Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome
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 tota...
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Format: | Article |
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Elsevier
2020-01-01
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Series: | Plant Communications |
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Online Access: | http://www.sciencedirect.com/science/article/pii/S2590346219300033 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Xiaoxuan Guo Xiaoning Zhang Yuan Qin Yong-Xin Liu Jingying Zhang Na Zhang Kun Wu Baoyuan Qu Zishan He Xin Wang Xinjian Zhang Stéphane Hacquard Xiangdong Fu Yang Bai |
spellingShingle |
Xiaoxuan Guo Xiaoning Zhang Yuan Qin Yong-Xin Liu Jingying Zhang Na Zhang Kun Wu Baoyuan Qu Zishan He Xin Wang Xinjian Zhang Stéphane Hacquard Xiangdong Fu Yang Bai Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome Plant Communications microbial load host-associated quantitative abundance profiling root microbiome |
author_facet |
Xiaoxuan Guo Xiaoning Zhang Yuan Qin Yong-Xin Liu Jingying Zhang Na Zhang Kun Wu Baoyuan Qu Zishan He Xin Wang Xinjian Zhang Stéphane Hacquard Xiangdong Fu Yang Bai |
author_sort |
Xiaoxuan Guo |
title |
Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome |
title_short |
Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome |
title_full |
Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome |
title_fullStr |
Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome |
title_full_unstemmed |
Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome |
title_sort |
host-associated quantitative abundance profiling reveals the microbial load variation of root microbiome |
publisher |
Elsevier |
series |
Plant Communications |
issn |
2590-3462 |
publishDate |
2020-01-01 |
description |
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. |
topic |
microbial load host-associated quantitative abundance profiling root microbiome |
url |
http://www.sciencedirect.com/science/article/pii/S2590346219300033 |
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doaj-5f92ffa278f64e51b8c7843085afe40e2020-11-25T02:54:24ZengElsevierPlant Communications2590-34622020-01-0111Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root MicrobiomeXiaoxuan Guo0Xiaoning Zhang1Yuan Qin2Yong-Xin Liu3Jingying Zhang4Na Zhang5Kun Wu6Baoyuan Qu7Zishan He8Xin Wang9Xinjian Zhang10Stéphane Hacquard11Xiangdong Fu12Yang Bai13State 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, ChinaState 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; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, ChinaState 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; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, ChinaState 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, ChinaState 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, ChinaState 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; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, ChinaState Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, ChinaState 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, ChinaState 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; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, ChinaState 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, ChinaShandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, ChinaMax Planck Institute for Plant Breeding Research, Cologne 50829, GermanyState Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences (CAS), Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China; Corresponding authorState 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; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China; Corresponding authorPlant-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.http://www.sciencedirect.com/science/article/pii/S2590346219300033microbial loadhost-associated quantitative abundance profilingroot microbiome |