The microbiome in plant-soil systems has a significant influence in promoting plant growth. Despite this, the extent of selectivity that the plant exerts on the microbiome in the continuum between the soil and internal plant tissues is not well understood. This study analysed the root microbiome of a legume, Melilotus officinalis (L.) Pall., sweet clover, and focused on dynamic shifts in the microbial community structure through the niches of bulk soil, rhizosphere, periderm, phloem and xylem, and further examined the effects of soil factors, root exudate metabolism, and root cell wall development on microbiome assemblages in different root compartments. Young and mature plants were sampled at 24 field sites and the microbial communities in different niches from bulk soil and rhizosphere through to root compartments were analysed by 16S rRNA gene sequencing. The microbiome composition changed from periderm to phloem to a greater extent than across other boundaries. Variation in microbiome composition was associated with geographic distance and soil properties for the bulk soil, rhizosphere and periderm niches. Root exudation influenced the rhizosphere microbiome assemblages in young and mature plants. The endophyte communities that occupied the phloem and xylem were most conserved and were independent of growing environments and root exudation. Symbiotic rhizobia able to nodulate M. officinalis were prominent colonisers of the periderm (∼15%) and xylem (∼6.2%), but were only a minor component in other soil-related niches (0.1%–2.5%). In xylem tissues, endophyte diversity was correlated with the total cell wall and lignin content across the sampled sites (r = 0.29–0.62). Our results demonstrate that selection of microbiome constituents occurs at different boundaries through bulk soil, rhizosphere, periderm, phloem and xylem, and is especially strong across the periderm boundary. The conserved endophyte community in the innermost tissues (phloem and xylem) was identified, and will be potentially advantageous to the development of specific beneficial microbial inoculants.

植物-土壤系统中的微生物组对促进植物生长具有重要影响。尽管如此，植物在土壤和植物内部组织之间的连续统一体中对微生物组的选择性程度尚不清楚。本研究分析了豆科植物Melilotus officinalis的根部微生物组(L.) Pall., sweet clover, 并通过大块土壤、根际、周皮、韧皮部和木质部的生态位关注微生物群落结构的动态变化，并进一步研究了土壤因素、根系分泌物代谢和根系的影响不同根室微生物组组合的细胞壁发育。对 24 个田间地点的幼苗和成熟植物进行采样，并通过 16S rRNA 基因测序分析从大块土壤和根际到根部的不同生态位中的微生物群落。与其他边界相比，微生物组组成从周皮到韧皮部的变化更大。微生物组组成的变化与大块土壤、根际和周皮生态位的地理距离和土壤特性有关。根系分泌物影响年轻和成熟植物的根际微生物群落组合。占据韧皮部和木质部的内生菌群落最为保守，不受生长环境和根系分泌物的影响。能够结瘤的共生根瘤菌M. officinalis是周皮 (~15%) 和木质部 (~6.2%) 的显着定殖者，但在其他与土壤相关的生态位 (0.1%–2.5%) 中仅占一小部分。在木质部组织中，内生菌多样性与采样点的总细胞壁和木质素含量相关（r = 0.29-0.62）。我们的研究结果表明，微生物组成分的选择发生在通过大块土壤、根际、周皮、韧皮部和木质部的不同边界，并且在周皮边界上尤其强烈。确定了最内层组织（韧皮部和木质部）中保守的内生菌群落，这对开发特定的有益微生物接种剂具有潜在的优势。