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Background <p>The rhizosphere microbiome underpins plant nutrition, health, and stress resilience, making it central to sustainable agriculture. Although soil physicochemical properties and environmental variability shape microbial communities, converging evidence shows that specific microbial taxa repeatedly associate with particular plant genotypes. This host-dependent stability implies that plant genomes impose selective filters on microbial assembly through root exudation, immunity, and developmental traits.</p> Scope <p>This review outlines a mechanistic framework that partitions rhizosphere microbiome assembly into two components: (i) an environment-driven microbiome shaped predominantly by edaphic conditions, climate, and management practices, and (ii) a host genetics-driven microbiome structured by plant molecular and physiological determinants. We aim to disentangle the assembly rules governing each component and assess their potential for targeted manipulation in crop improvement.</p> Key insights <p>The environment-driven component arises from microbial responses to nutrient availability, pH, moisture (including drought and salinity-driven osmotic/ionic stress), and agronomic inputs, and is dominated by ecological filtering and resource competition. The host-genetics-driven component arises from genotype-specific traits, including root architecture, exudate chemistry, and immune signaling pathways, that modulate colonization and persistence. This distinction highlights complementary leverage points: agronomic strategies to steer environment-driven processes and genetic dissection of loci controlling microbial recruitment. Major challenges include strong context dependency across soil–genotype combinations, limited power to link plant alleles to microbiome functions, and the lack of predictive models integrating host genetics, environment, and microbial dynamics.</p> Conclusion <p>A dual-strategy environmental optimization, combined with breeding to enhance the recruitment of beneficial microbes, offers a tractable route to microbiome-informed crop improvement and more resilient production systems.</p> Graphical Abstract <p></p>

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Decoding rhizosphere microbiome assembly: a dual framework of environment-driven and host genetics-driven components for sustainable agriculture

  • 期刊论文

  • 发表日期：

    2026年4月30日

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  • Muhammad Ikram,
  • Burhan Khalid,
  • Kamran Haider,
  • Maria Batool,
  • Maaz Ullah,
  • Muhammad Akif,
  • Tao Deng,
  • Jie Kuai,
  • Zhenghua Xu,
  • Jie Zhao,
  • Jing Wang,
  • Bo Wang,
  • Guangsheng Zhou

摘要

Background

The rhizosphere microbiome underpins plant nutrition, health, and stress resilience, making it central to sustainable agriculture. Although soil physicochemical properties and environmental variability shape microbial communities, converging evidence shows that specific microbial taxa repeatedly associate with particular plant genotypes. This host-dependent stability implies that plant genomes impose selective filters on microbial assembly through root exudation, immunity, and developmental traits.

Scope

This review outlines a mechanistic framework that partitions rhizosphere microbiome assembly into two components: (i) an environment-driven microbiome shaped predominantly by edaphic conditions, climate, and management practices, and (ii) a host genetics-driven microbiome structured by plant molecular and physiological determinants. We aim to disentangle the assembly rules governing each component and assess their potential for targeted manipulation in crop improvement.

Key insights

The environment-driven component arises from microbial responses to nutrient availability, pH, moisture (including drought and salinity-driven osmotic/ionic stress), and agronomic inputs, and is dominated by ecological filtering and resource competition. The host-genetics-driven component arises from genotype-specific traits, including root architecture, exudate chemistry, and immune signaling pathways, that modulate colonization and persistence. This distinction highlights complementary leverage points: agronomic strategies to steer environment-driven processes and genetic dissection of loci controlling microbial recruitment. Major challenges include strong context dependency across soil–genotype combinations, limited power to link plant alleles to microbiome functions, and the lack of predictive models integrating host genetics, environment, and microbial dynamics.

Conclusion

A dual-strategy environmental optimization, combined with breeding to enhance the recruitment of beneficial microbes, offers a tractable route to microbiome-informed crop improvement and more resilient production systems.

Graphical Abstract