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Metagenomic study of endophytic bacterial community of sweet potato (Ipomoea batatas) cultivated in different soil and climatic conditions

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Abstract

The aim of this study was to clarify effects of soil and climatic conditions on community structure of sweet potato bacterial endophytes by applying locked nucleic acid oligonucleotide-PCR clamping technique and metagenomic analysis. For this purpose, the soil samples in three locations were transferred each other and sweet potato nursery plants from the same farm were cultivated for ca. 3 months. After removal of plastid, mitochondria and undefined sequences, the averaged numbers of retained sequences and operational taxonomic units per sample were 20,891 and 846, respectively. Proteobacteria (85.0%), Bacteroidetes (6.6%) and Actinobacteria (6.3%) were the three most dominant phyla, accounting for 97.9% of the reads, and γ-Proteobacteria (66.3%) being the most abundant. Top 10 genera represented 81.2% of the overall reads in which Pseudomonas (31.9–45.0%) being the most predominant. The overall endophytic bacterial communities were similar among the samples which indicated that the soil and the climatic conditions did not considerably affect the entire endophytic community. The original endophytic bacterial community might be kept during the cultivation period.

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Acknowledgements

This study was supported in part by a Grant-in-Aid for Scientific Research (B) [16KT0032] from the Japan Society for the Promotion of Science (JSPS). We are thankful to Professor Makoto Ikenaga, Faculty of Agriculture, Kagoshima University for providing the information of mitochondrial primer sequence. We are also grateful to Laboratory of soil and ecological engineering, Shimane University for soil analysis.

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Authors and Affiliations

  1. The United Graduate School of Agricultural Sciences, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8553, Japan

    Ramesh Raj Puri & Kazuhito Itoh

  2. Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue, 690-8504, Shimane, Japan

    Fumihiko Adachi, Shohei Hayashi & Kazuhito Itoh

  3. Department of Agricultural Science and Business, Takushoku University, Hokkaido College, Memu 4558, Fukagawa, 074-8585, Hokkaido, Japan

    Masayuki Omichi

  4. Faculty of Agriculture, University of Miyazaki, Gakuen-Kibanadai-Nishi 1-1, Miyazaki, 889-2192, Japan

    Yuichi Saeki & Akihiro Yamamoto

  5. Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China

    Md Arshad Ali

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  1. Ramesh Raj Puri
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  2. Fumihiko Adachi
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Correspondence to Kazuhito Itoh.

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Puri, R.R., Adachi, F., Omichi, M. et al. Metagenomic study of endophytic bacterial community of sweet potato (Ipomoea batatas) cultivated in different soil and climatic conditions. World J Microbiol Biotechnol 35, 176 (2019). https://doi.org/10.1007/s11274-019-2754-2

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