Microbial dysbiosis and functional decline drive root-knot nematode outbreaks in continuous cropping systems

Abstract

The long-term practice of continuous cropping has been demonstrated to have a deleterious effect on the incidence of root-knot nematode disease. However, the extent to which the relationship among continuous cropping, root-knot nematode disease, and soil microbial community are understood remains limited. The present study systematically comparted physicochemical properties and microbial communities of disease-conducive soil from long-term continuous cropping systems and healthy soil. The results revealed that continuous cropping led to significant decreases in soil organic carbon, available nitrogen, and available potassium content, while simultaneously inducing changes in microbial α- and β-diversity. The analysis of microbial community composition revealed that disease-conducive soil exhibited a significant decrease in the abundance of potentially beneficial Actinobacteriota, Streptomyces and Bacillus, along with an abnormal enrichment of Acidobacteriota. Functional prediction based on FAPROTAX, Tax4Fun2 and BugBase analysis revealed impaired nitrogen fixation, nitrate denitrification, and nitrite denitrification and compromised methanol oxidation and methylotrophy in disease-conducive soil, disease-conducive soil also exhibits weaker capabilities in lipid metabolism, amino acid metabolism and secondary metabolite production compared to healthy soil, disease-conducive soil was enriched with aerobic Gram-negative bacteria, contrasting with healthy soil dominated by facultative anaerobic Gram-positive bacteria with higher contains mobile elements. The correlation analysis confirmed significant interactions among key microbial taxa, root-knot nematode biocontrol efficacy, and soil physicochemical properties. These findings demonstrate that long-term continuous cropping promotes root-knot nematode disease by disrupting soil nutrients, suppressing beneficial microbes, and impairing key metabolic functions, providing crucial insights for soil health management and biological disease control strategies.