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

Rice is the most cultivated food crop in Cambodia, providing a staple part of the diet and representing an important economic activity. However, yields remain low compared to regional standards, partly due to pests and diseases, including the root-knot nematode Meloidogyne graminicola which is found in 90% of Cambodian rice fields. Current control methods rely on water management and synthetic nematicides, which are environmentally damaging. In the search for sustainable alternatives to harmful nematicidal molecules, microbial biocontrol agents offer a promising solution. Thirteen rice field soils from three Cambodian provinces were sampled to identify potential suppressive activities and the responsible microbial taxa. An in vitro test based on larval mobility was developed to screen for antagonistic activities by challenging M. graminicola larvae with a soil suspension. A gradient of antagonism was observed, ranging from 30% to 95% inhibition of mobility, which was removed when the soil suspension was filtered. The soil microbiota was then sequenced using a metabarcoding approach and a threshold indicator taxa analysis was performed to identify bacterial and fungal genera strongly associated with the gradient. Analysis revealed a total of 105 taxa that increased with antagonism, including known antagonist genera of Meloidogyne spp. larvae and eggs such as Saccharopolyspora, Kitasatospora or Lysinibacillus. The isolation of these microorganisms should open new avenues for the use of biocontrol organisms to control M. graminicola in rice fields.