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Agronomy
Special Issues
Endophytic Fungi and Beneficial Microbes for Sustainable Crop Resilience
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Endophytic Fungi and Beneficial Microbes for Sustainable Crop Resilience

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Pest and Disease Management".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 3113

Special Issue Editors

Dr. Yi Cheng

E-Mail Website
Guest Editor
Institute of Bast Fiber Crops and Center of Southern Economic Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China
Interests: plant disease diagnosis; molecular detection; biological control; disease management
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Xiaofeng Su

E-Mail Website
Guest Editor
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
Interests: molecular biology; analysis of fungal pathogenicity; plant-microbe interaction; soil microorganism
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Global climate change, soil degradation, and excessive use of agrochemicals pose severe threats to crop productivity and food security, thereby creating an urgent need to explore eco-friendly strategies—such as harnessing endophytic fungi and beneficial microbes—to sustainably enhance crop resilience. Against this backdrop, this Special Issue aims to consolidate research on the role of these microorganisms in boosting crop resilience, with its scope covering microbial symbiosis mechanisms, stress tolerance (to drought, salinity, and pathogens), soil health improvement, and their applications in sustainable agriculture. Notably, the study of microbe-crop interactions dates back decades: early research focused on rhizobial nitrogen fixation and mycorrhizal nutrient uptake, and as sustainable agriculture gained global traction, the field has expanded to investigate the multifunctional roles of endophytic fungi in enhancing crop resilience. Now, current cutting-edge research includes deciphering microbial metabolic pathways that regulate crop stress responses, developing microbe-based biofertilizers and biopesticides, and applying omics technologies (genomics, metabolomics) to unravel the complex microbe-crop-soil interactions.

We welcome original research articles, reviews, and short communications that address microbial mechanisms for crop resilience, field validation of microbial products, and interdisciplinary studies linking microbial ecology to agricultural practice.

Dr. Yi Cheng
Prof. Dr. Xiaofeng Su
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. Agronomy is an international peer-reviewed open access semimonthly 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

  • endophytic fungi
  • beneficial microbes
  • sustainable crop resilience
  • stress tolerance
  • microbial symbiosis
  • soil health
  • omics technologies
  • biofertilizers
  • food security
  • agricultural sustainability

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Published Papers (3 papers)

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Research

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24 pages, 18806 KB  
Article
Effects of Gramineous and Leguminous Crops on Soil Microbial Community Structure and Diversity
by Zexian Mi, Zeyang Zheng, Botao Liu, Weitao Han, Xuehao Shan, Zhuofan Pu, Nuerbiyamu Rouzi, Xin Tan, Jianing Wei, Shaorong Hao and Hongliang Tang
Agronomy 2026, 16(3), 380; https://doi.org/10.3390/agronomy16030380 - 4 Feb 2026
Viewed by 441
Abstract
Different crops have varying effects on soil factors, and their associated microbial community compositions also differ. Currently, there is limited comparative research on crops with distant phylogenetic relationships, such as those between gramineous and leguminous species. In this study, a pot experiment combined [...] Read more.
Different crops have varying effects on soil factors, and their associated microbial community compositions also differ. Currently, there is limited comparative research on crops with distant phylogenetic relationships, such as those between gramineous and leguminous species. In this study, a pot experiment combined with high-throughput sequencing was conducted to enable a detailed comparison of microbial communities and soil factors across four crops: wheat, soybean, and two maize varieties. Compared to leguminous crops, differences between gramineous crops may be relatively smaller. The results showed that among the gramineous and leguminous crops, soybean had the lowest effect on soil electrical conductivity (EC) and available phosphorus (AP) (121.68 ± 2.70, 34.74 ± 1.02). The dominant fungi and bacteria phyla were Ascomycota and Proteobacteria; both were most abundant in the ZD958 variety, at 75.12% and 30.47%, respectively. The fungal diversity of ZD958 was most similar to that of W998, whereas the bacterial diversity of XY335 more closely resembled that of SB13. EC and AP were the key factors influencing fungal community composition, while alkali-hydrolyzable nitrogen (AN) was the key factor affecting bacterial community composition. These findings provide a basis for further in-depth research. Full article
(This article belongs to the Special Issue Endophytic Fungi and Beneficial Microbes for Sustainable Crop Resilience)
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18 pages, 3004 KB  
Article
Morphological and Molecular Profiling of Cercophora sp. and Studying Its Potential Effect on Legume Growth Performance Under Drought Conditions
by Bui Hanh Mai and Kazuhiko Narisawa
Agronomy 2025, 15(12), 2803; https://doi.org/10.3390/agronomy15122803 - 5 Dec 2025
Viewed by 691
Abstract
Cercophora species, typically known as saprobes or coprophiles, have occasionally been isolated from healthy roots and have recently been recognized as endophytes. Their dark-pigmented structures suggest adaptation traits similar to dark septate endophytes, although their symbiotic potential remains unclear. This study isolated and [...] Read more.
Cercophora species, typically known as saprobes or coprophiles, have occasionally been isolated from healthy roots and have recently been recognized as endophytes. Their dark-pigmented structures suggest adaptation traits similar to dark septate endophytes, although their symbiotic potential remains unclear. This study isolated and characterized Cercophora sp. NPKC241 from mung bean roots grown under artificial drought in soils with different fertilization histories, using PCR-based DNA sequencing and morphological observation. Its effects on legume growth were subsequently evaluated through pot inoculation experiments under drought. These experiments focused on mung bean, a species known to exhibit significant reductions in chlorophyll content and yield under drought conditions. Among 29 isolates, Cercophora sp. consistently promoted legume growth. In mung bean, it increased shoot and root mass, chlorophyll content, and root elongation under both optimal and water-limited conditions. Under drought, inoculated plants showed approximately threefold higher chlorophyll levels, two- to threefold greater biomass, and roots approximately 5 cm longer than the control, indicating mitigation of drought-induced physiological decline. These findings suggest that Cercophora sp. can act as a beneficial root-associated fungus, enhancing legume performance under drought. Future studies will further explore this interaction by underlying physiological mechanisms and the field-level application potential. Full article
(This article belongs to the Special Issue Endophytic Fungi and Beneficial Microbes for Sustainable Crop Resilience)
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Review

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24 pages, 689 KB  
Review
Recent Advances in Diagnosing and Managing Phytoplasma Diseases
by Zhecheng Xu, Liya Peng, Puhou Xing, Yu Gao, Yi Yu, Tuhong Wang, Zhiqiang Song, Wenjun Zhao, Yi Cheng and Qiulong Hu
Agronomy 2026, 16(5), 504; https://doi.org/10.3390/agronomy16050504 - 25 Feb 2026
Viewed by 1517
Abstract
Phytoplasmas are obligate intracellular parasitic bacteria that infect over 1000 plant species globally, causing devastating diseases characterized by yellowing, witches’ broom, phyllody, and significant yield losses in economically important crops. The unculturable nature of these pathogens has historically hindered their study; however, advances [...] Read more.
Phytoplasmas are obligate intracellular parasitic bacteria that infect over 1000 plant species globally, causing devastating diseases characterized by yellowing, witches’ broom, phyllody, and significant yield losses in economically important crops. The unculturable nature of these pathogens has historically hindered their study; however, advances in molecular biology and genomics have substantially accelerated progress over the past two decades. This review provides a comprehensive overview of current knowledge on phytoplasma diseases and control technologies. In terms of taxonomy, phytoplasmas are currently classified into 37 16Sr groups with over 150 subgroups based on 16S rRNA gene analysis, and approximately 50 ‘Candidatus Phytoplasma’ species have been formally named. Genomic studies have revealed that phytoplasmas possess highly reduced genomes (530–1350 kb) lacking many essential metabolic pathways, reflecting their obligate parasitic lifestyle. Regarding pathogenesis, secreted effector proteins such as SAP (Secreted Aster Yellows Witches’ Broom Protein), TENGU (tengu-su inducer), and SWP (Secreted Wheat Blue Dwarf Protein) manipulate plant hormone signaling and developmental processes, leading to characteristic disease symptoms. Detection technologies have evolved from traditional microscopy to molecular methods, including nested PCR, real-time quantitative PCR, loop-mediated isothermal amplification (LAMP), and CRISPR/Cas-based systems (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein), with AI-based image recognition and remote sensing emerging as promising tools for large-scale field monitoring. Integrated management strategies encompassing agricultural practices, insect vector control, biological control agents, induced resistance, and breeding for resistance are discussed. Finally, future research directions, including functional genomics, microbiome-based approaches, and precision agriculture technologies, are highlighted. This review aims to provide researchers and practitioners with a systematic reference for understanding phytoplasma biology and developing effective disease management strategies. Full article
(This article belongs to the Special Issue Endophytic Fungi and Beneficial Microbes for Sustainable Crop Resilience)
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