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Inoculation Strategies to Infect Plant Roots with Soil-Borne Microorganisms

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Plant microbiome engineering: from inoculation to genome editing.

Jyoti Yadav¹, Pushpa Gehlot¹, Priya Soni¹

¹Microbial Research Laboratory, Department of Botany, Mohanlal Sukhadia University, Udaipur, India.

Frontiers in Microbiology

|May 8, 2026

Summary

Precision microbiome engineering using synthetic biology and genome editing offers a path to enhance crop productivity and climate resilience. This approach integrates plant and microbial genetics for sustainable agriculture, moving beyond traditional methods.

Keywords:

CRISPR holobiont plant microbiome sustainable agriculture synthetic biology

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Area of Science:

Plant-microbe interactions
Synthetic biology
Agricultural biotechnology

Background:

Plant microbiomes are crucial for crop productivity and stress resilience.
Conventional methods like microbial inoculation have inconsistent field performance.
Existing reviews rarely integrate genome editing, microbiome stability, and climate-resilient agriculture.

Purpose of the Study:

To integrate genome editing, microbial ecology, and systems-level microbiome design for engineerable holobionts.
To frame plant-microbiome interactions within a unified conceptual framework for climate-smart agriculture.
To critically assess limitations and identify research priorities for large-scale deployment.

Main Methods:

Utilizing synthetic biology tools like CRISPR/Cas genome editing and RNA interference.
Designing synthetic microbial communities (SynComs) for targeted modification of plant traits and microbial pathways.
Applying AI-assisted decision frameworks, machine learning, and ecological modeling to analyze multi-omics data.

Main Results:

Advances in molecular biotechnology enable precision engineering of plant-microbe interactions.
Targeted modification of plant traits and microbial functions can improve nutrient cycling and stress tolerance.
Integration of genome editing and SynCom design allows for community-level functional complementarity.

Conclusions:

Bridging genome-enabled microbiome manipulation with ecological design principles offers a framework for climate-smart agriculture.
Addressing limitations in ecological stability, trait trade-offs, biosafety, and regulations is crucial for deployment.
Transitioning towards predictive, sustainable, and socially responsible agricultural biotechnology is a key research priority.