Rhizosphere Microbiome Association with Agronomic Productivity

Dear Colleagues,

The rhizosphere microbiome, encompassing plant-growth-promoting rhizobacteria (PGPR) and other beneficial microorganisms, serves as a critical determinant of plant growth, health, and resilience to environmental stresses. This dynamic microbial ecosystem is intricately shaped by bidirectional interactions with host plant composition and functional profiles, being influenced by root exudation patterns, plant genotype, and soil properties. Understanding the ecological principles governing rhizosphere microbiome assembly and their functional capacities represents a transformative pathway toward sustainable agriculture, offering viable alternatives to synthetic fertilizers and pesticides while enhancing ecosystem services.

This Special Issue aims to advance our mechanistic understanding of rhizosphere microbiome–plant interactions, with particular emphasis on PGPR-mediated processes and their translation into agronomic applications. We welcome cutting-edge research that explores the following topics:

• Fundamental Mechanisms:
• Microbial community assembly dynamics and ecological succession patterns;
• Plant–microbe molecular interactions, including signal transduction pathways and quorum sensing;
• Root exudate-mediated microbial recruitment and chemotaxis;
• Rhizosphere nutrient microenvironment modification and its cascading effects on microbial life history strategies.
• Advanced Methodological Approaches:
• Integrated multi-omics strategies (metagenomics, metatranscriptomics, metaproteomics, and metametabolomics) for comprehensive microbiome characterization;
• Design and validation of synthetic microbial communities (SynComs) using bottom-up and top-down approaches;
• High-throughput screening platforms for functional trait identification;
• Computational modeling and machine learning applications in microbiome prediction.

Translational Applications:

• Development of PGPR-based microbial consortia with enhanced colonization efficiency, functional stability, and predictable behaviors;
• Field-scale microbiome manipulation strategies and performance evaluation under diverse environmental conditions;
• Genotype-specific microbiome engineering using targeted plant breeding and agronomic interventions;
• Biofertilizer and biostimulant formulations for improved nutrient acquisition, stress mitigation, and biocontrol.

Recent breakthroughs have delineated environment-dominated and plant-genetic-dominated microbiome components, enabling precision manipulation using integrated approaches that combine agronomic practices with plant breeding strategies. We particularly encourage submissions addressing the functional redundancy and resilience of microbial communities, the role of rare taxa in ecosystem functions, and the development of predictive frameworks for microbiome-mediated crop improvement.

We invite original research articles, comprehensive reviews, methodological innovations, and perspective pieces that bridge fundamental microbiome science with practical agricultural applications, ultimately contributing to enhanced crop productivity, resource-use efficiency, and climate resilience in sustainable farming systems.

Dr. Yunpeng Gai
Guest Editor

Manuscript Submission Information

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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. Agronomy 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 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.

• rhizosphere microbiome
• plant–microbe interactions
• microbial community assembly
• root exudates
• agronomic productivity
• sustainable agriculture
• microbiome engineering
• crop yield
• stress tolerance
• beneficial microorganisms