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Updated: Feb 10, 2026
09:55
Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere
Published on: May 2, 2018
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Co-evolutionary associations between root-associated microbiomes and root transcriptomes in wild and cultivated rice
Lei Tian1, Shaohua Shi2, Lina Ma2
1Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China.
Plant Physiology and Biochemistry : PPB
|May 20, 2018
Summary
Wild rice (Oryza rufipogon) and cultivated rice (Oryza sativa) exhibit distinct metabolic pathways and root microbiomes. Understanding these associations offers insights for improving rice breeding through microbiome and transcriptome analysis.
Area of Science:
- Plant-microbe interactions
- Genomics and transcriptomics
- Microbiome research
Background:
- Plants and their root-associated microbiomes have a symbiotic relationship, influencing each other's metabolic processes.
- Wild rice (Oryza rufipogon) and cultivated rice (Oryza sativa) have evolved distinct metabolic pathways and root microbiomes.
- Investigating these co-evolutionary associations is crucial for advancing rice breeding strategies.
Purpose of the Study:
- To explore the co-evolutionary associations between metabolic pathways and root-associated microbiomes in wild and cultivated rice.
- To identify specific metabolic pathways and microbial communities linked to each rice type.
- To provide a basis for utilizing microbiome resources in rice improvement.
Main Methods:
- Transcriptome data analysis to identify plant metabolic pathways.
- 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing for root-associated microbiome profiling.
- Correlation analysis and redundancy analysis to link metabolic pathways with microbial communities.
Main Results:
- Differential correlations were observed between enriched pathways and microbiomes in wild versus cultivated rice.
- Wild rice showed positive associations between pathways like 'Glutathione metabolism' and specific bacterial/fungal taxa.
- Cultivated rice exhibited positive correlations between pathways such as 'Glycolysis/Gluconeogenesis' and microbial communities; Streptomyces significantly impacted gene expression in wild rice.
Conclusions:
- The study establishes a theoretical foundation for understanding root microbiome-transcriptome associations in rice.
- Findings highlight the practical significance of identifying and utilizing beneficial microbes from wild rice for crop improvement.
- Specific microbial species, like Streptomyces, can significantly influence plant gene expression, offering targets for agricultural applications.
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