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Plant–Microbe Interactions: 2nd Edition
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Plant–Microbe Interactions: 2nd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 30 July 2025 | Viewed by 2548

Special Issue Editor

Dr. Jian Jin

E-Mail Website
Guest Editor
Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
Interests: soil science; soil-plant interactions; plant-microbe interactions; crop development
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plants are offen affected by beneficial and pathogenic microorganisms. Microbiota are associated with crop growth and development due to their functions in mobilizing non-labile nutrients, mitigating abiotic and biotic stresses, and preventing pathogen infection. For example, Rhizobium can carry out nutrient transfer, fight pathogenic microorganisms, provide mineral nutrients to plants, and directly stimulate plant growth through phytohormones. The rhizosphere is the plant–soil interface colonized by bacterial and fungal communities that may exert growth-promoting and adaptive benefits to plants.

This Special Issue provides a platform for molecular mechanistic research on plant–microbe interactions and plant development. We warmly welcome your submissions of original papers and reviews based on results from molecular points of view.

This Special Issue is supervised by Dr. Jian Jin and assisted by our Topical Advisory Panel Member Dr. Xingguo Li (College of Horticulture & Landscape Architecture, Northeast Agricultural University, Harbin 150030, China).

Dr. Jian Jin
Guest Editor

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • plant
  • crop
  • rhizosphere microbiome
  • microbial colonization
  • quorum sensing
  • endophytic microbes

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Published Papers (4 papers)

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Research

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18 pages, 8355 KiB  
Article
Transcriptome Analysis Reveals Mechanisms of Stripe Rust Response in Wheat Cultivar Anmai1350
by Feng Gao, Jingyi Zhu, Xin Xue, Hongqi Chen, Xiaojin Nong, Chunling Yang, Weimin Shen and Pengfei Gan
Int. J. Mol. Sci. 2025, 26(12), 5538; https://doi.org/10.3390/ijms26125538 - 10 Jun 2025
Viewed by 412
Abstract
Wheat (Triticum aestivum L.) is the world’s most indispensable staple crop and a vital source of food for human diet. Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), constitutes a severe threat to wheat production and in [...] Read more.
Wheat (Triticum aestivum L.) is the world’s most indispensable staple crop and a vital source of food for human diet. Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), constitutes a severe threat to wheat production and in severe cases, the crop fails completely. Anmai1350 (AM1350) is moderately resistant to leaf rust and powdery mildew, and highly susceptible to sheath blight and fusarium head blight. We found that the length and area of mycelium in AM1350 cells varied at different time points of Pst infection. To investigate the molecular mechanism of AM1350 resistance to Pst, we performed transcriptome sequencing (RNA-seq). In this study, we analyzed the transcriptomic changes of the seedling leaves of AM1350 at different stages of Pst infection at 0 h post-infection (hpi), 6 hpi, 24 hpi, 48 hpi, 72 hpi, and 120 hpi through RNA-seq. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) was used to validate RNA-seq data. It was determined that there were differences in the differentially expressed genes (DEGs) of AM1350, and the upregulation and downregulation of the DEGs changed with the time of infection. At different time points, there were varying degrees of enrichment in the response pathways of AM1350, such as the ”MAPK signaling pathway–plant”, the “plant–pathogen interaction” pathway and other pathways. After Pst infected AM1350, the reactive oxygen species (ROS) content gradually increases. The ROS is toxic to Pst, promotes the synthesis of phytoalexins, and inhibits the spread of Pst. As a result, AM1350 shows resistance to Pst race CYR34. The main objective of this study is to provide a better understanding for resistance mechanisms of wheat in response to Pst infections and to avoid production loss. Full article
(This article belongs to the Special Issue Plant–Microbe Interactions: 2nd Edition)
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17 pages, 10422 KiB  
Article
Different Endophytes Colonized in Various Lotus Root Varieties and Their Associated Mealy and Crunchy Properties
by Yufei Wei, Xinyan Zhou, Meiping Gao, Yangxiu Ou, Yifeng Hu, Wen Jiang, Huiping Jiang and Shangdong Yang
Int. J. Mol. Sci. 2025, 26(10), 4529; https://doi.org/10.3390/ijms26104529 - 9 May 2025
Viewed by 308
Abstract
Lotus root texture significantly influences consumer preferences and market value, yet the role of endophytes in determining the distinct mealy (ML) and crunchy (CL) textural properties remains unclear. This study aimed to clarify the relationship between endophyte composition and metabolic characteristics underlying the [...] Read more.
Lotus root texture significantly influences consumer preferences and market value, yet the role of endophytes in determining the distinct mealy (ML) and crunchy (CL) textural properties remains unclear. This study aimed to clarify the relationship between endophyte composition and metabolic characteristics underlying the texture differences between ML and CL lotus root varieties. Two lotus root varieties (ML and CL) were analyzed for endophytic microbial communities using high-throughput sequencing methods. Metabolite profiling of cellulose, starch, pectin, soluble sugars, and proteins was conducted using standard biochemical assays. The findings revealed higher cellulose, starch, and pectin content in mealy lotus root (ML) varieties than those in crunchy lotus root (CL) varieties. Additionally, the functions of cellulose-degrading and protein-producing microorganisms, such as Firmicutes, Bacteroides, Exiguobacterium, Bradyrhizobium, and Basidiomycota, were primarily enriched in the ML varieties. In contrast, the CL varieties had specific dominant endophytic bacterial genera, such as Myxococcota, Geobacter, Paludibacteraceae, Rhodocyclaceae, Comamonadaceae, Micromonosporaceae, Sideroxydans, Bacillus, Lactococcus, Oxalobacteraceae, and Treponema. These results indicate that different endophytes are associated with the development of mealy and crunchy properties. Understanding these microbial–metabolic relationships offers practical implications for selective breeding and agricultural management aimed at texture improvement. Future research should elucidate the specific metabolic pathways regulated by these endophytes to facilitate targeted agricultural interventions. Full article
(This article belongs to the Special Issue Plant–Microbe Interactions: 2nd Edition)
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24 pages, 3462 KiB  
Article
Integrated Transcriptome and Metabolome Analysis Elucidates the Defense Mechanisms of Pumpkin Against Gummy Stem Blight
by Qian Zhao, Liyan Zhang, Weibo Han, Ziyu Wang and Jianzhong Wu
Int. J. Mol. Sci. 2025, 26(6), 2586; https://doi.org/10.3390/ijms26062586 - 13 Mar 2025
Viewed by 577
Abstract
Gummy stem blight (GSB) is a pervasive disease that causes considerable economic losses in cucurbit crops and poses a significant threat to pumpkin production. However, the molecular interaction mechanisms between pumpkin and the pathogen remain largely unexplored. In our previous research, we isolated [...] Read more.
Gummy stem blight (GSB) is a pervasive disease that causes considerable economic losses in cucurbit crops and poses a significant threat to pumpkin production. However, the molecular interaction mechanisms between pumpkin and the pathogen remain largely unexplored. In our previous research, we isolated and identified Stagonosporopsis cucurbitacearum (Sc) as the primary causative agent of pumpkin stem blight in Northeast China. Through whole-genome analysis, we identified several pathogenic genes associated with Sc infection in pumpkins. In this study, we performed a comprehensive comparative transcriptomic and metabolomic analysis of unvaccinated and Sc-inoculated pumpkins. We observed distinct differences in gene expression profiles, with these genes being significantly enriched in pathways related to plant–pathogen interactions, phytohormone signal transduction, and metabolic processes, including phenylpropanoid biosynthesis. Joint analysis revealed that the phenylpropanoid biosynthesis pathway was activated in Sc-infected pumpkins. Notably, two metabolites involved in the phenylpropanoid and flavonoid biosynthesis pathways, p-coumaric acid and quercetin, exhibited significant upregulation, suggesting their potential roles in conferring resistance to GSB. These findings enhance our understanding of the molecular mechanisms underlying the defense response against GSB infection in pumpkins and may provide valuable insights for developing strategies to control GSB disease. Full article
(This article belongs to the Special Issue Plant–Microbe Interactions: 2nd Edition)
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Review

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19 pages, 1007 KiB  
Review
Quorum Signaling Molecules: Interactions Between Plants and Associated Pathogens
by Xi Zheng, Junjie Liu and Xin Wang
Int. J. Mol. Sci. 2025, 26(11), 5235; https://doi.org/10.3390/ijms26115235 - 29 May 2025
Viewed by 514
Abstract
The morphogenesis and defense evolution of plants are intricately linked to soil microbial community dynamics, where beneficial and pathogenic bacteria regulate ecosystem stability through chemical signaling. A microbial communication mechanism known as quorum sensing (QS), which affects population density, virulence, and biofilm formation, [...] Read more.
The morphogenesis and defense evolution of plants are intricately linked to soil microbial community dynamics, where beneficial and pathogenic bacteria regulate ecosystem stability through chemical signaling. A microbial communication mechanism known as quorum sensing (QS), which affects population density, virulence, and biofilm formation, substantially impacts plant development and immune responses. However, plants have developed strategies to detect and manipulate QS signals, enabling bidirectional interactions that influence both plant physiology and the balance of the microbiome. In this review, QS signals from bacteria, fungi, and nematodes are systematically examined, emphasizing their recognition by plant receptors, downstream signaling pathways, and the activation of defense responses. Most significantly, attention is given to the role of fungal and nematode QS molecules in modulating plant microbe interactions. By elucidating these communication networks, we highlight their potential applications in sustainable agriculture, offering novel insights into crop health management and ecosystem resilience. Full article
(This article belongs to the Special Issue Plant–Microbe Interactions: 2nd Edition)
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