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Sci China Life Sci. 2018 Jun;61(6):613-621. doi: 10.1007/s11427-018-9284-4. Epub 2018 Mar 23.

Root microbiota shift in rice correlates with resident time in the field and developmental stage.

Zhang J1,2, Zhang N1,2,3, Liu YX1,2, Zhang X1,2,3, Hu B1, Qin Y1,2,3, Xu H1,2,3, Wang H1,2,3, Guo X1,2, Qian J1,2,3, Wang W1, Zhang P4,5, Jin T6,7, Chu C8, Bai Y9,10.

Author information

1
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
2
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.
3
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China.
4
China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China.
5
BGI-Qingdao, Qingdao, 266510, China.
6
China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China. jintao@genomics.cn.
7
BGI-Qingdao, Qingdao, 266510, China. jintao@genomics.cn.
8
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. ccchu@genetics.ac.cn.
9
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. ybai@genetics.ac.cn.
10
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. ybai@genetics.ac.cn.

Abstract

Land plants in natural soil form intimate relationships with the diverse root bacterial microbiota. A growing body of evidence shows that these microbes are important for plant growth and health. Root microbiota composition has been widely studied in several model plants and crops; however, little is known about how root microbiota vary throughout the plant's life cycle under field conditions. We performed longitudinal dense sampling in field trials to track the time-series shift of the root microbiota from two representative rice cultivars in two separate locations in China. We found that the rice root microbiota varied dramatically during the vegetative stages and stabilized from the beginning of the reproductive stage, after which the root microbiota underwent relatively minor changes until rice ripening. Notably, both rice genotype and geographical location influenced the patterns of root microbiota shift that occurred during plant growth. The relative abundance of Deltaproteobacteria in roots significantly increased overtime throughout the entire life cycle of rice, while that of Betaproteobacteria, Firmicutes, and Gammaproteobacteria decreased. By a machine learning approach, we identified biomarker taxa and established a model to correlate root microbiota with rice resident time in the field (e.g., Nitrospira accumulated from 5 weeks/tillering in field-grown rice). Our work provides insights into the process of rice root microbiota establishment.

KEYWORDS:

biomarker taxa; developmental stages; machine learning; modeling; residence time in the field; rice; root microbiota; time-series shift

PMID:
29582350
DOI:
10.1007/s11427-018-9284-4
[Indexed for MEDLINE]

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