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Purpose <p>The microbiome plays a crucial role in the growth, development and resistance of rice. However, most current studies have focused on a single compartment and lack a comprehensive study of compartment-specific microbiomes.</p> Methods <p>In this study, we collected 2,825 rice microbiome samples from published articles, identified specific core amplicon sequence variants (ASV) in different regions of rice using 4 methods including random forests, and predicted the functional profiles of these core ASVs using PICRUSt2.</p> Results <p>We analyzed rice across the six main compartments. The results indicated that, compared to other regions, Chinese researchers are currently more focused on microbial research, particularly in the rice rhizosphere. Proteobacteria dominated the microbial communities across all five compartments of rice plants. Community structure analysis revealed significant differences between the microbial communities in the aboveground and underground sections. The microbial communities in the underground sections exhibited a clear gradient across compartments. Screening and identification revealed significant differences between the core ASVs of the underground and aboveground sections, with almost no overlap. Proteobacteria were widely present in both the underground and aboveground sections, whereas Cyanobacteria were more abundant in the phyllosphere. Additionally, distinct functional profiles were observed between the ASVs in the aboveground and underground sections. Core ASVs in the aboveground section were associated with circadian rhythm-related functions, while those in the underground section were more involved in absorption and transport processes.</p> Conclusion <p>Our large-scale multi-regional analysis confirmed the compartment-specific microbiomes in rice, with these specific microbes exhibiting distinct functional roles. This study provides critical insights for rice microbiome breeding and related fields.</p>

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Compartment-specific core microbiomes and functions in rice

  • 期刊论文

  • 发表日期：

    2025年5月29日

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  • Linna Ma,
  • Yusha Bai,
  • Xiang Li,
  • Jingyu Li,
  • Feixue Li,
  • Yan Yue,
  • Yingguang Li,
  • Jingwen Guo,
  • Chen Ye,
  • Xinyue Mei,
  • Fei Du,
  • Yixiang Liu,
  • Min Yang,
  • Shusheng Zhu,
  • Huichuan Huang

摘要

Purpose

The microbiome plays a crucial role in the growth, development and resistance of rice. However, most current studies have focused on a single compartment and lack a comprehensive study of compartment-specific microbiomes.

Methods

In this study, we collected 2,825 rice microbiome samples from published articles, identified specific core amplicon sequence variants (ASV) in different regions of rice using 4 methods including random forests, and predicted the functional profiles of these core ASVs using PICRUSt2.

Results

We analyzed rice across the six main compartments. The results indicated that, compared to other regions, Chinese researchers are currently more focused on microbial research, particularly in the rice rhizosphere. Proteobacteria dominated the microbial communities across all five compartments of rice plants. Community structure analysis revealed significant differences between the microbial communities in the aboveground and underground sections. The microbial communities in the underground sections exhibited a clear gradient across compartments. Screening and identification revealed significant differences between the core ASVs of the underground and aboveground sections, with almost no overlap. Proteobacteria were widely present in both the underground and aboveground sections, whereas Cyanobacteria were more abundant in the phyllosphere. Additionally, distinct functional profiles were observed between the ASVs in the aboveground and underground sections. Core ASVs in the aboveground section were associated with circadian rhythm-related functions, while those in the underground section were more involved in absorption and transport processes.

Conclusion

Our large-scale multi-regional analysis confirmed the compartment-specific microbiomes in rice, with these specific microbes exhibiting distinct functional roles. This study provides critical insights for rice microbiome breeding and related fields.