Integrative Multi-Omics Framework Reveals Microbial and Chemical Biomarkers for Diagnosing Copper Contamination in False Yellowhead–Colonized Soils.

Long-term use of Bordeaux mixture in French vineyards has led to elevated copper levels in soils, many of which are now colonized by false yellowhead after vineyard abandonment. This species provides a relevant model to study plant–soil interactions under copper stress. This study investigated how soil copper contamination affects plant growth in microcosms, focusing on rhizosphere microbial communities and plant metabolomic responses. A multi-omics approach combining metabarcoding and untargeted metabolomics was used to identify biomarkers of copper contamination. Copper levels were quantified in soils, roots, and leaves. The results highlighted altered plant morphology, particularly reduced root growth and copper sequestration in roots. Microbial analyses showed an enrichment of Actinobacteria and Thermoleophilia in highly contaminated soils, while Deltaproteobacteria dominated uncontaminated soils. Metabolomic profiling highlighted flavonoids, quinic acid derivatives, and sesquiterpenes as key chemical markers of copper stress. By integrating microbial and chemical indicators, this study proposes a new framework for diagnosing copper contamination in soil, demonstrating the added value of multi-omic approaches to point out metal-specific stress signatures in soil-plant ecosystems. This study provides new, field-applicable biomarkers for environmental monitoring and open perspectives for assessing biosolution effects on copper-induced abiotic stress in agriculture practices.