It is not known how loss of rare soil microbes affects plant defence against aphids. Kurm et al. inoculated soil with a serial dilution of a microbial community and a presumed plant beneficial bacterium (Pseudomonas fluorescens). Subsequently, they measured plant biomass (Arabidopsis thaliana), defence-gene expression, and aphid numbers (Myzus persicae).
Microbial species loss affects plant biomass and Pseudomonas survival, but not plant gene expression or aphid numbers. Both aphids and Pseudomonas reduce plant biomass and defence gene expression. Kurm et al. conclude that rare microbes do not affect plant defence against aphids, but can reduce the establishment of introduced bacterial strains.
Kurm, V., van der Putten, W. H., Pineda, A., & Hol, W. H. G. (2018). Soil microbial species loss affects plant biomass and survival of an introduced bacterial strain, but not inducible plant defences. Annals of Botany, 121(2), 311–319. https://doi.org/10.1093/aob/mcx162