Advancements in molecular technology have reduced the constraints that the grain of observation, or the spatial resolution and volume of the sampling unit, has on the characterization of plant-associated microbiomes. With discrete ecological sampling and massive parallel sequencing, we can more precisely portray microbiome community assembly and microbial recruitment to host tissue over space and time. Here, we differentiate rarefied community richness and relative abundance in bacterial microbiomes of Salvia lyrata dependent on three spatial depths, which are discrete physical distances from the soil surface within the rhizosphere microhabitat as a proxy for the root system zones. To assess the impact of sampling grain on rarefied community richness and relative abundance, we evaluated the variation of these metrics between samples pooled prior to DNA extraction and samples pooled after sequencing. A distance-based redundancy analysis with the quantitative Jaccard distance revealed that rhizosphere microbiomes vary in richness between rhizosphere soil depths. At all orders of diversity, rarefied microbial richness was consistently lowest at the deepest samples taken (approximately 4 cm from soil surface) in comparison with other rhizosphere soil depths. We additionally show that finer grain sampling (i.e., three samples of equal volume pooled after sequencing) recovers greater microbial richness when using 16S rRNA gene sequencing to describe microbial communities found within the rhizosphere system. In summary, to further elucidate the extent host-specific microbiomes assemble within the rhizosphere, the grain at which bacterial communities are sampled should reflect and encompass fine-scale heterogeneity of the system.

分子技术的进步减少了观察的粒度或采样单元的空间分辨率和体积对植物相关微生物群表征的限制。通过离散的生态采样和大规模并行测序，我们可以更精确地描绘微生物组组装和微生物募集，以在空间和时间上容纳组织。在这里，我们区分丹参的细菌微生物群中稀有的群落丰富度和相对丰度取决于三个空间深度，这是根际微生境中距土壤表面的离散物理距离，作为根系区域的代理。为了评估采样谷物对稀疏群落丰富度和相对丰度的影响，我们评估了DNA提取之前收集的样品与测序后收集的样品之间这些指标的差异。基于距离的冗余分析和定量的Jaccard距离表明，根际土壤微生物在根际土壤深度之间的丰富度上有所不同。与其他根际土壤深度相比，在所有多样性水平上，在最深的样本中（距土壤表面约4 cm），稀有微生物的丰富度始终最低。我们还显示了更精细的谷物采样（即，当使用16S rRNA基因测序来描述根际系统中发现的微生物群落时，三个相同体积的样品在测序后合并）可回收更多的微生物。总之，为进一步阐明宿主特有的微生物群在根际内的聚集程度，采样细菌群落的谷物应反映并涵盖系统的小规模异质性。