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

Abstract

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 ofindica and japonica rice using high-throughput 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.

Graphical abstract

Keywords

rhizosphere / rhizoplane / root endosphere / microbial communities / microbial co-occurrence patterns

Highlight

	● 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.

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