Discovery of bacterial-derived bio-nematicides against root-knot nematodes through in vitro screening, GC–MS profiling, and molecular docking approaches

Root-knot nematodes are among the most economically destructive pathogens affecting tomato production worldwide. This study aimed to evaluate the nematicidal potential of bacteria cell-free culture filtrates against Meloidogyne spp. using integrated in vitro and in silico approaches. Seventeen bacterial isolates were obtained from soil and evaluated in vitro for their effects on egg hatching inhibition and J2 mortality of root-knot nematodes. The two most effective isolates were molecularly identified through 16S rRNA gene sequencing. Bioactive compounds present in their culture filtrates were characterized using GC–MS analysis. The nematicidal potential of the identified compounds was further assessed via molecular docking against nematode acetylcholinesterase (AChE). The in vitro results indicated that isolate BI-10 recorded the highest egg hatching inhibition (89.67%), while isolate BI-13 recorded the highest mortality rate (80.91%). Isolate BI-10 was identified as Stenotrophomonas beteli (accession No. PX508182), while BI-13 was identified as Enterobacter quasihormaechei (accession No PX508183). GC–MS analysis detected 79 bioactive compounds in the culture filtrates of both isolates, with relative abundances ranging from 0.52% to 6.42%. Molecular docking revealed that six compounds exhibited promising binding affinities to nematode AChE relative to oxamyl. The findings suggest that the secondary metabolites produced by BI-10 and BI-13 show potential as candidate bio-nematicidal agents. These findings highlight their promise as sustainable alternatives to chemical nematicides and support their future development as effective bionematicides for root-knot nematode management.