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

  • Ramesh Raj Puri
  • Fumihiko Adachi
  • Masayuki Omichi
  • Yuichi Saeki
  • Akihiro Yamamoto
  • Shohei Hayashi
  • Md Arshad Ali
  • Kazuhito ItohEmail author
Original Paper

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.

Keywords

Sweet potato Endophytic bacteria Microbial community Locked nucleic acid Metagenomics 

Notes

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.

Supplementary material

11274_2019_2754_MOESM1_ESM.docx (366 kb)
Supplementary file1 (DOCX 367 kb)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.The United Graduate School of Agricultural SciencesTottori UniversityTottoriJapan
  2. 2.Faculty of Life and Environmental ScienceShimane UniversityMatsueJapan
  3. 3.Department of Agricultural Science and BusinessTakushoku University, Hokkaido CollegeFukagawaJapan
  4. 4.Faculty of AgricultureUniversity of MiyazakiMiyazakiJapan
  5. 5.Institute of Biotechnology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina

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