Rhizosphere and Root Microbiome Analysis of Nematode-Parasitized Plants

During sampling, healthy and nematode-parasitized plants were pulled carefully from soil and shaken to remove large soil particles, leaving soil that was strongly attached to the roots. Rhizosphere soil and roots were separately collected from the sampled materials as described by Edwards et al. and Kwak et al. [70 (link), 71 (link)]. To obtain the bacterial community profiles specifically associated with RKN parasitism, galls induced by Meloidogyne spp. were separated from the surface-sterilized parasitized roots with a sterile scalpel [22 (link)]. Briefly, surface-sterilized parasitized roots were separated into two fractions: one contained the galls, whereas the other contained the non-swollen part of the parasitized root system. Together, for each sampled healthy plant, the rhizosphere soil and root fractions were isolated. For each nematode-parasitized plant, its rhizosphere soil and the two root fractions were obtained. In total, 75 samples (30 from rhizosphere soil, 30 from roots, and 15 from gall samples) were collected from healthy and parasitized plants, in the five different plant species (Additional Table S1). Similarly, 135 samples (57 rhizosphere soil, 57 root, and 21 gall samples) were collected from 9 or 10 growth stages, respectively, from the healthy and nematode-parasitized tomato plants (Additional Table S3).