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Insights into Endophytic Bacterial Community Structures of Seeds Among Various Oryza sativa L. Rice Genotypes

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Abstract

This study aimed to investigate the endophytic bacterial communities among various rice seed genotypes, to define the core microbiome and to further explore the relationship between rice genotypes and their endophytic bacterial flora. Simple sequence repeats molecular marker technology was used to investigate the genetic polymorphism in five different genotypes of rice. Endophytic bacterial communities in rice seeds were investigated using the Illumina-based 16S rRNA gene. The results showed that rice genotype had little impact on the diversity and richness of endophytic bacteria in seeds. The various rice genotypes do not have significantly different communities of endophytic bacterial in seeds, but the endophyte abundance distributions are obviously different, especially the dominant endophytic genera. Some phyla, such as Acidobacteria, Fusobacteria, Chlamydiae and Gemmatimonadetes, were first detected in rice seeds using high-throughput sequencing technique. As expected, five different rice genotypes were found to have a shared microbiome. At the genus level, Pantoea (28.33–72.77%), Acinetobacter (0.16–34.23%) and Xanthomonas (3.20–13.51%), which are probably the core microflora in indica rice seeds, served as the dominant genera that coexisted in all rice seeds tested. However, the current studies cannot confirm the correlation of rice phylogeny and seed bacterial microbiome clearly, but provide some clues of technical possibility and valuable experiences for the future study.

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Acknowledgements

We thank Prof. Yang-Sheng Li of Wuhan University for offering rice seeds. We thank Dr. Yan-Zhong Luo of Biotechnology Research Institute, Chinese Academy of Agricultural Sciences for excellent technical assistance.

Funding

This work was supported by the National Natural Science Foundation of China (Grant No. 31670005).

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Author notes

  1. Jun Zhang and Caiwen Zhang have contributed equally to this paper.

Authors and Affiliations

  1. Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Jun Zhang, Caiwen Zhang, Ruijie Zhang, Jusheng Gao, Xia Zhao, Juanjuan Zhao, Dongfang Zhao & Xiaoxia Zhang

  2. State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China

    Jing Yang

  3. Qiyang Agro-ecosystem of National Field Experimental Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Qiyang, 426182, China

    Jusheng Gao

  4. China Center of Industrial Culture Collection (CICC), China National Research Institute of Food and Fermentation Industries, Beijing, 100015, China

    Caiwen Zhang

  5. State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou, 510070, China

    Jun Zhang

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  1. Jun Zhang
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Zhang, J., Zhang, C., Yang, J. et al. Insights into Endophytic Bacterial Community Structures of Seeds Among Various Oryza sativa L. Rice Genotypes. J Plant Growth Regul 38, 93–102 (2019). https://doi.org/10.1007/s00344-018-9812-0

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