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Composition and Diversity of Endophytic Bacterial Communities in the Seeds of Upland Rice Resources from Different Origin Habitats in China

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Abstract

The cultivation of high-quality upland rice, which is known to be drought tolerant and widely adaptable, can help solve the challenges of food and water shortages for the world’s rising populations, so it is of great significance to sustainable agricultural development. Certain microbial agents can further enhance plant drought resistance, such as the endophytic bacteria that live in plant seeds without causing infection, making them a vital resource that can improve upland rice cultivation and yield. In this study, high-throughput sequencing technology based on the Illumina MiSeq platform was used to investigate the structure and diversity of endophytic bacterial communities in the seeds of 12 upland rice varieties from different areas in Yunnan Province, China. The results showed that 39 endophytic operational taxonomic units (OTUs) were found to coexist in all samples. At the phylum level, the dominant phyla in the 12 seed samples were Proteobacteria (66.92–99.98%). At the genus level, Pantoea (9.75–99.24%), Pseudomonas (0.11–37.24%), Curtobacterium (0.01–19.90%), Microbacterium (0.01–14.95%), Methylobacterium (0.40–5.86%), Agrobacterium (0.01–4.53%), Sphingomonas (0.04–1.56%), Aurantimonas (0.01–1.45%) and Rhodococcus (0.11–1.09%) were found to be the dominant genera coexisting in all the tested upland rice seeds tested, representing the core microbiota in upland rice seeds. Furthermore, correlation analysis showed that upland rice habitat environmental factors, such as climate, precipitation and altitude, exert significant effects on the composition and diversity of the endophytic bacterial communities in the upland rice seeds. The findings of this study contribute significantly to understanding the relationship between upland rice and its endophytic bacteria, which can be developed to enhance drought tolerance and yield in this important crop.

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Data Availability

All data generated or analyzed during this study are included in this published article and its supplementary information files.

Abbreviations

OTU:

Operational Taxonomic Units

PCoA:

Principal Coordinates Analysis

RDA:

Redundancy Analysis

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Acknowledgements

We would like to thank the research team of Prof. Huajun Zheng of Shanghai-MOST Key Laboratory of Health and Disease Genomics of Chinese National Human Genome Center at Shanghai for its platform and technical support in high-throughput sequencing and Bioinformatics analysis.

Funding

The research was supported by the National foreign expert Program of China (No. QN2021105002L), the Open Research Fund of Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs (MRCP-2018–5), the Fundamental Research Funds for the Central Universities (No. FRF-TP-20-044A2; FRF-MP-20–39) and the Open Research Fund of State Key Laboratory of Hybrid Rice (Hunan Hybrid Rice Research Center) (No. 2017KF04).

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Author notes

  1. Zhishan Wang and Yongqiang Zhu have contributed equally to this work.

Authors and Affiliations

  1. School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China

    Zhishan Wang & Yang Liu

  2. State Key Laboratory of Hybrid Rice (Hunan Hybrid Rice Research Center), Changsha, 410125, China

    Ni Li & Weiping Wang

  3. Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China

    Yongqiang Zhu

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  1. Zhishan Wang
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  2. Yongqiang Zhu
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  3. Ni Li
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  4. Weiping Wang
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  5. Yang Liu
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Contributions

WZS and ZYQ designed and participated in all experimental procedures, performed data analysis, and drafted the manuscript. LN participated in the plant samples cultivation. WWP and LY supervised the study and critically revised the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Weiping Wang or Yang Liu.

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Wang, Z., Zhu, Y., Li, N. et al. Composition and Diversity of Endophytic Bacterial Communities in the Seeds of Upland Rice Resources from Different Origin Habitats in China. J Plant Growth Regul 42, 2433–2442 (2023). https://doi.org/10.1007/s00344-022-10714-1

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  • DOI: https://doi.org/10.1007/s00344-022-10714-1

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