Department of Plant Pathology, University of Minnesota, Minneapolis, USA.
USDA-ARS, Plant Science Research Unit, Saint Paul, MN, USA.
Microb Ecol. 2019 Oct;78(3):753-763. doi: 10.1007/s00248-019-01318-6. Epub 2019 Mar 9.
Soil microbiota play important and diverse roles in agricultural crop nutrition and productivity. Yet, despite increasing efforts to characterize soil bacterial and fungal assemblages, it is challenging to disentangle the influences of sampling design on assessments of communities. Here, we sought to determine whether composite samples-often analyzed as a low cost and effort alternative to replicated individual samples-provide representative summary estimates of microbial communities. At three Minnesota agricultural research sites planted with an oat cover crop, we conducted amplicon sequencing for soil bacterial and fungal communities (16S and ITS2) of replicated individual or homogenized composite soil samples. We compared soil microbiota from within and among plots and then among agricultural sites using both sampling strategies. Results indicated that single or multiple replicated individual samples, or a composite sample from each plot, were sufficient for distinguishing broad site-level macroecological differences among bacterial and fungal communities. Analysis of a single sample per plot captured only a small fraction of the distinct OTUs, diversity, and compositional variability detected in the analysis of multiple individual samples or a single composite sample. Likewise, composite samples captured only a fraction of the diversity represented by the six individual samples from which they were formed, and, on average, analysis of two or three individual samples offered greater compositional coverage (i.e., greater number of OTUs) than a single composite sample. We conclude that sampling design significantly impacts estimates of bacterial and fungal communities even in homogeneously managed agricultural soils, and our findings indicate that while either strategy may be sufficient for broad macroecological investigations, composites may be a poor substitute for replicated samples at finer spatial scales.
土壤微生物在农业作物营养和生产力方面发挥着重要而多样的作用。尽管人们越来越努力地描述土壤细菌和真菌组合，但要区分采样设计对群落评估的影响仍然具有挑战性。在这里，我们试图确定复合样本（通常作为重复个体样本的低成本和低工作量替代方法进行分析）是否可以提供微生物群落的代表性综合估计。在明尼苏达州的三个农业研究点，我们对种植燕麦覆盖作物的土壤细菌和真菌群落（16S 和 ITS2）进行了扩增子测序，这些样本来自重复的个体样本或均匀化的复合土壤样本。我们使用两种采样策略比较了不同样地内和样地间以及不同农业点间的土壤微生物群。结果表明，单个或多个重复的个体样本，或每个样地的一个复合样本，足以区分细菌和真菌群落的广泛站点水平的宏观生态差异。每个样地分析一个样本仅捕获了在分析多个个体样本或单个复合样本时检测到的独特 OTU、多样性和组成变异性的一小部分。同样，复合样本仅捕获了由它们形成的六个个体样本中代表的多样性的一小部分，并且平均而言，分析两个或三个个体样本比单个复合样本提供了更大的组成覆盖度（即更多的 OTU）。我们得出结论，采样设计即使在同质管理的农业土壤中也会显著影响细菌和真菌群落的估计，我们的研究结果表明，虽然这两种策略都可能足以进行广泛的宏观生态学研究，但在更精细的空间尺度上，复合样本可能是重复样本的较差替代品。
