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Microorganisms
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Feature Papers in Plant–Microbe Interactions in North America
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Feature Papers in Plant–Microbe Interactions in North America

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 1887

Special Issue Editor

Dr. Nazrul Islam

E-Mail Website
Guest Editor
Agriculture and Agri-Food Canada (AAFC), Morden Research and Development Centre, 101 Route 100, Morden, MB R6M 1Y5, Canada
Interests: soil and crop microbiomes; sustainable agriculture; metagenomics; microbial inoculants; biofertilizers; biopesticides; nutrient cycling; disease suppression; plant growth promotion; climate change resilience; biodiversity; environmental impact; food security; farming practices
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue, entitled "Feature Papers in Plant–Microbe Interactions in North America", invites the submission of pioneering research that deepens our understanding of plant–microbe relationships and their potential to revolutionize sustainable agriculture. This Special Issue aims to focus on advanced insights from metagenomics, proteomics, metabolomics, and bioinformatics, which collectively reveal how microbial communities can improve plant resilience to environmental challenges. Given the urgency of adapting agriculture to climate change, these studies are critical for developing crop systems resilient to biotic and abiotic stresses.

With a focus on microbial roles in enhancing soil health, crop productivity, and disease resistance, this Special Issue encourages the submission of research that defines key hypotheses, identifies new interactions, and proposes actionable strategies. Studies should illustrate how plant-associated microbes can contribute to food security, especially in diverse agroecological contexts, by optimizing nutrient uptake, reducing reliance on chemical inputs, and suppressing pathogens naturally. In addition, the integration of these findings into economically viable farming systems will address agricultural sustainability, benefiting both producers and ecosystems.

Through high-quality transformative research, this Special Issue aims to provide essential data for agricultural policymakers to craft informed, evidence-based strategies that promote resilient, low-impact food production systems. Contributions that bridge the gap between plant–microbe science and real-world applications in sustainable food production, with a commitment to advancing the future of resilient agriculture and economic viability, will be highly valued.

Dr. Nazrul Islam
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 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. Microorganisms 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 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 interaction
  • plant-associated microbes
  • biotic and abiotic stresses
  • agricultural sustainability

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Published Papers (3 papers)

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Research

20 pages, 1944 KiB  
Article
Comparison and Analysis of the Genomes of Three Strains of Botrytis cinerea Isolated from Pomegranate
by Alberto Patricio-Hernández, Miguel Angel Anducho-Reyes, Alejandro Téllez-Jurado, Rocío Ramírez-Vargas, Andrés Quezada-Salinas and Yuridia Mercado-Flores
Microorganisms 2025, 13(7), 1605; https://doi.org/10.3390/microorganisms13071605 - 8 Jul 2025
Abstract
Gray mold disease, caused by the fungus Botrytis cinerea, affects a wide variety of plants. In this study, we conducted several in vitro tests and genomic analyses on three strains of this fungus (BcPgIs-1, BcPgIs-3, MIC) previously isolated from diseased pomegranate fruits, [...] Read more.
Gray mold disease, caused by the fungus Botrytis cinerea, affects a wide variety of plants. In this study, we conducted several in vitro tests and genomic analyses on three strains of this fungus (BcPgIs-1, BcPgIs-3, MIC) previously isolated from diseased pomegranate fruits, collected at two geographic locations in Mexico. Our goal was to identify possible differences among these strains. The development of the three strains in distinct culture media, the production of extracellular enzymes, and their effect on the progression of infection in pomegranate fruits were evaluated. The genomes were sequenced using the Illumina platform and analyzed with various bioinformatics tools. All strains possess genetic determinants for virulence and cell wall polymer degradation, but MIC exhibited the highest pectinolytic activity in vitro. This strain also produced sclerotia in a shorter time (7 days) in PDA medium. BcPgls-3 demonstrated the highest conidia production across all the culture media used. Both BcPgls-3 and MIC damaged all the pomegranate fruits 8 days after inoculation, while the BcPgls-1 required up to 9 days. Sequencing of the three strains yielded high-quality sequences, resulting in a total of 17 scaffolds and genomes that exceed 41 million bp, with a GC content of approximately 42%. Phylogenomic analysis indicated that the MIC strain is situated in a group separate from BcPgIs-1 and BcPgIs-3. BcPgIs-3 possesses more coding sequences, but MIC has more genes for CAZymes and peptidases. The three strains share 10,174 genes, while BcPgIs-3 and MIC share 851. These findings highlight the differences among the strains studied, which may reflect their adaptive capacities to their environment. Results contribute to our understanding of the biology of gray mold in pomegranates and could assist in developing more effective control strategies. Full article
(This article belongs to the Special Issue Feature Papers in Plant–Microbe Interactions in North America)
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14 pages, 3921 KiB  
Article
First Report of Phytophthora mengei Causing Root Rot and Canker in Avocado (Persea americana) in Michoacán, Mexico
by Alejandra Mondragón-Flores, Alejandro Soto-Plancarte, Gerardo Rodríguez-Alvarado, Patricia Manosalva, Salvador Ochoa-Ascencio, Benjamin Hoyt, Nuria Gómez-Dorantes and Sylvia Patricia Fernández-Pavía
Microorganisms 2025, 13(7), 1471; https://doi.org/10.3390/microorganisms13071471 - 24 Jun 2025
Viewed by 512
Abstract
Mexico is the world’s leading producer of avocado (Persea americana); however, its productivity is threatened by various diseases, especially root rot caused by Phytophthora. While P. cinnamomi is the most commonly reported species worldwide, this study identified P. [...] Read more.
Mexico is the world’s leading producer of avocado (Persea americana); however, its productivity is threatened by various diseases, especially root rot caused by Phytophthora. While P. cinnamomi is the most commonly reported species worldwide, this study identified P. mengei for the first time as a causal agent of root rot and trunk canker in avocado orchards in the state of Michoacán, México. The morphological and molecular characterization of four isolates (three from canker and one from root rot) confirmed their identity: semi-papillate sporangia and plerotic oospores with paragynous antheridia, with sequence identities of 99.87% (ITS) and 100% (COI) with type sequences of P. mengei. Pathogenicity tests demonstrated the ability to infect roots, stems, and fruits, although with a low reisolation percentage in roots (10%), suggesting an opportunistic pathogen behavior. Sensitivity tests to potassium phosphite (EC50 of 3.67 μg/mL−1 a.i.) and metalaxyl-M (0.737 μg/mL−1 a.i.) revealed possible limitations for chemical control. These findings position P. mengei as an emerging pathogen with important implications for integrated crop management. To the best of our knowledge, this is the first report of P. mengei causing root rot and trunk canker in avocado in Michoacán, Mexico. Full article
(This article belongs to the Special Issue Feature Papers in Plant–Microbe Interactions in North America)
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17 pages, 2322 KiB  
Article
Cultivable and Non-Cultivable Approach to Bacteria from Undisturbed Soil with Plant Growth-Promoting Capacity
by Lorena Jacqueline Gómez-Godínez, Pedro Cisneros-Saguilán, Dulce Darina Toscano-Santiago, Yair Eduardo Santiago-López, Saúl Neftalí Fonseca-Pérez, Magali Ruiz-Rivas, José Luis Aguirre-Noyola and Gabriel García
Microorganisms 2025, 13(4), 909; https://doi.org/10.3390/microorganisms13040909 - 16 Apr 2025
Cited by 1 | Viewed by 893
Abstract
Undisturbed soils are essential ecosystems with high microbial diversity. Microorganisms present in the soil can regulate biogeochemical cycles, making available and transforming different minerals in the soil, such as nitrogen, phosphorus and sulfur. In this study, the microbiota of undisturbed soils was characterized [...] Read more.
Undisturbed soils are essential ecosystems with high microbial diversity. Microorganisms present in the soil can regulate biogeochemical cycles, making available and transforming different minerals in the soil, such as nitrogen, phosphorus and sulfur. In this study, the microbiota of undisturbed soils was characterized using an integrated approach of 16S rRNA ribosomal gene amplicon analysis and classical microbiology techniques. Phylum-level analyses revealed a high abundance of Proteobacteria, Acidobacteria, Verrucomicrobia and Actinobacteria, key groups in nutrient recycling, organic matter decomposition and plant-microorganism interaction. In the genus analysis, Nitrospira spp., Candidatus Koribacter spp., Burkholderia spp., Bacillus spp., Flavobacterium spp. and Pedomicrobium spp. were identified, with important functions in nitrification, plant growth promotion, organic matter degradation, and recovery of degraded soils. On the other hand, by using selective and differential media, it was possible to demonstrate the presence of microorganisms such as Enterobacter spp. and Hafnia spp., with the ability to solubilize phosphorus and potassium and produce siderophores, which are likely contributing to the biogeochemical cycles and plant growth within the soil studied. Full article
(This article belongs to the Special Issue Feature Papers in Plant–Microbe Interactions in North America)
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