Exploring the Diversity of Endophytic Microorganisms: From Microbial Ecology to Agronomic Applications—2nd Edition

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Agroecology Innovation: Achieving System Resilience".

Deadline for manuscript submissions: 15 December 2026 | Viewed by 2067

Special Issue Editors


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Departamento de Biomedicina, Biotecnología y Salud Pública, Laboratorio de Microbiología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Spain
Interests: plant pathogens; pathogenic fungi; endophytic microorganisms; Botrytis cinerea; molecular biology of microorganisms
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Departamento de Biomedicina, Biotecnología y Salud Pública, Laboratorio de Microbiología, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Puerto Real, Spain
Interests: plant pathogens; pathogenic fungi; endophytic microorganisms; Botrytis cinerea; molecular biology of microorganisms
Special Issues, Collections and Topics in MDPI journals

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Guest Editor

Special Issue Information

Dear Colleagues,

The Special Issue, titled "Exploring the Diversity of Endophytic Microorganisms: From Microbial Ecology to Agronomic Applications—2nd Edition", continues to advance our understanding of endophytic microorganisms, essential microbial communities that inhabit plant tissues. This Special Issue invites original research and review articles that investigate the interactions between these microorganisms and their host plants, their ecological roles, and their practical applications in agriculture. Key goals include further exploring the biodiversity of endophytic microbes, deepening insights into plant–microbe interactions from ecological and functional perspectives, and expanding their potential in crop improvement, sustainable farming, and plant disease management. The scope encompasses studies on the characterization of endophytic communities in diverse plant species, their contributions to plant growth and health, the development of endophyte-based strategies for crop enhancement, and the integration of microbial ecology into innovative agricultural practices. This Special Issue serves as a valuable platform for researchers in microbiology, ecology, biotechnology, and agronomy to share their findings and contribute to the growing body of knowledge in this vital field.

Dr. Carlos Garrido
Dr. Victoria E. González-Rodríguez
Dr. Hernando José Bolivar Anillo
Guest Editors

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Keywords

  • endophytic microorganisms
  • plant–microbe interactions
  • endophytic communities
  • innovative agronomic applications
  • microorganisms and host plants

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Related Special Issue

Published Papers (2 papers)

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Research

14 pages, 2250 KB  
Article
Azadirachtin and Its Nanoformulation Reshape the Maize Phyllosphere Microbiome While Maintaining Overall Microbial Diversity
by Ai-Ting Song, Yu-Ning Li, Hao Wu, Muhammad Zeeshan and Zhi-Xiang Zhang
Agronomy 2026, 16(3), 334; https://doi.org/10.3390/agronomy16030334 - 29 Jan 2026
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Abstract
The phyllosphere microbiome is an important component of plant-associated ecosystems, and its structure is susceptible to biotic stress and agricultural interventions. However, the non-target effects of plant-derived pesticides and their nanoformulations on the phyllosphere microbial community remain unclear. By using 16S rRNA amplicon [...] Read more.
The phyllosphere microbiome is an important component of plant-associated ecosystems, and its structure is susceptible to biotic stress and agricultural interventions. However, the non-target effects of plant-derived pesticides and their nanoformulations on the phyllosphere microbial community remain unclear. By using 16S rRNA amplicon sequencing, we investigated the non-target effects of azadirachtin (Aza) and its nanoformulation (O-carboxymethyl chitosan-loaded azadirachtin, O-cmc-aza) on the phyllosphere microbial community of maize, including Spodoptera frugiperda herbivory stress (Attack) as an additional treatment. The results showed that all three treatments significantly altered the phyllosphere microbial community structure, while the overall microbial diversity indices remained stable. Specifically, the Attack treatment significantly enriched bacterial genera such as Akkermansia and Burkholderia-Caballeronia-Paraburkholderia; the Aza treatment mainly increased the abundance of taxa such as Stenotrophomonas and Herbaspirillum, which have been associated in the literature with plant growth promotion; and the O-cmc-aza treatment specifically enriched microbial groups such as Ralstonia and Sphingomonas, which have been reported to include strains involved in pollutant degradation and nitrogen cycling, while reducing the ACE index but maintaining high community evenness. Our results indicated that azadirachtin and its nanoformulations induced compositional changes in the phyllosphere microbiome, without causing marked decline in microbial diversity. This study provides data support for evaluating plant-derived pesticides and nanoformulations with respect to their non-target effect on phyllosphere microbial communities in green agricultural systems. Full article
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24 pages, 1080 KB  
Article
Multifunctional Endophytic Fungi from Ginger (Zingiber officinale) with Antimicrobial, Enzymatic, and Antioxidant Potential
by Rogelio Borrego, Alejandro Bódalo, Inmaculada Izquierdo-Bueno, Javier Moraga, María Carbú, Hernando José Bolivar-Anillo, María Dolores Vela-Delgado, Jesús M. Cantoral, Carlos Garrido and Victoria E. González-Rodríguez
Agronomy 2025, 15(12), 2711; https://doi.org/10.3390/agronomy15122711 - 25 Nov 2025
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Abstract
Endophytic fungi were isolated from ginger (Zingiber officinale) tubers and identified through molecular characterization of ITS and 28S rRNA regions. Nine species were obtained, belonging to the genera Aspergillus, Penicillium, Plectosphaerella, and Pseudogymnoascus. Several isolates, particularly Penicillium [...] Read more.
Endophytic fungi were isolated from ginger (Zingiber officinale) tubers and identified through molecular characterization of ITS and 28S rRNA regions. Nine species were obtained, belonging to the genera Aspergillus, Penicillium, Plectosphaerella, and Pseudogymnoascus. Several isolates, particularly Penicillium melinii, Aspergillus ustus, and Plectosphaerella cucumerina, exhibited strong antagonistic activity against Botrytis cinerea (up to 98.6% growth inhibition), while moderate effects were observed against Colletotrichum acutatum, Staphylococcus aureus and Klebsiella pneumoniae. All isolates produced at least one extracellular enzyme, with lipolytic and cellulolytic enzymes being the most frequently observed, and showed measurable antioxidant activity (EC50 values ranging from 21.7 to 673.6 µg/mL). P. melinii and P. cucumerina demonstrated the highest radical scavenging capacities. These findings reveal the multifunctional potential of ginger-associated endophytic fungi as sustainable sources of bioactive compounds, with promising applications in biocontrol, food preservation, and industrial biotechnology. Full article
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