Metabarcoding reveals preservation of non-target nematode communities to fipronil applied to control Pratylenchus spp. in ratoon sugarcane

Root-lesion nematodes (Pratylenchus spp.) significantly inhibit sugarcane growth and are prevalent in Okinawa, Japan. However, no synthetic nematicide is currently registered for ratoon sugarcanes under Japanese regulations. Furthermore, there is a potential risk that nematicide use could harm non-target free-living nematodes, which may contribute to soil health and fertility. To address these challenges, we investigated the nematicidal efficacy of the insecticide fipronil, which interferes with GABA receptors, against root-lesion nematodes, aiming to improve yield and quality in ratoon sugarcane. Simultaneously, we assessed its potential side-effects on the non-target free-living nematode community. We first determined an appropriate dose of fipronil to control root-lesion nematodes in ratoon canes in pot trials. We then conducted multi-year field experiments to assess a yield response to fipronil treatment and its side-effects on the soil nematode community using metabarcoding analysis with next-generation sequencing. Fipronil treatment significantly decreased root-lesion nematodes in ratoon cane roots (42–51 % to control) three months after application, resulting in significant increases in yield by 4–20 % and Brix value by 2–3 %. Impact of fipronil on the abundance of soil nematodes and their community structure was negligible, as revealed by metabarcoding analysis. Diversity indices, functional metrics, and maturity index showed no significant difference between treatments. Furthermore, principal component analysis and differential abundance testing (ANCOM-BC) showed no dominant and impacted nematode taxon due to fipronil treatment. Our findings suggest that fipronil (0.3 kg a.i./ha) is appropriate to control root-lesion nematodes in ratoon sugarcane, providing yield increase without evident side-effects on the overall non-target nematode community.