore suspension (104 spores/mL) had no adverse effects on three crops: hulless barley (Hordeum vulgare var. coeleste L.), wheat (Triticum aestivum L.), and potato (Solanum tuberosum L.). These findings suggest that F. oxysporum strain JZ-5 warrants further investigation as a potential bioherbicide for controlling three problematic weed species—Chenopodium album L. (common lambsquarters), Elsholtzia densa Benth. (dense-flowered elsholtzia), and Lamium amplexicaule L. (henbit deadnettle)—in cultivated fields of hulless barley (Hordeum vulgare var. coeleste L.), wheat (Triticum aestivum L.), and potato (Solanum tuberosum L.). This discovery provides valuable fungal resources for ecologically sustainable weed management strategies, contributing significantly to the advancement of sustainable agricultural practices. Full article
(This article belongs to the Special Issue Fungal Biology and Interactions—3rd Edition)
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14 pages, 6707 KiB  
Article
Diplodia fraxini: The Main Pathogen Involved in the Ash Dieback of Fraxinus angustifolia in Croatia
by Jelena Kranjec Orlović, Carlo Bregant, Benedetto T. Linaldeddu, Lucio Montecchio, Ida Volenec, Katarina Uidl and Danko Diminić
Microorganisms 2025, 13(6), 1238; https://doi.org/10.3390/microorganisms13061238 - 28 May 2025
Viewed by 390
Abstract
Fraxinus angustifolia, the main ash species in Croatia in terms of economic and ecological importance, is affected by a severe dieback initially attributed to the fungal pathogen Hymenoscyphus fraxineus. Recently, another pathogen, Diplodia fraxini, has been shown to play a [...] Read more.
Fraxinus angustifolia, the main ash species in Croatia in terms of economic and ecological importance, is affected by a severe dieback initially attributed to the fungal pathogen Hymenoscyphus fraxineus. Recently, another pathogen, Diplodia fraxini, has been shown to play a key role in ash dieback in several European countries. Therefore, because the dieback symptoms of ash trees observed in Croatia are typical of Botryosphaeriaceae attacks, the aim of this study was to define the etiology of F. angustifolia dieback. To this end, symptomatic shoots and branches and cross-sections of the main stem were sampled from 20 symptomatic trees at eight locations and analyzed for the presence of D. fraxini and other possible fungal pathogens. Diplodia fraxini was the fungus most frequently associated with branch cankers and dieback; it was isolated from 17 trees in all sites monitored, and its pathogenicity towards F. angustifolia was confirmed. The fungus was also associated with wood necrosis at the base of the trunk in two trees. Other fungi, namely H. fraxineus, Diaporthe eres, Diplodia seriata, Botryosphaeria dothidea, Armillaria gallica, and Lentinus tigrinus, were isolated sporadically. Full article
(This article belongs to the Special Issue Fungal Biology and Interactions—3rd Edition)
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