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Jiang L, Ke D, Sun B, Zhang J, Lyu S, Yu H, Chen P, Mao X, Liu Q, Chen W, Fan Z, Huang L, Yin S, Deng Y, Li C. Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process. Microbiol Spectr 2024; 12:e0333023. [PMID: 38470483 DOI: 10.1128/spectrum.03330-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/15/2024] [Indexed: 03/13/2024] Open
Abstract
The root-associated microbiota has a close relation to the life activities of plants, and its composition is affected by the rhizospheric environment and plant genotypes. Rice (Oryza sativa) was domesticated from the ancestor species Oryza rufipogon. Many important agricultural traits and adversity resistance of rice have changed during a long time of natural domestication and artificial selection. However, the influence of rice genotypes on root microbiota in important agricultural traits remains to be explained. In this study, we performed 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing to generate bacterial and fungal community profiles of O. rufipogon and O. sativa, both of which were planted in a farm in Guangzhou and had reached the reproductive stage. We compared their root microbiota in detail by alpha diversity, beta diversity, different species, core microbiota, and correlation analyses. We found that the relative abundance of bacteria was significantly higher in the cultivated rice than in the common wild rice, while the relative abundance of fungi was the opposite. Significant differences in agricultural traits between O. rufipogon and O. sativa showed a high correlation with core microorganisms in the two Oryza species, which only existed in either or had obviously different abundance in both two species, indicating that rice genotype/phenotype had a strong influence on recruiting specific microorganisms. Our study provides a theoretical basis for the in-depth understanding of rice root microbiota and the improvement of rice breeding from the perspective of the interaction between root microorganisms and plants.IMPORTANCEPlant root microorganisms play a vital role not only in plant growth and development but also in responding the biotic and abiotic stresses. Oryza sativa is domesticated from Oryza rufipogon which has many excellent agricultural traits especially containing resistance to biotic and abiotic stresses. To improve the yield and resistance of cultivated rice, it is particularly important to deeply research on differences between O. sativa and O. rufipogon and find beneficial microorganisms to remodel the root microbiome of O. sativa.
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Affiliation(s)
- Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Da Ke
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Shuwei Lyu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Pingli Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Qing Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Li Huang
- Healthtimegene Institute, Shenzhen, China
| | - Sanjun Yin
- Healthtimegene Institute, Shenzhen, China
| | - Yizhen Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Chen Li
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
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