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<p><UnorderedList Mark="Bullet"> <ItemContent> <p>Gammaproteobacteria were recruited and Bacteroidia were filtered by rice roots.</p> </ItemContent> <ItemContent> <p>Nutrients cycling and beneficial bacteria were enriched by <i>indica</i> compared to <i>japonica</i>.</p> </ItemContent> <ItemContent> <p><i>Indica</i> rice microbiomes prioritize modular organization, while <i>japonica</i> networks favor dense. interactions.</p> </ItemContent> </UnorderedList></p><p>The root microdomain represents a “hot spot” where microorganisms play a pivotal role in driving ecological processes and interact intimately with the host plants. In this study, we investigated 11 <i>indica</i> and 4 <i>japonica</i> rice varieties as test crops and analyzed the structural and functional characteristics of the microbial communities in the rhizosphere, rhizoplane and root endosphere of <i>indica</i> and <i>japonica</i> rice using highthroughput sequencing technology. Our findings reveal that, during the assembly process within the root microdomain, community diversity gradually decreases, while the filtering effect of the rice root intensifies from the rhizosphere to the root endosphere. Gammaproteobacteria tended to be recruited by both <i>indica</i> and <i>japonica</i> rice, while Clostridia and Betaproteobacteria were specifically recruited by <i>japonica</i> rice to colonize the rhizoplane and root endosphere. In contrast, Bacteroidia were depleted in the root microdomain of both <i>indica</i> and <i>japonica</i> rice, whereas Deltaproteobacteria and Nitrospira were specifically depleted in the root microdomain of <i>indica</i> rice. Compared to <i>japonica</i> rice, the bacteria enriched in the root microdomain of <i>indica</i> rice were primarily affiliated with Bacillales, Pseudomonadales, and Nitrospirales. Moreover, the <i>indica</i> rice had a lower number of instances of co-occurrence (edge/node ratio), network density and degree, while displayed a higher number of modularity, among-module connectivities, average path length and closeness centrality compared with <i>japonica</i> rice. These findings provide detailed insights into the assembly process of the microbiome in the root microdomain of different rice cultivars, as well as host genotype-regulated changes in microbial communities.</p>

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Host genotype-driven assembly of bacterial communities in the rice root microdomains

  • 期刊论文

  • 发表日期：

    2025年7月3日

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  • Yi Wan,
  • Zhi Ma,
  • Jiaping Lang,
  • Xuebin Xu,
  • Caihong Shao,
  • Jianping Chen,
  • Tida Ge,
  • Haoqing Zhang

摘要

Gammaproteobacteria were recruited and Bacteroidia were filtered by rice roots.

Nutrients cycling and beneficial bacteria were enriched by indica compared to japonica.

Indica rice microbiomes prioritize modular organization, while japonica networks favor dense. interactions.

The root microdomain represents a “hot spot” where microorganisms play a pivotal role in driving ecological processes and interact intimately with the host plants. In this study, we investigated 11 indica and 4 japonica rice varieties as test crops and analyzed the structural and functional characteristics of the microbial communities in the rhizosphere, rhizoplane and root endosphere of indica and japonica rice using highthroughput sequencing technology. Our findings reveal that, during the assembly process within the root microdomain, community diversity gradually decreases, while the filtering effect of the rice root intensifies from the rhizosphere to the root endosphere. Gammaproteobacteria tended to be recruited by both indica and japonica rice, while Clostridia and Betaproteobacteria were specifically recruited by japonica rice to colonize the rhizoplane and root endosphere. In contrast, Bacteroidia were depleted in the root microdomain of both indica and japonica rice, whereas Deltaproteobacteria and Nitrospira were specifically depleted in the root microdomain of indica rice. Compared to japonica rice, the bacteria enriched in the root microdomain of indica rice were primarily affiliated with Bacillales, Pseudomonadales, and Nitrospirales. Moreover, the indica rice had a lower number of instances of co-occurrence (edge/node ratio), network density and degree, while displayed a higher number of modularity, among-module connectivities, average path length and closeness centrality compared with japonica rice. These findings provide detailed insights into the assembly process of the microbiome in the root microdomain of different rice cultivars, as well as host genotype-regulated changes in microbial communities.