Linking microbial community composition of three rootstock genotypes to apple replant disease susceptibility

Apple replant disease (ARD) is a worldwide issue of complex biotic origin. The exact aetiology has yet to be fully elucidated and environmentally friendly and economically feasible countermeasures are sparse. The breeding of tolerant apple rootstock genotypes shows some promise as reduced sensitivity on selected ARD-affected soils has been shown for some rootstock genotypes. By adding insights into the root-associated microbiome, we aimed to complement previously published results, examining the response in growth, gene expression and production of phenolic compounds in roots of seven Malus genotypes in ARD soil. We selected the two least susceptible rootstock genotypes of the previous study, EMR.2 and G.935, in addition to the susceptible rootstock genotype M.26. The objective of this study was to gain insights into the bacterial community composition of the rhizosphere and root endosphere of less susceptible rootstock genotypes in comparison to the susceptible one.

In an Illumina-based sequencing approach, the composition of rhizosphere as well as endophytic bacterial communities was investigated for apple plants in ARD soil and disinfected ARD soil. ARD impacted the rhizosphere stronger than the endosphere, where rootstock genotype influence was stronger. G.935 generally showed a more distinct and diverse microbiome than the other two rootstock genotypes. In bacterial communities, the relative abundance of Pseudomonadota decreased in ARD samples, while Actinomycetota increased. In the endosphere, this was mostly accounted for by Streptomyces. A qPCR approach confirmed the high abundance of Streptomyces. Interestingly, another qPCR approach did not indicate a high abundance of plant pathogenic Streptomyces in the same samples.

ARD strongly influenced the bacterial microbiome in the rhizosphere and, to a lesser extent, the root endophytic microbiome. The distinct and more diverse bacterial microbiome of G.935 might help against biotic stress, such as ARD. However, EMR.2 was previously found to be less susceptible to ARD, too, suggesting additional factors must play a role and additional research is necessary. Pathogenicity of Streptomyces could not be proven but repeatedly high abundance of root endophytic Streptomyces under ARD conditions indicate an important role.