Cambodian rice field soils infested by Meloidogyne spp. unveil a potential source of natural pest biocontrol agents

Rice is a key staple crop and economic resource in Cambodia. Yet national yields are below regional averages due to the prevalence of persistent biotic stressors, including the rice root-knot nematode Meloidogyne graminicola. This pathogen is highly prevalent in Cambodian rice cropping systems, where current control measures primarily rely on water management and chemical nematicide treatment approaches that are often environmentally detrimental and unsustainable. Microbial biocontrol agents could offer a promising alternative for long-term nematode suppression. This study focused on soils from 13 rice fields in three Cambodian provinces to assess their suppressiveness against M. graminicola. An in vitro bioassay assessing second-stage juvenile (J2) mobility responses to soil suspensions revealed 30–95 % antagonistic activity. Nematofaunal communities were characterized alongside microbial community profiled using 16S and 18S metabarcoding. Threshold Indicator Taxa ANalysis (TITAN) was conducted to identify taxa associated with suppressive activity. Suppressive soils were found to be enriched with 105 bacterial and fungal taxa overall, along with several site-specific indicator taxa associated with localized antagonistic activity. These included known nematode antagonist taxa such as Saccharopolyspora, Kitasatospora, Lysinibacillus and Mortierella, as well as potential keystone taxa like Ohtaekwangia. Several previously unreported taxa were also associated with nematode inhibition. These findings revealed diverse microbial candidates with potential biocontrol activity against M. graminicola, thereby offering a stepping stone for the development of sustainable microbe-based rice nematode management strategies.