State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China.
CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), Beijing 100101, China.
Plant Commun. 2019 Sep 16;1(1):100003. doi: 10.1016/j.xplc.2019.100003. eCollection 2020 Jan 13.
Plant-associated microbes are critical for plant growth and survival under natural environmental conditions. To date, most plant microbiome studies involving high-throughput amplicon sequencing have focused on the relative abundance of microbial taxa. However, this technique does not assess the total microbial load and the abundance of individual microbes relative to the amount of host plant tissues. Here, we report the development of a host-associated quantitative abundance profiling (HA-QAP) method that can accurately examine total microbial load and colonization of individual root microbiome members relative to host plants by the copy-number ratio of microbial marker gene to plant genome. We validate the HA-QAP method using mock experiments, perturbation experiments, and metagenomic sequencing. The HA-QAP method eliminates the generation of spurious outputs in the classical method based on microbial relative abundance, and reveals the load of root microbiome to host plants. Using the HA-QAP method, we found that the copy-number ratios of microbial marker genes to plant genome range from 1.07 to 6.61 for bacterial 16S rRNA genes and from 0.40 to 2.26 for fungal internal transcribed spacers in the root microbiome samples from healthy rice and wheat. Furthermore, using HA-QAP we found that an increase in total microbial load represents a key feature of changes in root microbiome of rice plants exposed to drought stress and of wheat plants with root rot disease, which significantly influences patterns of differential taxa and species interaction networks. Given its accuracy and technical feasibility, HA-QAP would facilitate our understanding of genuine interactions between root microbiome and plants.
植物相关微生物对于植物在自然环境条件下的生长和存活至关重要。迄今为止，大多数涉及高通量扩增子测序的植物微生物组研究都集中在微生物类群的相对丰度上。然而，该技术不能评估微生物的总负荷和单个微生物的丰度相对于宿主植物组织的数量。在这里，我们报告了一种宿主相关定量丰度分析（HA-QAP）方法的开发，该方法可以通过微生物标记基因与植物基因组的拷贝数比值，准确地检测单个根微生物成员相对于宿主植物的总微生物负荷和定殖情况。我们使用模拟实验、扰动实验和宏基因组测序来验证 HA-QAP 方法。HA-QAP 方法消除了基于微生物相对丰度的经典方法中产生虚假输出的问题，并揭示了根微生物组对宿主植物的负荷。使用 HA-QAP 方法，我们发现健康水稻和小麦根微生物组样本中细菌 16S rRNA 基因的微生物标记基因与植物基因组的拷贝数比值范围为 1.07 至 6.61，真菌内部转录间隔区的拷贝数比值范围为 0.40 至 2.26。此外，使用 HA-QAP，我们发现总微生物负荷的增加是暴露于干旱胁迫的水稻植物和根腐病小麦植物的根微生物组变化的一个关键特征，这显著影响了差异分类群和物种相互作用网络的模式。鉴于其准确性和技术可行性，HA-QAP 将有助于我们理解根微生物组与植物之间的真实相互作用。
