Rice domestication influences the composition and function of the rhizosphere bacterial chemotaxis systems

• Published in: Plant and soil Vol. 466; no. 1/2; pp. 81 - 99
• Main Authors: Sun, Yu, Tian, Lei, Chang, Jingjing, Shi, Shaohua, Zhang, Jianfeng, Xie, Hongwei, Cai, Yaohui, Chen, Dazhou, Kuramae, Eiko E., van Veen, Johannes A., Li, Weiqiang, Tran, Lam-Son Phan, Tian, Chunjie
• Format: Journal Article
• Language: English
• Published: Cham Springer Science + Business Media 01.09.2021; Springer International Publishing; Springer; Springer Nature B.V
• Subjects: Agriculture; Analysis; Bacteria; bacterial communities; Biomedical and Life Sciences; Chemotaxis; Composition; Cultivation; Domestication; Ecology; Exudates; Gene sequencing; Genes; Grain cultivation; Identification and classification; Life Sciences; Metabolites; Metabolomics; Metagenomics; Methods; Microorganisms; Oryza; Physiological aspects; Plant Physiology; Plant Sciences; REGULAR ARTICLE; Rhizosphere; Rice; RNA sequencing; rRNA 16S; soil; Soil bacteria; Soil microbiology; Soil microorganisms; Soil Science & Conservation; wild rice; United States; Netherlands; China; Rhizosphere; Rice domestication; Bacterial chemotaxis systems; Root metabolites; Bacterial community
• ISSN: 0032-079X; 1573-5036
• DOI: 10.1007/s11104-021-05036-2

Aims Specific soil bacteria can sense and respond to the selective rhizosphere recruitment of root exudates using unique systems of chemotaxis that mediate plant-microbe and microbe-microbe interactions. This study investigates how the bacterial chemotaxis systems have been impacted by selection during the domestication of rice ( Oryza species). Methods Shotgun metagenomic sequencing and 16S rRNA gene amplicon sequencing were performed to investigate the bacterial chemotaxis systems and chemotactic bacteria in the rhizospheres of wild and cultivated rice. Metabolomics analysis was performed to examine the root metabolites of different accessions of rice. Results The bacterial chemotaxis genes exhibited a higher abundance in the rhizospheres of wild rice than cultivated rice, and that the compositional profile of chemotaxis genes was distinctly different between types of rice. Differential selection of chemotaxis systems was at least partially driven by changes in the metabolite profiles of rice roots that were affected by domestication. A core group of chemotactic bacteria was also identified, and specific chemotactic bacteria were found to function as hub taxa in the rhizosphere bacterial community. Conclusion The present study provides novel insights into the composition and function of the bacterial chemotaxis systems in the rhizospheres of wild and domesticated rice. It also provides a new perspective on the impact of rice domestication on the assembly of rhizomicrobiome.