Mapping soil nematode communities in Thai paddy fields using eDNA metabarcoding and morphological analysis

Soil nematodes are microscopic roundworms that play diverse roles in soil ecosystems, including as rice pathogens that cause significant economic losses worldwide. Despite their ecological and agricultural importance to Thailand’s rice production, the diversity and distribution of soil nematodes in Thai rice paddies remain poorly characterized. In this study, 30 soil samples from 17 provinces across Thailand were analyzed using both morphological identification and environmental DNA (eDNA) metabarcoding. Traditional nematode extraction identified 17 genera, comprising 5 plant-parasitic, 7 free-living, and 5 predatory nematodes. The 18S rRNA-based eDNA metabarcoding approach detected a broader diversity, identifying 15 plant-parasitic, 14 free-living, and 6 predatory genera. Both methods frequently detected Hirschmanniella and Meloidogyne among the most prevalent plant-parasitic genera, while others such as Rotylenchus , Pratylenchus , and Helicotylenchus , were presented at only a few sites, suggesting more restricted distributions. Notably, eDNA metabarcoding detected several genera containing known pest species that were not recovered by traditional methods, including Basiria, Mesocriconema, Paralongidorus, and Tylenchorhynchus . This study represents the first application of eDNA metabarcoding to characterize plant-parasitic nematodes in Thai rice paddies, highlighting their widespread presence and emphasizing the need for proactive, combined eDNA and traditional monitoring and management strategies.