Abstract
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.
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Data availability
Shotgun metagenomic sequencing and 16S rRNA gene amplicon sequencing data are available on NCBI under the Bioproject accession number PRJNA632564 and PRJNA639671, respectively.
Code availability
Not applicable.
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Funding
This work was supported by the National Natural Science Foundation of China (41920104008, 42007034), the National Key Research and Development Program of China (2016YFC0501202), the Science Foundation of Chinese Academy of Sciences (XDA23070501), the Cooperative Project between CAS and Jilin Province of China (2019SYHZ0039) and the Science and Technology Development Project of Jilin Province of China (20190303070SF, 20200501003GX, YDZJ202101ZYTS006). Publication number 7205 of the Netherlands Institute of Ecology (NIOO-KANW).
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CT conceived and designed the study; JZ and WL helped with the experiment design; HX, YC and DC carried out the experiments; LT and SS collected the samples; YS, LT and JC analyzed the data and prepared figures and tables with the input of WL and L-SPT; YS, WL, L-SPT and CT wrote the manuscript. EEK and JAvV helped with the improvement of the manuscript. All authors read and approved the final manuscript.
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Sun, Y., Tian, L., Chang, J. et al. Rice domestication influences the composition and function of the rhizosphere bacterial chemotaxis systems. Plant Soil 466, 81–99 (2021). https://doi.org/10.1007/s11104-021-05036-2
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DOI: https://doi.org/10.1007/s11104-021-05036-2