Response of Tomato Rhizosphere Bacteria to Root-Knot Nematodes, Fenamiphos and Sampling Time Shows Differential Effects on Low Level Taxa

A factorial taxonomic metabarcoding study was carried out to determine the effect of root-knot nematodes (Meloidogyne incognita, RKN) and the nematocide fenamiphos on the rhizosphere microbiome of tomato. Plants inoculated (or not) with RKN second-stage juveniles (J2), and treated (or not) with the nematocide, were tested in a 6 months greenhouse assay using a RKN-free soil proceeding from an organic crop. Rhizosphere soil was sampled at J2 inoculation, 3 months later (before the second nematocidal treatment), and again after 3 months. At each sampling, the RNAs were extracted and the 16S rRNA V4 regions sequenced with a Next Generation Sequencing (NGS) protocol. Changes in bacteria metagenomic profiles showed an effect of the treatments applied, with different representations of taxa in samples receiving nematodes and fenamiphos, at the two sampling times. In general, a tendence was observed toward an increase number of OTUs at 6 months, in all treatments. β-Proteobacteria were the most abundant class, for all treatments and times. When compared to soil before transplanting, the presence of tomato roots increased frequency of Actinobacteria and Thermoleophilia, reducing abundance of Solibacteres. At lowest taxonomic levels the samples clustered in groups congruent with the treatments applied, with OTUs differentially represented in relation to RKN and/or fenamiphos applications. Bacillus, Corynebacterium, Streptococcus, and Staphylococcus were more represented at 6 months in samples inoculated with RKN. The nematodes with the nematocide application increased the emergence of rare OTUs or reduced/enhanced the abundance of other taxa, from different lineages.