Root‐Microbiome Signaling Under Co‐Contaminant Stress: Rhizosphere Reassembly, Microbial Detoxification, and Plant Resilience Through Multiomics

Agricultural soils contain mixture of metals, pesticides, antibiotics, pharmaceuticals, and plastics. Their combined effects are shaped by contaminant chemistry, root activity, and microbial interactions at the rhizosphere interface. This review develops a mechanistic framework linking co-contaminant exposure with root sensing, exudate reprogramming, microbiome reassembly, multitrophic interactions, microbial detoxification, and plant stress adaptation. We distinguish taxonomic shifts from functional resilience and microbial resistance from plant protection. Particular attention is given to cross-kingdom interactions and microbial processes that control contaminant sequestration, transformation, nutrient availability, and host signaling. Multi-omics approaches are evaluated alongside stable-isotope probing, synthetic communities, metabolite supplementation, and genetic validation to identify candidate mechanisms for targeted causal validation. We then discuss microbiome engineering strategies for moving beyond descriptive community profiling toward predictive and function-oriented rhizosphere engineering. These strategies can be guided by contaminant fate and plant performance. By integrating contaminant chemistry, root-microbiome signaling, microbial functional responses, and plant adaptation, this review provides a mechanistic framework for understanding and engineering rhizosphere resilience under co-contaminant stress.