Root Microbiome Shifts in Nematode-Infected Plants

To assess the effects of Meloidogyne spp. on root-associated microbiota, rhizosphere soil and root samples of healthy and parasitized plants were collected in Shunchang County of Fujian province, China (26° 38′–27° 121′ N, 117° 29′–118° 14′ E) in June 2016 (Additional Table S1). Samples of three vegetables, tomato (Solanum lycopersicum), lettuce (Lactuca sativa L. var. ramosa Hort.), and celery (Apium graveolens L.), were collected from a vegetable farm, monitored for RKN parasitism for at least 5 years before sample collection [67 ]. The field prevalence of RKN for the three crops were approximately 30–50%. Two perennial plants, Snakegourd fruit (Trichosanthes kirilowii Maxim.) and citrus (Citrus reticulata Blanco), attacked by RKN for at least 2 years (severe parasitism, with > 75% roots with galls, and swollen by > 75%), were separately collected from orchards with RKN. The collected lettuce and celery roots showed a low RKN parasitism symptom (less than one third roots with galls), and tomato root with a moderate RKN parasitism symptom (more than half of roots with galls) (Additional Table S1). At least three replicated healthy or nematode-parasitized plants were sampled for each plant species. The collected plants were used to separate rhizosphere soil and root samples for the 16S rRNA gene-based high-throughput sequencing and bacterial community analysis (Additional Table S1).