Dynamics of bacterial root endophytes of <em>Malus domestica</em> plants grown in field soils affected by apple replant disease.

Apple replant disease (ARD) is a worldwide problem for tree nurseries and orchards leading to reduced plant growth and fruit quality. The etiology of this complex phenomenon is poorly understood, but shifts of the bulk soil and rhizosphere microbiome seem to play an important role. Since roots are colonized by microbes from the rhizosphere, studies of the endophytic microbiome in relation to ARD are meaningful. In this study, culture-independent and culture-dependent approaches were used in order to unravel the endophytic root microbiome of apple plants 3, 7, and 12 months after planting in ARD-affected soil and ARD-unaffected control soil at two different field sites. Next to a high diversity of Pseudomonas in roots from all soils, molecular barcoding approaches revealed an increase in relative abundance of endophytic Actinobacteria over time in plants grown in ARD and control plots. Furthermore, several amplicon sequence variants (ASVs) linked to Streptomyces, which had been shown in a previous greenhouse ARD biotest to be negatively correlated to shoot length and fresh mass, were also detected in roots from both field sites. Especially in roots of apple plants from control soil, these Streptomyces ASVs increased in their relative abundance over time. The isolation of 150 bacterial strains in the culture-dependent approach revealed a high diversity of members of the genus Pseudomonas, confirming the data of the molecular barcoding approach. However, only partial overlaps were found between the two approaches, underlining the importance of combining these methods in order to better understand this complex disease and develop possible countermeasures. Overall, this study suggests a key role of Streptomyces in the etiology of ARD in the field

Molecular barcoding reveals the genus <em>Streptomyces</em> as associated root endophytes of apple (<em>Malus domestica</em>) plants grown in soils affected by apple replant disease.

Apple replant disease (ARD) occurs when apple is repeatedly planted at the same site, leading to growth reductions and losses in fruit yield and quality. Up to now the etiology is poorly understood, but soil (micro)biota are known to be involved. Since endophytes often colonize plants via the rhizosphere this study aimed at comparing the bacterial endophytic root microbiome in plants growing in ARD affected and unaffected soils from three different sites based on greenhouse biotests using a molecular barcoding approach. The initial endophytic microbiome of the starting material (in vitro propagated plants of the apple rootstock M26) did not significantly affect the overall richness and diversity of the endophytic community in plants after 8 weeks of growth in the respective soils, but some genera of the initial microbiome managed to establish in apple roots. Proteobacteria were the dominant phylum in all samples. No differences in diversity or number of amplicon sequence variants (ASVs) between plants grown in ARD soil and unaffected soil was observed. However, several ASVs of high abundance uniquely found in plants grown in ARD affected soils were Streptomyces. In soil from all three sites these Streptomyces were negatively correlated to plant growth parameters. Future inoculation experiments using selected Streptomyces isolates have to prove if bacteria from this genus are opportunists or part of the ARD complex. For the first time, the bacterial endophytic community of apple roots grown in ARD affected soils was characterized which will help to understand the etiology of ARD and develop countermeasures