Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes

Abstract

Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, as effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics, and agricultural practices, more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes. Based on a network analysis of potential microbe-microbe associations, we further found that several fungal taxa potentially preying on nematodes [Dactylellina (Orbiliales), Rhizophydium (Rhizophydiales), Clonostachys (Hypocreales), Pochonia (Hypocreales), and Purpureocillium (Hypocreales)] co-occurred in the soybean rhizosphere at a small spatial scale. Overall, this study suggests how \"consortia\" of anti-nematode microbes can derive from indigenous (resident) microbiomes, thereby providing basic information for managing anti-nematode microbial communities in agroecosystems.