# Microbial biocontrol agents and the rhizosphere microbiome: integrating ecological function and climate resilience in sustainable agriculture

## TL;DR

This review explores how beneficial microbes in the soil can help crops withstand stress and reduce reliance on chemicals, promoting sustainable agriculture.

## Contribution

The paper introduces a microbiome-informed framework for designing microbial biocontrol agents to enhance crop resilience and sustainability.

## Key findings

- Microbial biocontrol agents can modulate rhizosphere communities and improve plant tolerance to abiotic stress.
- Precision-designed synthetic microbial communities and trait-based screening are proposed to optimize microbiome function.
- Key challenges include inoculant persistence and microbiome-level trade-offs affecting field effectiveness.

## Abstract

The growing challenges of food insecurity, soil degradation, and climate-induced stresses are exposing the limitations of chemically intensive crop protection systems. In this context, the rhizosphere microbiome, comprising complex microbial networks that regulate plant growth, nutrient acquisition, and immune responses, has emerged as a promising focus for more sustainable agricultural practices. Microbial biocontrol agents (BCAs) are increasingly recognized not only for their pathogen-suppressive properties but also for their potential to modulate rhizosphere microbial communities and contribute to plant tolerance to abiotic stressors. This review synthesizes recent advances in understanding the ecological and mechanistic interplay between BCAs and the rhizosphere microbiome, highlighting how microbial inoculants can influence community assembly, functional processes, and microbiome resilience under biotic and abiotic stress conditions. Drawing on molecular and ecological evidence, the synthesis integrates current knowledge of BCA-mediated regulation of plant defense signalling, nutrient cycling, and stress-associated responses. Key knowledge gaps related to inoculant persistence, ecological compatibility, and microbiome-level trade-offs that limit field-scale effectiveness are also identified. To address these challenges, a microbiome-informed conceptual framework is proposed, emphasizing precision-designed synthetic microbial communities (SynComs), trait-based screening, host–microbiome co-optimization, and integration of BCAs into resilient Integrated Pest Management (IPM) strategies. In summary, this review provides a systems-level perspective on how rhizosphere microbiome dynamics can be leveraged to support sustainable climate-smart crop production.