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Endophytic Fungi–Plant Interactions and Ecology
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Endophytic Fungi–Plant Interactions and Ecology

A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungi in Agriculture and Biotechnology".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 2363

Special Issue Editors

Dr. Zhenjiang Chen

E-Mail Website
Guest Editor
State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China
Interests: plant; endophytic fungi
Dr. Gensheng Bao

E-Mail Website
Guest Editor
College of Animal Husbandry and Veterinary Medicine, Qinghai University, Xining, China
Interests: hemiparasite; endophytic fungi

Special Issue Information

Dear Colleagues,

Endophytic fungi live symbiotically inside plant tissues without causing apparent harm. They play vital roles in enhancing plant growth, immunity, stress tolerance, and nutrient acquisition. During nutrient deficiency, endophytic fungi prioritize allocating more photosynthetic products to themselves, promoting their growth and the synthesis of stress-resistant substances. In turn, endophytic fungi allocate more resources to help the host resist stress. Endophytic fungi have a significant impact on the physical and chemical properties and microbial communities of soil by affecting litter decomposition and/or root metabolism. Yet, critical gaps remain in our understanding, including how climate change alters the specificity of these interactions, the molecular crosstalk driving mutualistic nutrient exchange, and how endophyte diversity scales to influence plant community resilience. This Special Issue will explore the evolving field of endophytic fungi-plant interactions through the lenses of climate change impact, molecular communication, and ecosystem resilience. It aims to deepen our understanding of how global environmental changes alter the specificity and dynamics of fungal endophyte symbioses with plants. Emphasis will be placed on the molecular crosstalk mechanisms that facilitate mutualistic nutrient exchange and the functional diversity of endophyte communities. Additionally, contributions are invited that investigate how endophyte diversity and interactions at multiple scales influence plant community structure, ecosystem stability, and resilience in the aspect of environmental stressors. This issue seeks multidisciplinary studies ranging from molecular biology to community ecology and environmental modeling to guide future sustainable ecosystem management.

Key Points:

  • Impact of anthropogenic and environmental stressors (e.g., pollution, drought, and invasive species) on endophyte-plant interactions.
  • Application of endophytic fungi in climate-resilient agriculture, grassland, and ecosystem restoration, including biocontrol, biofertilization, and phytoremediation.
  • Functional implications of altered endophyte diversity on plant growth and stress adaptation.
  • Integration of transcriptomics, metabolomics, and ecological data to elucidate endophyte functions.
  • Impacts of changing endophyte populations on soil microbiomes and biogeochemical cycles amid global change.

Reviews, original research, and communications are welcome for submission for this Special Issue.

Dr. Zhenjiang Chen
Dr. Gensheng Bao
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 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-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Journal of Fungi 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 2600 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

  • fungal endophytes
  • plant–soil-microbe interaction
  • functional diversity
  • climate change
  • ecosystem restoration

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Published Papers (3 papers)

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Research

19 pages, 13468 KB  
Article
Morphological Diversity of Epichloë sinensis from Festuca sinensis Germplasm on the Qinghai–Tibet Plateau
by Junying Liu, Jiawen Sun, Yanqun Zhao, Zhongxiang Li, Mei Zhang, Longxuan Cui, Jinhui Shen, Yang Luo, Yue Gao, Wei Zhou, Taixiang Chen, Tian Wang, Mingxiang Du, Wencong Liu, Chao Xia, Tao Hu and Pei Tian
J. Fungi 2026, 12(3), 166; https://doi.org/10.3390/jof12030166 - 25 Feb 2026
Viewed by 579
Abstract
Epichloë sinensis engages in mutualistic symbiosis with Festuca sinensis on the Qinghai–Tibet Plateau. The influence of variation within the Epichloë genus on morphology in this context is poorly understood, as is the influence of environmental factors (e.g., temperature, precipitation, and altitude). Accordingly, a [...] Read more.
Epichloë sinensis engages in mutualistic symbiosis with Festuca sinensis on the Qinghai–Tibet Plateau. The influence of variation within the Epichloë genus on morphology in this context is poorly understood, as is the influence of environmental factors (e.g., temperature, precipitation, and altitude). Accordingly, a total of 122 fungal endophyte strains were isolated from 270 F. sinensis seeds collected from different locations on the Qinghai–Tibet Plateau, and their morphological characteristics were observed. The colonies were white on the front, dark brown in the center on the back, and light brown or yellow around the PDA medium, exhibiting typical characteristics of E. sinensis. Morphological diversity was categorized into (1) colony features (six types based on texture, shape, and cracks), (2) growth rates (51 strains that produce spores: 0.23–0.78 mm/d; 71 strains that do not produce spores: 0.11–0.93 mm/d), and (3) hyphal width (51 strains that produce spores: 0.60–2.57 μm; 71 strains that do not produce spores: 0.95–2.10 μm). Correlation analyses revealed that temperature and altitude had significant effects on these traits. Phylogenetic relationships showed that 17 strains probably were E. sinensis, and only 4 strains probably were the endophyte E. poae. One strain was haploid and may have originated from E. festucae. All 22 tested strains lacked genes associated with toxic alkaloid biosynthesis (ergot alkaloid) but harbored regulatory genes for the insect-resistant alkaloid peramine, demonstrating potential for use in developing new germplasm in Festuca species. Full article
(This article belongs to the Special Issue Endophytic Fungi–Plant Interactions and Ecology)
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23 pages, 4608 KB  
Article
Environmental Drivers Override Host Phylogeny in a Locoweed–Endophyte Symbiosis
by Yue-Yang Zhang, Tong-Tong Wang and Yan-Zhong Li
J. Fungi 2026, 12(2), 87; https://doi.org/10.3390/jof12020087 - 28 Jan 2026
Viewed by 673
Abstract
Plant endophytes, often termed the “second genome”, critically shape host adaptability. However, the complexity of their interactions, regulated by microbial traits, host species, and environment, has limited both our understanding of symbiosis and the application of beneficial endophytes. The symbiosis between locoweeds ( [...] Read more.
Plant endophytes, often termed the “second genome”, critically shape host adaptability. However, the complexity of their interactions, regulated by microbial traits, host species, and environment, has limited both our understanding of symbiosis and the application of beneficial endophytes. The symbiosis between locoweeds (Oxytropis and Astragalus species) and the endophyte Alternaria sect. Undifilum, which produces the neurotoxin swainsonine, serves as an ideal model for investigating these relationships. Through extensive national surveys (2021–2023) across China’s major locoweed habitats, combining field sampling with cultivation, molecular, quantitative, and modeling approaches, a central question emerged: To what extent are the distribution and function of this symbiosis shaped by the contemporary environment versus host evolutionary history? The results showed that: (1) Among 32 surveyed species of Oxytropis, Astragalus, and Sphaerophysa, the endophyte Alternaria sect. Undifilum colonized 11 species. In colonized plants, endophyte loads ranged from 0.02 to 58.87 pg/ng total DNA, and swainsonine concentrations varied from 0.00003% to 1.00%. (2) Environmental factors, rather than host phylogeny, were the key driver governing the geographical distribution and expression of the symbiosis. (3) Low temperature and drought stress regulated the symbiotic relationship and chemical defense through both direct effects on the symbionts and indirect pathways involving grazing pressure. This study demonstrates that the environment is the core force dominating the geographical pattern and functional expression of the locoweed–endophyte symbiosis at ecological scales. These findings provide new perspectives for understanding the general principles of plant–endophyte symbiosis and establish a scientific foundation for predicting and utilizing endophyte resources in changing environments. Full article
(This article belongs to the Special Issue Endophytic Fungi–Plant Interactions and Ecology)
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14 pages, 3902 KB  
Article
Ascomycetous Endophytic Fungi Drive Root Fungal Community Assembly in Wheat Under Moderate Drought
by Zixuan Yao, Yadi Chen, Guanqun Wang, Yonghui Hong, Shuqiu Jiang, Xuhang Jiang, Fanyu Zhao, Chen Zhou, Yuxiang Zhou, Hening Tang, Min Zhu, Jinfeng Ding, Chunyan Li, Weifeng Xu, Wenshan Guo, Jianhua Zhang, Ying Li and Xinkai Zhu
J. Fungi 2026, 12(2), 82; https://doi.org/10.3390/jof12020082 - 25 Jan 2026
Viewed by 690
Abstract
Drought stress severely limits wheat growth, development and yield. Endophytic fungi play a crucial role in plant growth and drought resistance. In agricultural production, they hold significant application potential as biocontrol agents capable of mitigating drought-induced damage. However, the mechanisms underlying changes in [...] Read more.
Drought stress severely limits wheat growth, development and yield. Endophytic fungi play a crucial role in plant growth and drought resistance. In agricultural production, they hold significant application potential as biocontrol agents capable of mitigating drought-induced damage. However, the mechanisms underlying changes in endophytic fungal community structure under drought stress remain unclear. Our study employed amplicon sequencing to investigate the structure of endophytic fungal communities in wheat roots under different water treatments, comparing structural and functional changes between different treatments. Results revealed that drought stress led to the greatest accumulation of relative abundance in the phylum Ascomycota (86.4%). At the genus level, Stachybotrys (increase 994.2%), Fusarium (increase 94.6%) and Aspergillus (increase 295.6%) showed the most significant increases in relative abundance. Co-occurrence network and Sankey diagram analysis revealed that wheat roots formed a drought-specific endophytic fungal community centered around Stachybotrys, Fusarium and Aspergillus, which indirectly enhanced crop drought tolerance. Our findings provide a theoretical foundation for future agricultural strategies to improve crop drought resistance through precise regulation of microbial communities. Full article
(This article belongs to the Special Issue Endophytic Fungi–Plant Interactions and Ecology)
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