Enhancing soil citrulline degrading function to mitigate soil-borne Fusarium wilt

Continuous cropping often exacerbates soil-borne diseases, particularly Fusarium wilt, yet the intricate rhizosphere relationships among phyto-derived metabolites, pathogens, and particular microbial functions remain poorly understood. Here, we observe that citrulline accumulation during continuous cropping is positively correlated with Fusarium wilt severity by enhancing fusaric acid production in Fusarium oxysporum. Metagenomic analyses reveal that citrulline turnover-related functions, represented by functional modules including M00978, are significantly enriched in healthy rhizosphere soils but are notably reduced in Fusarium-conducive soils. The functional genes, arcB and argH, are identified in Pseudomonas putida YDTA3, with arcB being essential for citrulline-degradation via knockout experiments. The inoculation of an arcB-expressing indigenous Escherichia consortium (EO-arcB) in three independent continuous cropping systems of cucurbit crops demonstrates that enhancing and maintaining the soil citrulline-degrading function mitigates soil-borne Fusarium wilt. In summary, this study advances our understanding of rhizosphere interactions underlying Fusarium wilt disease occurrence and offers a promising biocontrol strategy. In this study, the authors show that citrulline accumulation exacerbates Fusarium wilt and that enhancing the soil’s citrulline-degrading function, particularly via the arcB gene, significantly reduces disease in continuous cucurbitaceous cropping systems.