The microbiome as the second genome: engineering the phytobiome for climate-resilient agriculture

The plant microbiome, often referred to as the ‘second genome,’ is a key yet underutilized determinant of plant health and ecosystem function. As climate change accelerates, harnessing this microbial resource is critical for food security and carbon mitigation. The phytobiome is not passive but an engineerable system that can enhance crop resilience under environmental stress. Climate stress disrupts plant–microbe interactions and destabilizes microbial networks, potentially triggering adverse soil carbon feedbacks. This review presents a framework for phytobiome engineering that integrates synthetic microbial consortia, plant-driven microbiome selection, and ecological design to improve stress tolerance and soil carbon sequestration. By incorporating multi-omics, artificial intelligence, and predictive modeling, we propose a data-driven approach to microbiome stewardship. However, field-scale implementation remains challenging due to ecological complexity and context dependency. Future research should prioritize long-term field validation and integrative modeling to support sustainable, climate-resilient agricultural systems worldwide.