Comparative analysis of the rhizosphere and endophytic microbiomes across apple rootstock genotypes in replant orchard soils

Apple replant disease (ARD), caused by a complex of soil-borne pathogens, negatively impacts tree health and productivity in new orchard plantings at sites previously planted to apple. Use of new disease tolerant apple rootstock genotypes may diminish growth limiting effects of ARD, however the influence of rootstock genotype on modulating the rhizosphere and endophytic microbiome to enable ARD tolerance is not fully understood. Composition of the rhizosphere and root endophytic microbiomes was characterized across a diversity of apple rootstock genotypes. A series of tolerant (G.210, G.41, G.890, and G.935) and susceptible (M.26 and M.9) rootstock cultivars were consecutively planted into orchard replant soil containing a known pathogen complex. Amplicon sequencing was used to determine simultaneously the presence of a broad taxonomic range of organisms and their relative abundance. Microbial communities exhibited significant differences in composition between the rhizosphere and endophytic environments in terms of species diversity, content, and abundance. Significant differences in composition of the endophytic and rhizosphere microbiomes were observed between rootstock genotypes. Among rootstock endophytic fungal communities, rootstock G.890 samples consistently harbored the highest percentage of arbuscular mycorrhizal fungal species (>5% of total). Ilyonectria spp., which may function as a pathogen of apple, were detected at high relative abundance in the endosphere of all genotypes, with the highest relative abundance in M.26. These results provide further insight into rhizosphere and endophytic microbial communities of apple rootstocks, which could be exploited or manipulated to improve tree fruit agricultural management practices with respect to plant nutrition and disease control.

苹果再植病害（ARD），由一组土壤传播的病原体引起，对曾在苹果种植地再植的新果园的树木健康和生产力产生负面影响。使用新型耐病苹果砧木基因型可能减少ARD的生长限制效应，然而，砧木基因型对调节根际和内生微生物群以实现ARD耐受性的影响尚不完全明了。在不同苹果砧木基因型的根际和根内生微生物群的组成进行了表征。一系列耐病砧木品种（G.210、G.41、G.890和G.935）和易感砧木品种（M.26和M.9）依次种植于含有已知病原体复合体的果园再植土壤中。通过扩增子测序同时确定了一广泛分类范围的生物体及其相对丰度。微生物群落在其物种多样性、内容和丰度方面，在根际和内生环境中表现出显著的组成差异。在砧木基因型之间观察到内生和根际微生物群的组成存在显著差异。在砧木内生真菌群落中，砧木G.890样本持续携带最高比例的丛枝菌根真菌物种（占总数的5%以上）。可能作为苹果病原体的Ilyonectria属物种在所有基因型的内生组织中检测到高相对丰度，其中M.26的相对丰度最高。这些结果进一步揭示了苹果砧木的根际和内生微生物群落，这些群落可以被利用或操纵，以改善树木水果农业管理实践，特别是在植物营养和病害控制方面。