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Microorganisms
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Chemical Communication in Plant–Microbe Beneficial Interactions Between Plants and Rhizosphere...
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Chemical Communication in Plant–Microbe Beneficial Interactions Between Plants and Rhizosphere Microorganisms

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

Deadline for manuscript submissions: closed (30 November 2025) | Viewed by 9337

Special Issue Editors

Prof. Dr. Haichao Feng

E-Mail Website
Guest Editor
College of Agriculture, Henan University, Zhengzhou, China
Interests: plant growth-promoting rhizobacteria
Prof. Dr. Yunpeng Liu

E-Mail Website
Guest Editor
Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
Interests: plant–microbe interactions

Special Issue Information

Dear Colleagues,

Rhizosphere microbiomes are crucial for plant health, such as growth promotion, disease resistance, etc. Harnessing the power of beneficial microbes in the rhizosphere to improve plant performance is a vital goal of sustainable agriculture. However, the precise management of rhizosphere microbes for crop growth and health remains challenging because we lack a comprehensive understanding of the plant–rhizobacteria relationship.

In this Special Issue, we will present the latest findings on the interaction between microbes and roots, the root colonization of chemotaxis, attachment, root exudates, rhizomicrobiome, bacterial chemotaxis, biofilms, etc. High-quality original research, reviews, mini-reviews, and perspectives related to this multi-disciplinary area are welcome.

Prof. Dr. Haichao Feng
Prof. Dr. Yunpeng Liu
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 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. 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 growth-promoting rhizobacteria (PGPR)
  • root exudates
  • colonization
  • chemotaxis
  • attachment
  • biofilm
  • rhizomicrobiome
  • plant health
  • recruitment
  • biocontrol

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Published Papers (5 papers)

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Research

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20 pages, 2272 KB  
Article
The Synergistic Effects of Jasmonic Acid and Arbuscular Mycorrhizal Fungi in Enhancing the Herbicide Resistance of an Invasive Weed Sphagneticola trilobata
by Hu’anhe Xiong, Misbah Naz, Rui Chen, Mengting Yan, Zongzhi Gong, Zhixiang Shu, Ruike Zhang, Guangqian Ren, Shanshan Qi, Zhicong Dai and Daolin Du
Microorganisms 2025, 13(12), 2817; https://doi.org/10.3390/microorganisms13122817 - 10 Dec 2025
Abstract
The invasive plant Sphagneticola trilobata (Asteraceae), known for its rapid growth and strong adaptability, has spread widely across tropical and subtropical regions worldwide, posing a serious threat to local plant diversity. Traditional weed control approaches have limited effectiveness, and the overuse of chemical [...] Read more.
The invasive plant Sphagneticola trilobata (Asteraceae), known for its rapid growth and strong adaptability, has spread widely across tropical and subtropical regions worldwide, posing a serious threat to local plant diversity. Traditional weed control approaches have limited effectiveness, and the overuse of chemical herbicides such as glyphosate not only leads to resistance but also harms the environment. This study elucidated the important roles of jasmonic acid (JA) and arbuscular mycorrhizal fungi (AMF) in jointly promoting the herbicide resistance of S. trilobata. Firstly, the herbicide tolerance of S. trilobata was tested. Then, a field experiment was conducted to test the relation between AMF colonization and herbicide resistance in S. trilobata by high-throughput sequencing, and the metabolomics analysis was conducted to test the secondary metabolite difference by AMF colonization. Lastly, a greenhouse experiment was conducted to assess the synergistic effects of JA and AMF on S. trilobata’s herbicide resistance. Results showed that invasive S. trilobata has stronger glyphosate tolerance than its native congener. The field experiment showed that glyphosate treatment significantly increased the AMF colonization in S. trilobata and altered the composition of the rhizosphere AMF community. Metabolomics analysis revealed that AMF colonization upregulates the expression of stress-related metabolites, especially JA content. The greenhouse experiment further validated that both AMF colonization and JA application could enhance the stem and root length and plant biomass. Under glyphosate application, AMF and JA enhanced plant growth and relative chlorophyll content, while reducing relative flavonol and anthocyanin contents. Furthermore, the interaction of AMF and JA treatments led to a significant synergistic effect in plant growth and resistance to glyphosate. Our findings emphasize the necessity to simultaneously consider eliminating the promoting effects of JA and AMF on the herbicide resistance when implementing chemical control management strategies for the control of S. trilobata. This study provides new theoretical bases and sustainable control strategies for invasive plant management, as well as important references for research on plant-microbe interactions and stress resistance mechanisms. Full article
(This article belongs to the Special Issue Chemical Communication in Plant–Microbe Beneficial Interactions Between Plants and Rhizosphere Microorganisms)
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27 pages, 4292 KB  
Article
Alleviating Overgrazing Stress and Promoting Grassland Plant Regeneration via Root Exudate-Mediated Recruitment of Beneficial Bacteria
by Ting Yuan, Jiatao Zhang, Shaohong Zhang, Shuang Liang, Changhong Zhu, Weibo Ren and Jialu Liang
Microorganisms 2025, 13(6), 1225; https://doi.org/10.3390/microorganisms13061225 - 27 May 2025
Viewed by 927
Abstract
Overgrazing (OG) is an important driver of grassland ecosystem degradation and productivity decline. Plants may effectively cope with OG stress by regulating their synergistic interactions with plant growth-promoting rhizobacteria (PGPR) through root exudates. However, the synergistic regulatory mechanisms remain unclear. Under OG stress, [...] Read more.
Overgrazing (OG) is an important driver of grassland ecosystem degradation and productivity decline. Plants may effectively cope with OG stress by regulating their synergistic interactions with plant growth-promoting rhizobacteria (PGPR) through root exudates. However, the synergistic regulatory mechanisms remain unclear. Under OG stress, Leymus chinensis recruited the specific PGPR strain Paraburkholderia graminis (B24) by regulating specific root exudate compounds, including amino acids, alkaloids, and organic acids, which enhance B24 chemotaxis and biofilm formation. The B24 inoculation systematically regulated the transcription of key plant growth and development genes, including those involved in nutrient transport and cell wall expansion, which enhanced nutrient uptake and promoted the overall growth of L. chinensis. Furthermore, B24 regulated the homeostasis of endogenous L. chinensis through the synergistic effects of hormones and the trade-off between growth and defense. Integrated transcriptomic and metabolomic analyses revealed that B24 regulation enhanced carbon and nitrogen metabolism, and energy supply after mowing, forming a holistic adaptive mechanism that enabled L. chinensis to effectively recover from mowing-induced stress, thereby improving its adaptability and regenerative capacity. This study provides a scientific basis and support for elucidating the response mechanisms of how grassland plants cope with OG stress, optimizing grassland management, and rapidly restoring and enhancing grassland productivity. Full article
(This article belongs to the Special Issue Chemical Communication in Plant–Microbe Beneficial Interactions Between Plants and Rhizosphere Microorganisms)
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21 pages, 3107 KB  
Article
Four Decades of Bacillus Biofertilizers: Advances and Future Prospects in Agriculture
by Xinmai Wu, Yan Liu, Baolei Jia, Lili Tao, Han Li, Jingbang Wang, Ziqi Yuan, Xiaobao Sun and Yanlai Yao
Microorganisms 2025, 13(1), 187; https://doi.org/10.3390/microorganisms13010187 - 17 Jan 2025
Cited by 10 | Viewed by 5998
Abstract
Over the past four decades, Bacillus biofertilizers, which are microbial formulations based on Bacillus species, have significantly contributed to sustainable agriculture by enhancing crop growth, improving soil health, and reducing the dependency on chemical fertilizers. Bacillus species, particularly known for their ability to [...] Read more.
Over the past four decades, Bacillus biofertilizers, which are microbial formulations based on Bacillus species, have significantly contributed to sustainable agriculture by enhancing crop growth, improving soil health, and reducing the dependency on chemical fertilizers. Bacillus species, particularly known for their ability to promote plant growth, fix nitrogen, solubilize phosphorus, and produce growth-promoting substances such as phytohormones and antibiotics, have emerged as key players in the development of eco-friendly agricultural solutions. This research utilizes bibliometric analysis based on 3,242 documents sourced from the Web of Science database to map the development, key contributions, and innovation within the field from 1985 to 2023. This study identifies exponential growth in research output, particularly from 2003 onwards, indicating a robust interest and expanding research base predominantly in China, India, and the United States. We segmented the research timeline into three distinct phases, each marked by varying growth rates and research foci. This paper presents novel insights into the geographical and institutional distributions of research, highlighting the predominant role of developing countries in advancing Bacillus-based technologies. Key research hotspots have evolved from basic applications to complex interactions involving synthetic microbial communities and advanced multi-omics techniques. Our findings demonstrate a trend towards more strategic and technologically integrated approaches to developing Bacillus biofertilizers, reflecting broader shifts towards more sustainable agricultural systems. This study not only charts historical progress, but also proposes future research trajectories aimed at enhancing the application and effectiveness of microbial fertilizers across diverse ecosystems. Full article
(This article belongs to the Special Issue Chemical Communication in Plant–Microbe Beneficial Interactions Between Plants and Rhizosphere Microorganisms)
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Review

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19 pages, 1608 KB  
Review
Agrobacterium fabrum (tumefaciens) Chemosensory System: A Typical Model of One Histidine Kinase for Two Coupling Proteins and Multiple Response Regulators
by Jinjing Liu, Mengya Feng, Nan Xu, Hao Wang and Minliang Guo
Microorganisms 2025, 13(11), 2556; https://doi.org/10.3390/microorganisms13112556 - 9 Nov 2025
Viewed by 419
Abstract
Bacteria utilize chemotaxis to sense the surrounding chemical signals to seek a more favorable survival environment. The chemotaxis process includes signal sensing, signal transduction, and signal response (i.e., regulating flagellar rotation to control motility). Agrobacterium fabrum, as a soil-born facultative phytopathogen, can [...] Read more.
Bacteria utilize chemotaxis to sense the surrounding chemical signals to seek a more favorable survival environment. The chemotaxis process includes signal sensing, signal transduction, and signal response (i.e., regulating flagellar rotation to control motility). Agrobacterium fabrum, as a soil-born facultative phytopathogen, can survive in diverse environments from bulk soil, the rhizosphere, to the plant-associated niches, and needs to cope with diverse challenges from various survival environments. It must recognize a variety of environmental signals and thus has evolved a chemosensory signaling system more complicated than the prototypical chemotaxis system. The chemosensory system of A. fabrum possesses one histidine kinase, but more chemoreceptors, coupling proteins (2 CheWs), and response regulators (2 CheYs and 1 CheB) than the well-studied prototypical system in the model bacterium Escherichia coli, which has only one CheW, one CheY, and fewer chemoreceptors. More response regulators imply that the chemosensory system may involve other physiological functions beyond chemotaxis. In this review, we outline the recent advances in the prototypical chemosensory signaling system and discuss the functions of protein components in A. fabrum’s chemosensory system by comparing those proteins with the homologous proteins observed in the paradigm and other closely related species. Meanwhile, we place particular emphasis on reviewing the data about the chemosensory system of A. fabrum, propose a “one-system two-pathways” model depicting that A. fabrum possibly utilizes one histidine kinase to assemble two chemosensory signaling pathways, and envision future directions for studying this system. The insights provided will aid in understanding the diversity of chemosensory signaling pathways in other organisms and the molecular mechanism mediating the signal crosstalk among chemosensory signaling pathways. Full article
(This article belongs to the Special Issue Chemical Communication in Plant–Microbe Beneficial Interactions Between Plants and Rhizosphere Microorganisms)
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13 pages, 743 KB  
Review
Harnessing the Rhizosphere Microbiome for Selenium Biofortification in Plants: Mechanisms, Applications and Future Perspectives
by Ruixin Fu, Mengyuan Zhu, Yanrong Zhang, Junmin Li and Haichao Feng
Microorganisms 2025, 13(6), 1234; https://doi.org/10.3390/microorganisms13061234 - 28 May 2025
Viewed by 1441
Abstract
The rhizosphere microbiome plays a critical role in promoting crop health and productivity. Selenium (Se), a beneficial trace element for plants, not only enhances resistance to both abiotic and biotic stresses but also modulates soil microbial communities. Se biofortification of crops grown in [...] Read more.
The rhizosphere microbiome plays a critical role in promoting crop health and productivity. Selenium (Se), a beneficial trace element for plants, not only enhances resistance to both abiotic and biotic stresses but also modulates soil microbial communities. Se biofortification of crops grown in seleniferous soils using selenobacteria represents an eco-friendly and sustainable biotechnological approach. Crops primarily absorb selenium from the soil in its oxidized forms, selenate and selenite, and subsequently convert it into organic Se compounds. However, the role of Se-oxidizing bacteria in soil Se transformation, bioavailability, and plant uptake remains poorly understood. In this review, systematic collection and analysis of research on selenobacteria, including both Se-oxidizing and Se-reducing bacteria, are therefore essential to elucidate their functions in enhancing crop growth and health. These insights can (i) deepen our mechanistic understanding of microbially mediated Se cycling and stress resilience and (ii) offer a novel framework for nanomicrobiome engineering aimed at promoting sustainable food production. Full article
(This article belongs to the Special Issue Chemical Communication in Plant–Microbe Beneficial Interactions Between Plants and Rhizosphere Microorganisms)
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