Impact of apple replant disease on different apple rootstock genotypes and the composition of their bacterial root endophyte communities

Apple replant disease (ARD) is a global issue known for decades. It occurs on replanting apple onto a site that has previously been cultivated with apple and leads to reduced growth and yield. Although the cause is known to be of biotic origin, the exact aetiology has not been elucidated to date. A major reason for this is the heterogeneity of ARD at different sites, leading to inconsistent findings pertaining to pathogens and other factors throughout. Research to improve our understanding of this disease and to develop alternative countermeasures is direly needed. The microbiome and plant response was assessed across multiple different ARD-soils employing greenhouse and climate chamber experiments. Additionally, the performance of proposed ARD-tolerant rootstocks as mitigation strategy was examined. Furthermore, previous research has indicated a possible role of root endophytic Streptomyces due to their high abundance in ARD-affected roots as well as negative correlation to plant growth. Therefore, in this thesis special emphasis was put onto the bacterial endophyte community within ARDaffected roots. 16S rRNA amplicon sequencing was utilised to discover diversity and community composition. Supporting qPCRs were also performed. The strong heterogeneity of ARD characteristics between different sites was confirmed. Growth depression on different ARD soils correlated with increased expression of the biphenyl synthase 3 gene (BIS3) and phytoalexin production. Potentially tolerant rootstocks and wildtype accessions did not display consistently improved growth across different ARD soils compared to the ARD-susceptible rootstock M.26. A significant influence of the apple genotype on the root endophytic bacteria composition and diversity was revealed. Here, Geneva rootstock G.935 featured a distinct microbiome compared to East Malling rootstocks M.26 and EMR.2. However, neither diversity, nor composition of bacterial root endophytes was, at large, clearly connected to ARD severity. Streptomyces were detected in high abundance via amplicon sequencing and qPCR, though the abundance did not correlate with plant growth across many tested soils, indicating that they probably accumulate due to opportunistic reasons. In support of this, qPCR detection resulted in no significant amounts of Streptomyces carrying the plant pathogenicity indicator gene thaxtomin synthase (txtAB). Massilia was identified as another important genus, the relative abundance of which correlated positively with plant growth. Concluding, the impact of ARD heterogeneity on experimental design and development of countermeasures was discussed. Furthermore, future microbiome research should focus on microbial functionality over composition and potential techniques to address this are explored.