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Plants
Special Issues
Interactions Between Plants and Beneficial Microorganisms
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Interactions Between Plants and Beneficial Microorganisms

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Protection and Biotic Interactions".

Deadline for manuscript submissions: 30 April 2026 | Viewed by 2537

Special Issue Editor

Prof. Dr. Juan Francisco Jimenez-Bremont

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Guest Editor
Plant Molecular Biotechnology Laboratory, Molecular Biology Division, Instituto Potosino de Investigación Científica y Tecnológica, A. C., San Luis Potosi 78216, Mexico
Interests: plant molecular biology; CAM plant research; plant responses to abiotic stress
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are pleased to invite submissions for the Special Issue "Interactions Between Plants and Beneficial Microorganisms". Studying the interactions between beneficial microorganisms and plants has gained significant importance in biotechnology. These interactions play a crucial role in sustainable agriculture by enhancing plant nutrient uptake, disease resistance, and tolerance to abiotic stress conditions. This Special Issue will focus on recent advances to understand the positive impact of microorganisms on plants. We aim to bring together research exploring the interactions between plant-associated bacteria and fungi, the molecular mechanisms underlying these interactions, and their applications in promoting plant growth and enhancing responses to biotic and abiotic stresses.

Dr. Juan Francisco Jimenez-Bremont
Guest Editor

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. Plants 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 2700 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

  • plant–microbe interactions
  • beneficial microorganisms
  • abiotic and biotic stress tolerance
  • plant growth promotion
  • microbial applications in agriculture

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

Published Papers (3 papers)

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Research

15 pages, 2221 KB  
Article
Assessment of Bacterial Diversity and Rhizospheric Community Shifts in Maize (Zea mays L.) Grown in Soils with Contrasting Productivity Levels
by Sebastian Cano-Serrano, Hugo G. Castelán-Sánchez, Helen Oyaregui-Cabrera, Luis G. Hernández, Ma. Cristina Pérez-Pérez, Gustavo Santoyo and Ma. del Carmen Orozco-Mosqueda
Plants 2026, 15(1), 130; https://doi.org/10.3390/plants15010130 - 2 Jan 2026
Viewed by 626
Abstract
The resident microbiota in agricultural soils strongly influences crop health and productivity. In this study, we evaluated the prokaryotic diversity of two clay soils with similar physicochemical characteristics but contrasting levels of maize (Zea mays L.) and wheat (Triticum aestivum L.) [...] Read more.
The resident microbiota in agricultural soils strongly influences crop health and productivity. In this study, we evaluated the prokaryotic diversity of two clay soils with similar physicochemical characteristics but contrasting levels of maize (Zea mays L.) and wheat (Triticum aestivum L.) production using 16S rRNA gene sequencing. Yield records showed significant differences in grain production over five consecutive years. When comparing prokaryotic alpha diversity between the “non-productive” and “productive” soils, no major differences were found, and the abundance of ammonia-oxidizing archaea (AOA) and bacterial genera such as Arthrobacter, Neobacillus, and Microvirga remained consistent across soils. Analysis of the top 20 genera showing the greatest abundance shifts by compartment (bulk soil vs. rhizosphere) revealed that genera such as Priestia, Neobacillus, Sporosarcina, and Pontibacter decreased in the rhizosphere of the non-productive soil, while in the productive soil, these genera remained unchanged. In the non-productive soil, genera such as Flavisobacter decreased in abundance in the rhizosphere, whereas Arthrobacter increased. Principal coordinates analysis (PCoA) showed no clear clustering by compartment (bulk vs. rhizosphere), but two distinct clusters emerged when grouping by soil type (productive vs. non-productive). Interaction networks varied by soil type: non-productive soils showed positive Candidatus–Bacillus and negative Massilia links, while productive soils were dominated by Flavisolibacter and negative Pontibacter. Across soils, Rhizobium–Bradyrhizobium associations were positive, whereas Neobacillus and Priestia were negative. These findings highlight that a few potential beneficial microbiota and their interactions may be key drivers of soil productivity, representing targets for microbiome-based agricultural management. Full article
(This article belongs to the Special Issue Interactions Between Plants and Beneficial Microorganisms)
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19 pages, 2835 KB  
Article
Pseudomonas simiae WCS417 and Debaryomyces hansenii Induce Iron Deficiency Responses in Rice (Oryza sativa L.) Through Phytosiderophore Production and Gene Expression Modulation
by Jorge Núñez-Cano, Francisco J. Ruiz-Castilla, Francisco J. Romera, José Ramos and Carlos Lucena
Plants 2025, 14(24), 3769; https://doi.org/10.3390/plants14243769 - 10 Dec 2025
Cited by 1 | Viewed by 572
Abstract
Iron (Fe) is an essential micronutrient for crop productivity, but its low availability in alkaline and calcareous soils limits the growth of rice (Oryza sativa L.), which employs a combined strategy for its acquisition based on the release of phytosiderophores (PS) and [...] Read more.
Iron (Fe) is an essential micronutrient for crop productivity, but its low availability in alkaline and calcareous soils limits the growth of rice (Oryza sativa L.), which employs a combined strategy for its acquisition based on the release of phytosiderophores (PS) and the use of specific transporters. In this study, the effect of the rhizospheric bacterium Pseudomonas simiae WCS417 and the halotolerant yeast Debaryomyces hansenii CBS767 as inducers of responses to Fe deficiency in rice grown under hydroponic conditions was evaluated. Plants were inoculated in nutrient solutions with and without Fe, and PS production and the expression of genes associated with biosynthesis and transport were determined by qRT-PCR. The results showed that both microorganisms significantly increased PS production compared to controls, especially under Fe-deficient conditions, although P. simiae also exerted an effect under Fe sufficiency. Furthermore, induction of key genes (OsNAAT, OsIRO2, OsTOM1, OsYSL15, and OsIRT1), as well as genes related to the ethylene pathway (OsEIN2, OsACS2, and OsACO3), was observed, pointing to a regulatory role for this hormone in the response. In conclusion, P. simiae and D. hansenii act as inducers of Fe acquisition mechanisms in rice, offering a sustainable biotechnological approach to improve iron nutrition in limiting environments. Full article
(This article belongs to the Special Issue Interactions Between Plants and Beneficial Microorganisms)
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14 pages, 1207 KB  
Article
Inoculation with Trichoderma atroviride and T. virens Induces ROS Overaccumulation and Compromises Pathogen Resistance in Arabidopsis 35S::TaEPL1-3 Plants
by Ever Trinidad Astorga-Arzola, Enrique González-Pérez, Alicia Becerra Flora and Juan Francisco Jiménez-Bremont
Plants 2025, 14(17), 2794; https://doi.org/10.3390/plants14172794 - 6 Sep 2025
Cited by 1 | Viewed by 818
Abstract
Recent studies showed that constitutive expression of the cerato-platanin protein EPL1 from Trichoderma atroviride in the Arabidopsis thaliana 35S::TaEPL1-3 line promotes plant growth and pathogen resistance. Here, the effect of inoculating this line with T. atroviride and T. virens on growth and defense [...] Read more.
Recent studies showed that constitutive expression of the cerato-platanin protein EPL1 from Trichoderma atroviride in the Arabidopsis thaliana 35S::TaEPL1-3 line promotes plant growth and pathogen resistance. Here, the effect of inoculating this line with T. atroviride and T. virens on growth and defense responses was evaluated. Inoculated 35S::TaEPL1-3 plantlets exhibited increased fresh weight and more lateral roots compared to uninoculated controls. Infection assays on 28-day-old 35S::TaEPL1-3 and Col-0 (WT) leaves (pre-inoculated at 15 days with T. atroviride, T. virens, or both) revealed that dual Trichoderma inoculation compromised the transgenic line’s resistance to Pseudomonas syringae and Botrytis cinerea compared to WT. It was previously reported that the 35S::TaEPL1-3 line accumulates elevated levels of reactive oxygen species (ROS). Therefore, ROS levels were examined to determine whether they were further influenced by inoculation with Trichoderma species. Dual inoculation triggered higher H2O2 accumulation in 35S::TaEPL1-3 compared to WT. In addition, high ROS levels were observed when the 35S::TaEPL1-3 line was co-inoculated with both Trichoderma species and subsequently challenged with both pathogens. These findings showed that elevated ROS levels may compromise priming activation in the 35S::TaEPL1-3 line (constitutively expressing the Epl1 elicitor) during co-inoculation with T. atroviride (Epl1-secreting) and T. virens (Sm1-secreting), where synergistic elicitor accumulation could potentially lead to defense signal dysregulation and consequent loss of resistance in transgenic plants. Full article
(This article belongs to the Special Issue Interactions Between Plants and Beneficial Microorganisms)
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