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Agronomy
Special Issues
New Insights into Plant–Microbe Interaction
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New Insights into Plant–Microbe Interaction

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

Deadline for manuscript submissions: 10 October 2026 | Viewed by 2248

Special Issue Editors

Dr. Eliana Dell'olmo

E-Mail Website
Guest Editor
Council for Agricultural Research and Economics, Research Centre for Vegetable and Ornamental Crops, Via Cavalleggeri 25, 84098 Pontecagnano, Italy
Interests: legumes; plant pathology; beneficial microorganisms; bacterial biofilm
Special Issues, Collections and Topics in MDPI journals
Dr. Loredana Sigillo

E-Mail Website
Guest Editor
Council for Agricultural Research and Economics, Research Centre for Vegetable and Ornamental Crops, Via Cavalleggeri 25, 84098 Pontecagnano, Italy
Interests: pathogen identification and characterization; disease resistance; phytopathology; bacteriology; plant virus
Special Issues, Collections and Topics in MDPI journals
Dr. Giulia Semenzato

E-Mail Website
Guest Editor Assistant
Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
Interests: bacterial endophytes; PGPB; plant-microorganism interaction

Special Issue Information

Dear Colleagues,

Legumes and vegetables have become important sources of nutrition for humans, but the cultivation and management of these crops can be particularly challenging due to the susceptibility of these species to biotic and abiotic stress.

In this Special Issue, we welcome contributions on emerging diseases of legume species and vegetable crops, the development of novel biocontrol agents against pathogens, and the characterization of novel beneficial microorganisms that improve health and resistance to biotic and abiotic stress. We are also interested in studies exploring the molecular basis of plant–microbe interaction including the plant–pathogen, plant–beneficial microorganism, and pathogen–beneficial microorganism interactions. Papers on microbial genomes analyses are also encouraged.

We invite experts and researchers to submit their reviews, original research, and opinion pieces addressing topics within the scope of this Special Issue.

Dr. Eliana Dell'olmo
Dr. Loredana Sigillo
Guest Editors

Dr. Giulia Semenzato
Guest Editor Assistant

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

  • legumes
  • vegetable crops
  • pathogens
  • beneficial microorganisms
  • microbiome
  • microbial community

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

22 pages, 10382 KB  
Article
Uncovering Viral Diversity and Host Responses in Saffron via Nanopore RNA Sequencing
by Marzieh Shamshiri, Conchi Sánchez, Jesús Mª Vielba, Nieves Vidal, Masoud Shams-Bakhsh and Saleta Rico
Agronomy 2026, 16(8), 803; https://doi.org/10.3390/agronomy16080803 - 14 Apr 2026
Viewed by 497
Abstract
Saffron (Crocus sativus L.) is a high-value crop vulnerable to potyvirus infections threatening its yield and quality. In this study, we combined Oxford Nanopore long-read sequencing with exploratory transcriptomic profiling to characterize the saffron virome and to describe expression profiles associated with [...] Read more.
Saffron (Crocus sativus L.) is a high-value crop vulnerable to potyvirus infections threatening its yield and quality. In this study, we combined Oxford Nanopore long-read sequencing with exploratory transcriptomic profiling to characterize the saffron virome and to describe expression profiles associated with two distinct infection histories: (i) saffron plants experimentally inoculated with cucumber mosaic virus (CMV; Cucumovirus CMV) and turnip mosaic virus (TuMV; Potyvirus rapae) under controlled greenhouse conditions, and (ii) saffron plants naturally infected by diverse viruses. We identified six plant-infecting viral families in both conditions, including Potyviridae, Geminiviridae, Caulimoviridae, Tymoviridae, Aspiviridae, and Partitiviridae. Transcriptomic profiling revealed distinct expression profiles associated with each infection background. Given the limitations of the experimental design, gene expression differences are interpreted descriptively. We describe pathway enrichments associated with antiviral responses. Naturally infected plants exhibited a broad-spectrum, tolerance-based response characterized by the upregulation of photosynthesis-related genes, calcium-mediated signaling components, and stress-responsive transcription factors. In contrast, virus-inoculated plants activated a targeted antiviral program involving RNA silencing, autophagy, ubiquitin-mediated proteolysis, and hormonal regulation. Both GO and KEGG enrichment analyses supported these findings, highlighting photosynthesis and metabolic flexibility in naturally infected plants versus hypersensitive response, RNA surveillance, and lignin biosynthesis in virus-inoculated plants. This work provides a comprehensive view of the saffron virome and offers a hypothesis-generating overview of transcriptional responses associated with natural versus experimental virus infections. These findings advance the understanding of the saffron virome and provide a valuable resource for breeding virus-resistant cultivars. Full article
(This article belongs to the Special Issue New Insights into Plant–Microbe Interaction)
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24 pages, 15371 KB  
Article
The Complete Genome of Rhizobium favelukesii LPU83T: Insights into Plastic pSym and Its Symbiotic Incompatibility with a Broad Range of Legume Hosts
by Abril Luchetti, Catalina D’Addona, Lucas G. Castellani, María Delfina Cabrera, Daniel Wibberg, Carolina Vacca, Linda Fenske, Jochen Blom, Anika Winkler, Tobias Busche, Christian Rückert-Reed, Jörn Kalinowski, Andreas Schlüter, Alfred Pühler, Karsten Niehaus, Antonio Lagares, María Florencia Del Papa, Mariano Pistorio and Gonzalo Torres Tejerizo
Agronomy 2026, 16(5), 523; https://doi.org/10.3390/agronomy16050523 - 27 Feb 2026
Viewed by 805
Abstract
Achieving completeness of multipartite bacterial genomes has been a difficult task, especially in rhizobia. In this study, we performed a deep bioinformatic analysis of the newly re-sequenced genome of Rhizobium favelukesii LPU83T. This strain was isolated from acid soils in Argentina [...] Read more.
Achieving completeness of multipartite bacterial genomes has been a difficult task, especially in rhizobia. In this study, we performed a deep bioinformatic analysis of the newly re-sequenced genome of Rhizobium favelukesii LPU83T. This strain was isolated from acid soils in Argentina and is capable of nodulating several leguminous plants, although it is unable to fix nitrogen efficiently in any of them. Oxford Nanopore sequencing allowed us to completely assemble the symbiotic plasmid of the strain, pRfaLPU83b, and we discovered that it harbors three intact prophages and a high density of insertion sequences (ISs). These characteristics show why it is often so difficult to complete the symbiotic plasmids of rhizobial strains and the importance of having long-read sequencing methods. Upon detailed analysis of this replicon, we identified a complete conjugation system with gene structure consistent with quorum sensing-associated systems that may have contributed to the genetic mosaic structure of the strain. Furthermore, we identified in the symbiotic plasmid of R. favelukesii LPU83T a large proportion of the symbiotic genes previously identified as essential for Biological Nitrogen Fixation (BNF) in symbiosis with alfalfa, with a high percentage of identity with respect to those of Sinorhizobium meliloti 2011. Among the determinants related to BNF, we found genes encoding the HrrP and SapA peptidases in the LPU83 genome, previously described and related to the degradation of nodule-specific cysteine-rich peptides. These peptides are essential for bacteroid differentiation and, therefore, efficient BNF. Our results show that despite having these genes, they are not directly responsible for the inefficient BNF phenotype of LPU83. Full article
(This article belongs to the Special Issue New Insights into Plant–Microbe Interaction)
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