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Microorganisms
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Endophytic Fungus as Producers of New and/or Bioactive Substances, Second...
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Endophytic Fungus as Producers of New and/or Bioactive Substances, Second Edition

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

Deadline for manuscript submissions: 31 October 2026 | Viewed by 3014

Editor

Prof. Dr. Cecilia Veronica Nunez

E-Mail Website
Guest Editor
Bioprospection and Biotechnology Laboratory, National Institute of Amazonian Research, Manaus 69067-375, Brazil
Interests: endophytic fungus; bioactive natural products; phytochemistry; in vitro plant cell culture
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

This Special Issue is the continuation of our previous Special Issue entitled “Endophytic Fungus as Producers of New and/or Bioactive Substances”.

In recent years, fungi have attracted more attention from natural product chemists because of their great potential for producing new chemical entities and bioactive substances. They can also produce substances similar to those produced by their host plant, which can be very useful in industrial applications. Sometimes, they may produce other molecules with very different chemical skeletons. Thus, this Special Issue will highlight fungi as producers of natural products (especially micromolecules, such as terpenes, flavonoids, alkaloids, etc.), though other biomolecules are also welcome. This Special Issue of Microorganisms will also provide a scientific platform for scientists performing chemical and biological studies related to endophytic fungus. Original studies and reviews are particularly welcome.

Prof. Dr. Cecilia Veronica Nunez
Guest Editor

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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized 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

  • endophytic fungus
  • natural products 
  • terpenes 
  • alkaloids 
  • flavonoids 
  • peptides 
  • nuclear magnetic resonance 
  • bioactivity

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Published Papers (3 papers)

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Research

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22 pages, 6017 KB  
Article
RdDM-Dependent Epigenetic Regulation Coordinates Systemic Immunity and Compatibility with Trichoderma atroviride in Arabidopsis thaliana
by Maria Montserrat Rosendo-Vargas, Valeria Ávila-Castillo, Kumari Rashmi and Sergio Casas-Flores
Microorganisms 2026, 14(4), 914; https://doi.org/10.3390/microorganisms14040914 - 18 Apr 2026
Cited by 1 | Viewed by 731
Abstract
Epigenetic regulation plays a central role in modulating plant immune responses and interactions with beneficial microbes. In this study, we investigated the contribution of RNA-directed DNA methylation (RdDM) components—DCL3; AGO9; DCL1; and the de novo DNA methyltransferases CMT3, DRM1, and DRM2—to the interaction [...] Read more.
Epigenetic regulation plays a central role in modulating plant immune responses and interactions with beneficial microbes. In this study, we investigated the contribution of RNA-directed DNA methylation (RdDM) components—DCL3; AGO9; DCL1; and the de novo DNA methyltransferases CMT3, DRM1, and DRM2—to the interaction between Arabidopsis thaliana, Trichoderma atroviride, and foliar pathogens. We show that DCL3 and AGO9 differentially regulate basal and inducible immunity, negatively affecting resistance to the necrotrophic fungus Botrytis cinerea, while promoting defense against the hemibiotrophic bacterium Pseudomonas syringae pv. tomato DC3000. Transcriptional analyses revealed that RdDM components modulate the balance between jasmonic acid/ethylene (JA/ET) and salicylic acid (SA) signaling pathways, influencing the amplitude and coordination of defense responses. In addition, DCL3 and DCL1 appear to be required for the full expression of T. atroviride-mediated systemic resistance, whereas AGO9 and DNA methyltransferases contribute to efficient root colonization. Notably, mutants in these pathways displayed enhanced basal resistance but impaired responsiveness to beneficial microbial signals, revealing a trade-off between constitutive defense activation and inducible systemic protection. Consistent with this, alterations in RdDM components were also associated with changes in plant growth dynamics under specific conditions, supporting a role for epigenetic regulation in coordinating growth–defense trade-offs. Together, our findings support a model in which epigenetic regulation controls defense responsiveness, enabling plants to balance immune activation, growth and compatibility toward beneficial microbes. Full article
(This article belongs to the Special Issue Endophytic Fungus as Producers of New and/or Bioactive Substances, Second Edition)
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14 pages, 1903 KB  
Article
Low Nitrogen Concentration and Acidic pH Enhance the Antifungal Activity Against Botrytis cinerea of an Endophytic Alternaria sp. Isolated from Opuntia ficus-indica
by Leonora Mendoza, Camilo Aguirre, Rodolfo Parada, Hristo Parada, Paulo Castro, Freddy Navarro, Araceli Vidal and Milena Cotoras
Microorganisms 2026, 14(2), 376; https://doi.org/10.3390/microorganisms14020376 - 5 Feb 2026
Viewed by 1038
Abstract
Endophytic fungi from the Cactaceae family are an underexplored source of bioactive secondary metabolites with potential applications in sustainable agriculture. This study investigated an endophytic fungus obtained from healthy cladodes of Opuntia ficus-indica growing in the Chilean Andean Precordillera. The influence of culture [...] Read more.
Endophytic fungi from the Cactaceae family are an underexplored source of bioactive secondary metabolites with potential applications in sustainable agriculture. This study investigated an endophytic fungus obtained from healthy cladodes of Opuntia ficus-indica growing in the Chilean Andean Precordillera. The influence of culture conditions, specifically pH and nitrogen concentration, on the production of diffusible and volatile antifungal compounds against the phytopathogen Botrytis cinerea was evaluated using dual-culture (confrontation) and sandwiched Petri dish assays. Morphological characteristics and molecular analyses confirmed that the isolate belongs to the genus Alternaria. Antifungal activity increased significantly under acidic conditions and limited nitrogen availability. The strongest inhibition by volatile compounds occurred at pH 4.5 and the lowest concentration of ammonium tartrate. Furthermore, ethyl acetate extracts at 40 mg/L obtained from Alternaria sp. cultures grown at pH 4.5 with 2.3 g/L ammonium tartrate inhibited B. cinerea mycelial growth by 60%. The study provides a framework for improving the yield of antifungal metabolites produced by Alternaria, contributing to the development of biofungicides for gray mold control. Full article
(This article belongs to the Special Issue Endophytic Fungus as Producers of New and/or Bioactive Substances, Second Edition)
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27 pages, 586 KB  
Systematic Review
Endophytic Fungi as a Promising Source of Bioactive Compounds for Wound Healing: A Systematic Review
by Marina Borges Guimarães, Carolina Castello Branco Rangel Helbourn, Gustavo Oliveira Gonçalves, Maria Beatriz Macedo Gonçalves, Damaris Silviera, Yris Maria Fonseca Bazzo, Paula Elaine Diniz do Reis and Pérola Oliveira Magalhães
Microorganisms 2026, 14(4), 918; https://doi.org/10.3390/microorganisms14040918 - 18 Apr 2026
Viewed by 782
Abstract
Endophytic fungi (EF) inhabit internal plant tissue in a mutually beneficial symbiotic relationship with their host plant. EF synthesizes metabolites that are structurally similar or identical to those found in their host plants, which include alkaloids, flavonoids, terpenoids, phenolic compounds, polysaccharides, proteins, lipids, [...] Read more.
Endophytic fungi (EF) inhabit internal plant tissue in a mutually beneficial symbiotic relationship with their host plant. EF synthesizes metabolites that are structurally similar or identical to those found in their host plants, which include alkaloids, flavonoids, terpenoids, phenolic compounds, polysaccharides, proteins, lipids, and organic acids. These molecules have promising therapeutic effects, such as antimicrobial, antioxidant, anti-inflammatory, and antitumor activities. Wound healing has earned attention in recent years because of its relation to chronic pathological diseases. This systematic review scanned the available scientific literature database about the wound-healing properties of EF biomolecules. Amongst 994 works, 24 were screened after abstract and full-text reading. The studies were published between 2014 and 2026, in twelve countries. In total, 16 studies presented in vivo assays, 11 studies presented in vitro assays, and 3 studies presented both assays. Most studies identified molecules, which include melanin, benzoic acid, terpenes, sesquiterpenes (purpurolide), extracellular polysaccharides, exopolysaccharides, carotenoids, fatty acids, proteins, pyrones, quinones, and hydrocarbon acids, among others. A meta-analysis was not conducted due to high heterogeneity across extracts, methodologies, and outcomes. All studies showed wound-healing properties from EF extracts. The findings suggest a positive effect of EF extracts on wound-healing properties and the need for standardized in vitro and in vivo protocols. Full article
(This article belongs to the Special Issue Endophytic Fungus as Producers of New and/or Bioactive Substances, Second Edition)
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