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Agronomy
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Exploring the Diversity of Endophytic Microorganisms: From Microbial Ecology to...
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Exploring the Diversity of Endophytic Microorganisms: From Microbial Ecology to Agronomic Applications

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 March 2025 | Viewed by 2957

Special Issue Editors

Dr. Carlos Garrido

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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
Dr. Victoria E. González-Rodríguez

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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
Dr. Hernando José Bolivar Anillo

E-Mail Website
Guest Editor
Programa de Microbiología, Facultad de Ciencias Básicas y Biomédicas, Universidad Simón Bolívar, Barranquilla 080002, Colombia
Interests: biocontrol; endophytic microorganisms; Botrytis cinerea
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The Special Issue titled "Exploring the Diversity of Endophytic Microorganisms: From Microbial Ecology to Agronomic Applications" aims to deepen the understanding of endophytic microorganisms, crucial microbial entities that reside within plant tissues. This issue invites original research and articles that delve into the interactions between these microorganisms and host plants, their implications in microbial ecology, and their practical applications in agronomy. The objectives include uncovering new aspects of endophytic microbial biodiversity, understanding plant–microbe interactions from an ecological and functional perspective, and exploring practical applications in crop improvement, agricultural sustainability, and plant disease management. The scope encompasses studies on the characterization of endophytic communities in different plant species, analysis of endophytes' effects on plant growth and health, development of agronomic strategies using endophytes for crop enhancement, and research linking microbial ecology to innovative agronomic applications. This Special Issue serves as a unique platform for researchers in microbiology, ecology, biotechnology, and agronomy to present their findings and contribute to advancing knowledge in this vital field.

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

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

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Published Papers (4 papers)

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Research

34 pages, 6063 KiB  
Article
Exploring the Genome of the Endophytic Fungus Botrytis deweyae: Prediction of Novel Secondary Metabolites Gene Clusters: Terpenes and Polyketides
by Victor Coca-Ruiz, Josefina Aleu, Carlos Garrido and Isidro G. Collado
Agronomy 2024, 14(11), 2747; https://doi.org/10.3390/agronomy14112747 - 20 Nov 2024
Viewed by 212
Abstract
Fungi have played a pivotal role in human history, from the dangers of fungal toxins to the revolutionary discovery of penicillin. Fungal secondary metabolites (SMs), such as polyketides (PKs) and terpenes, have attracted considerable interest due to their diverse biological activities. Botrytis deweyae [...] Read more.
Fungi have played a pivotal role in human history, from the dangers of fungal toxins to the revolutionary discovery of penicillin. Fungal secondary metabolites (SMs), such as polyketides (PKs) and terpenes, have attracted considerable interest due to their diverse biological activities. Botrytis deweyae, an endophytic fungus, exhibits behaviors that are notably distinct from those of its necrotrophic relatives within the genus Botrytis. This study explores the importance of terpenes and PK gene clusters and their conservation between species. In addition, new putative biosynthetic gene clusters corresponding to those families were identified. Consequently, the new PKS BdPKS22-26 were also identified in other Botrytis species and other fungi. In addition, those new gene clusters identified in this work show differences in the degree of conservation and are phylogenetically closely related to some of the 21 PKSs previously described in the reference strain Botrytis cinerea B05.10. Moreover, a new gene cluster related to terpenes in B. deweyae B1 and B. cinerea B05.10 was also identified that had never been detected before. This new gene cluster is well conserved among other Botrytis species in many phylogenetically distant fungal lineages. Understanding the genetic basis and conservation of these putative biosynthetic gene clusters sheds light on the metabolic potential and ecological roles of B. deweyae and related fungal species. Full article
(This article belongs to the Special Issue Exploring the Diversity of Endophytic Microorganisms: From Microbial Ecology to Agronomic Applications)
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14 pages, 1437 KiB  
Article
Differences in Early Root Endophytic Bacterial Communities between Japanese Sake Rice Cultivars and Table Rice Cultivars
by Sibel Sokel, Solomon Oloruntoba Samuel, Kazuki Suzuki and Naoki Harada
Agronomy 2024, 14(8), 1769; https://doi.org/10.3390/agronomy14081769 - 12 Aug 2024
Viewed by 670
Abstract
Sake, which is produced mainly from japonica rice (Oryza sativa subsp. japonica), is one of the most important alcohol products in Japan. In this study, we aimed to investigate a hypothesis that the early root endophytic bacterial communities in Japanese sake [...] Read more.
Sake, which is produced mainly from japonica rice (Oryza sativa subsp. japonica), is one of the most important alcohol products in Japan. In this study, we aimed to investigate a hypothesis that the early root endophytic bacterial communities in Japanese sake rice cultivars would be distinct from those in table rice cultivars, comparing four sake rice cultivars and two table rice cultivars. Rice roots in the vegetative stage were collected 0, 3, and 6 weeks after transplanting, and 16S rRNA gene amplicon sequencing revealed significant differences in bacterial community composition diversity between the sake and table rice cultivars. The root endophytic bacterial communities at the transplanting differed significantly between the rice cultivars, indicating differences in each seed-derived endophytic community. After an overall dominance of Pantoea and Methylobacterium-Methylorubrum at the transplanting, the endophytic community was gradually replaced by soil-derived bacteria that varied by the rice cultivars. Notably, PERMANOVA results showed that the rice endophytic bacterial community composition differed significantly between the sake and table rice cultivars (p < 0.001). These results highlight the distinct root endophytic bacterial composition in the sake rice cultivars compared to those in the table rice cultivars, supporting our hypothesis. Full article
(This article belongs to the Special Issue Exploring the Diversity of Endophytic Microorganisms: From Microbial Ecology to Agronomic Applications)
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13 pages, 3433 KiB  
Article
Drought Stress Increases the Complexity of the Bacterial Network in the Rhizosphere and Endosphere of Rice (Oryza sativa L.)
by Chunyan Wu, Xiaoqin Zhang, Yinxiu Liu, Xu Tang, Yan Li, Tao Sun, Guochao Yan and Chang Yin
Agronomy 2024, 14(8), 1662; https://doi.org/10.3390/agronomy14081662 - 29 Jul 2024
Viewed by 773
Abstract
The root microbiota plays a crucial role in assisting the plant host in combating various biotic and abiotic stresses, notably drought, which poses a significant threat to global food security. Despite extensive efforts to understand the shifts in rhizosphere and endosphere bacteriomes, there [...] Read more.
The root microbiota plays a crucial role in assisting the plant host in combating various biotic and abiotic stresses, notably drought, which poses a significant threat to global food security. Despite extensive efforts to understand the shifts in rhizosphere and endosphere bacteriomes, there remains a gap in comprehending how drought stress influences the co-occurring network patterns within these compartments and their ecological functional potentials. To address this gap, a pot experiment was conducted with two treatments: continuous flooding as a control and drought treatment. Bulk soil, rhizosphere, and endosphere samples were collected and subjected to high-throughput sequencing and bioinformatics analysis. The results revealed that drought stress significantly reduced the rice biomass but increased the Shannon diversity index in both the rhizosphere and endosphere bacterial communities with no observable effect on richness across compartments. Additionally, drought treatment markedly altered the community structure and bacterial assemblages in these compartments, resulting in the specific enrichment of Actinobacteriota, Gemmatimonadetes, and Patescibacteria, while Bacteroidetes and Firmicutes were depleted in the rhizosphere and endosphere. Furthermore, drought heightened the complexity of the co-occurring networks and the proportions of positive links across all sampling compartments; this effect was accompanied by an increase in the number of connectors in the bulk soil and rhizosphere, as well as module hubs in the rhizosphere. Functional potential prediction indicated that drought stress significantly altered multiple potential ecological functions across all sampling compartments, particularly enriching functions related to the oxidation of sulfur, manganese, and hydrogen in the bulk soil, while functions associated with iron oxidation were significantly depleted in the rhizosphere. Overall, our results demonstrate that under drought stress, rice may specifically enrich certain bacterial taxa and enhance their positive interactions within its root system to improve adaptation. Full article
(This article belongs to the Special Issue Exploring the Diversity of Endophytic Microorganisms: From Microbial Ecology to Agronomic Applications)
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15 pages, 3931 KiB  
Article
Poly-γ-Glutamic Acid-Induced Assemblage of Root Endophytic Microbiota Enhances Disease Resistance in Chrysanthemum Plants
by Feng Cui, Lin Zhu and Cheng Zhou
Agronomy 2024, 14(7), 1577; https://doi.org/10.3390/agronomy14071577 - 19 Jul 2024
Viewed by 741
Abstract
Plant microbiota composition changes with the environment and host state, suggesting potential for engineering. However, engineering plant microbiomes is promising but currently undeveloped. This study investigated the role of root-associated bacterial microbiomes in poly-γ-glutamic acid (γ-PGA)-induced plant disease resistance. γ-PGA treatment significantly reduced [...] Read more.
Plant microbiota composition changes with the environment and host state, suggesting potential for engineering. However, engineering plant microbiomes is promising but currently undeveloped. This study investigated the role of root-associated bacterial microbiomes in poly-γ-glutamic acid (γ-PGA)-induced plant disease resistance. γ-PGA treatment significantly reduced wilt disease caused by Fusarium oxysporum f. sp. chrysanthemi (Foc). Quantitative PCR analysis revealed a 73.2% reduction in Foc abundance in the roots following γ-PGA exposure. However, the disease suppression effect of γ-PGA was notably weakened in sterilized soils or soils treated with bactericide, indicating the essential role of root-associated microbiomes in this process. 16S rRNA gene amplicon sequencing showed that γ-PGA treatments increased the abundance of Proteobacteria, particularly the family Burkholderiaceae, in the roots. Metabolite analysis further indicated that γ-PGA treatment significantly elevated salicylic acid (SA) levels, suggesting that SA played a critical role in the assembly of the root microbiome under γ-PGA treatment. Further experiments confirmed the antagonistic activity and induced systemic resistance (ISR) of Burkholderia sp. against Fusarium wilt. Burkholderia sp. CM72 was found to enhance plant disease resistance through antibiosis and activation of jasmonic acid (JA)-related pathways. In summary, γ-PGA significantly improved plant disease resistance by modulating the SA pathway and promoted the colonization of beneficial microbiota, particularly with Burkholderia sp. Full article
(This article belongs to the Special Issue Exploring the Diversity of Endophytic Microorganisms: From Microbial Ecology to Agronomic Applications)
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