Vermicompost-mediated shifts in soil microbiome and functional potential suppress root-knot nematode (Meloidogyne incognita) in tomato

Abstract

The root-knot nematode (Meloidogyne incognita) poses a major constraint to global crop productivity, underscoring the urgent need for sustainable and eco-friendly management strategies. This study assessed the efficacy of vermicompost in suppressing M. incognita using a combination of in vitro bioassays, greenhouse pot experiments, and polyhouse validation trials. In vitro assays showed that vermicompost extract significantly increased juvenile mortality by 63.6 % (p < 0.001), a performance comparable to the synthetic nematicide carbofuran (98.8 %). Under polyhouse conditions, the combined application of fluopyram and vermicompost (T3) yielded the lowest gall density (29 galls per plant), while vermicompost alone (37.2 galls) and fluopyram alone (45 galls) also showed significant reduction (p < 0.001). Microbial community profiling based on 16S rRNA sequencing revealed that vermicompost selectively enriched beneficial bacterial taxa. Complementary GC–MS analysis of the acetone extract identified 20 bioactive compounds, including Glycidyl palmitate (10.37 %), Hexatriacontane (5.47 %), and Dodecane, 4,6-dimethyl (4.99 %), all recognized for their antimicrobial and nematicidal properties. Functional prediction (PICRUSt2) indicated enrichment of pathways associated with secondary metabolite biosynthesis, signal transduction, and nutrient cycling, reflecting a functionally active and disease-suppressive microbiome. Our study highlights that vermicompost-mediated nematode suppression results from a synergistic interaction between its bioactive metabolites and enriched microbial communities. This positions vermicompost as a promising sustainable alternative for integrated nematode management in agricultural system.