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Soil-root interface influences the assembly of the endophytic bacterial community in rice plants


To highlight the importance of the soil-root interface in bacterial root colonization, we performed 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform to characterize the bacterial endophytes of rice plants grown by two experiments – soil and hydroponic, considering their soil, solution, and endosphere compartments. We hypothesized that rice plants from both experiments would exhibit dissimilar endophytic bacterial communities. Alpha-diversity (richness (ASVs), Shannon index, Faith’s phylogenetic diversity, and Pielou’s evenness) for bacterial endophytes was lower in the soil experiment than in the hydroponic experiment. However, the rhizospheric soil exhibited higher microbial diversity and richness than the hydroponic solution after 6 weeks. Proteobacteria and Firmicutes were the most dominant phyla in both experiments, while several other bacterial taxa showed major differences at genus levels. A Venn diagram revealed that 5 overlapping bacterial genera were shared by the endosphere and rhizosphere/solution compartments of both experiments. Principal coordinate analysis (PCoA) based on weighted UniFrac distances showed a clear distinction between microbial communities of all sampled compartments. Furthermore, PERMANOVA results showed that the endophyte communities of both experiments differed significantly (p < 0.001). Overall, this study suggests that the soil-root interface plays a significant role in determining the bacterial endophyte community in rice plants, and the different patterns of endophytic colonization of the rice roots in both experiments were likely influenced by factors that may include bacterial motility, biofilm formation, as well as the decreased effects of root exudates due to dissolution in the solution of the hydroponic experiment.

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Data availability

The 16S rRNA gene amplicon sequences for this study were deposited in the DDBJ under the following accession number: DRR316996-DRR317103. A table of bacterial community compositions after QIIME2 processing is also available in Microsoft Excel format as supplementary material (ESM_1.xlsx).


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This work was the result of using research equipment shared in the MEXT Project for promoting public utilization of advanced research infrastructure (program for supporting the introduction of the new sharing system) at Niigata University, Grant Number JPMXS0421100320.

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Correspondence to Kazuki Suzuki.

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Supplementary file1 (XLSX 494 KB)

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Samuel, S.O., Suzuki, K., Asiloglu, R. et al. Soil-root interface influences the assembly of the endophytic bacterial community in rice plants. Biol Fertil Soils 58, 35–48 (2022).

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  • Bacterial endophytes
  • Hydroponic experiment
  • Plant–microbe interaction
  • Soil experiment
  • Soil-root interface