Microorganisms play an important role in plant growth, health and ecological function. It is necessary to explore the microbial community because of the significant ecological and economic value of apples (Malus x domestica). However, the related bacterial communities in different ecological habitats are not clear in the unique scion/rootstock combinations of apples. In this study, the Illumina Miseq platform was used to analyze the bacterial communities in different niches (bulk soil, rhizosphere soil and roots) of two scion/rootstock combinations [Fuji/Malus xiaojinensis Cheng et Jiang (Mx) and Fuji/Malus baccata (L.) Borkh. (Mb)]. The relationship between the microbial community, soil properties, and plant characters was explored. The results showed that the diversity of the bacterial community decreased from bulk soil to rhizosphere soil and then to roots. In addition, at the phylum level, Proteobacteria, Actinobacteria and Acitinobacteria were dominant and had notable divergence in different ecological niches. Distinct niches had remarkable effects on the diversity and composition of the bacterial community according to PCoA. The rootstock genotype had an effect on the bacterial composition but no effect on the diversity. pH, soil organic matter (SOM), alkaline hydrolyzable nitrogen (AN) were the main factor affecting the structure of bacterial community in rhizosphere soil, as shown by Pearson analysis. Bacteria taxa in the roots were affected by starch, fructose, sucrose and sorbitol. This study showed the microbial community structure in different ecological niches of different scion/rootstock combinations and provided some evidence for understanding the microbial-plant interaction of apple rootstocks.

微生物在植物生长、健康和生态功能中起着重要作用。由于苹果 ( Malus x domestica )具有重要的生态和经济价值，因此有必要探索微生物群落。然而，在苹果独特的接穗/砧木组合中，不同生态生境中的相关细菌群落并不明确。在本研究中，使用 Illumina Miseq 平台分析了两种接穗/砧木组合 [Fuji/ Malus xiaojinensis Cheng et Jiang (Mx) 和 Fuji/ Malus baccata] 不同生态位（土体土壤、根际土壤和根系）中的细菌群落(L.) 博克。(MB)]。探索了微生物群落、土壤特性和植物性状之间的关系。结果表明，细菌群落的多样性从土体土壤到根际土壤再到根系依次递减。此外，在门水平上，变形菌门、放线菌门和不动杆菌门占主导地位，在不同的生态位有显着差异。根据 PCoA，不同的生态位对细菌群落的多样性和组成具有显着影响。砧木基因型对细菌组成有影响，但对多样性没有影响。皮尔逊分析表明，pH、土壤有机质（SOM）、碱性可水解氮（AN）是影响根际土壤细菌群落结构的主要因素。根中的细菌类群受淀粉、果糖、蔗糖和山梨糖醇的影响。该研究揭示了不同接穗/砧木组合的不同生态位的微生物群落结构，为了解苹果砧木的微生物-植物相互作用提供了一些证据。