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


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.


Sweet potato Endophytic bacteria Microbial community Locked nucleic acid Metagenomics 



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)


  1. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169PubMedPubMedCentralGoogle Scholar
  2. Amplicon PCR, Clean-Up PCR, Index PCR (2013) 16S metagenomic sequencing library preparation, pp 1–28Google Scholar
  3. Andreote FD, De Araújo WL, De Azevedo JL et al (2009) Endophytic colonization of potato (Solanum tuberosum L.) by a novel competent bacterial endophyte, Pseudomonas putida strain P9, and its effect on associated bacterial communities. Appl Environ Microbiol 75:3396–3406CrossRefGoogle Scholar
  4. Duffy BK, Défago G (1999) Environmental factors modulating antibiotic and siderophore biosynthesis by Pseudomonas fluorescens biocontrol strains. Appl Environ Microbiol 65:2429–2438PubMedPubMedCentralGoogle Scholar
  5. Gaiero JR, McCall CA, Thompson KA et al (2013) Inside the root microbiome: bacterial root endophytes and plant growth promotion. Am J Bot 100:1738–1750CrossRefGoogle Scholar
  6. Garbeva P, Van Overbeek LS, Van Vuurde JWL et al (2001) Analysis of endophytic bacterial communities of potato by plating and denaturing gradient gel electrophoresis (DGGE) of 16S rDNA based PCR fragments. Microb Ecol 41:369–383CrossRefGoogle Scholar
  7. Gottel NR, Castro HF, Kerley M et al (2011) Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microbiol 77:5934–5944CrossRefGoogle Scholar
  8. Huong NL, Itoh K, Suyama K (2007) Diversity of 2,4-dichlorophenoxyacetic acid (2,4-d) and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)-degrading bacteria in Vietnamese soils. Microbes Environ 22:243–256CrossRefGoogle Scholar
  9. Ikenaga M, Sakai M (2014) Application of Locked Nucleic Acid (LNA) oligonucleotide–PCR clamping technique to selectively PCR amplify the SSU rRNA genes of bacteria in investigating the plant-associated community structures. Microbes Environ 29:286–295CrossRefGoogle Scholar
  10. Ikenaga M, Tabuchi M, Oyama T et al (2015) Development of LNA oligonucleotide-PCR clamping technique in investigating the community structures of plant-associated bacteria. Biosci Biotechnol Biochem 79:1556–1566CrossRefGoogle Scholar
  11. Jackson CR, Randolph KC, Osborn SL et al (2013) Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables. BMC Microbiol 13:1–12CrossRefGoogle Scholar
  12. Jaric M, Segal J, Silva-Herzog E et al (2013) Better primer design for metagenomics applications by increasing taxonomic distinguishability. BMC Proc 7:1–10CrossRefGoogle Scholar
  13. Khan Z, Doty SL (2009) Characterization of bacterial endophytes of sweet potato plants. Plant Soil 322:197–207CrossRefGoogle Scholar
  14. Klindworth A, Pruesse E, Schweer T et al (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41:1–11CrossRefGoogle Scholar
  15. Magnani GS, Cruz LM, Weber H et al (2013) Culture-independent analysis of endophytic bacterial communities associated with Brazilian sugarcane. Genet Mol Res 12:4549–4558CrossRefGoogle Scholar
  16. Marques JM, da Silva TF, Vollu RE et al (2015) Bacterial endophytes of sweet potato tuberous roots affected by the plant genotype and growth stage. Appl Soil Ecol 96:273–281CrossRefGoogle Scholar
  17. Miller CM, Miller RV, Garton-Kenny D et al (1998) Ecomycins, unique antimycotics from Pseudomonas viridiflava. J Appl Microbiol 84:937–944CrossRefGoogle Scholar
  18. Moronta-Barrios F, Gionechetti F, Pallavicini A et al (2018) Bacterial microbiota of rice roots: 16S-based taxonomic profiling of endophytic and rhizospheric diversity, endophytes isolation and simplified endophytic community. Microorganisms 6:14CrossRefGoogle Scholar
  19. Oliver JD (2010) Recent findings on the viable but nonculturable state in pathogenic bacteria. FEMS Microbiol Rev 34:415–425CrossRefGoogle Scholar
  20. Oteino N, Lally RD, Kiwanuka S et al (2015) Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates. Front Microbiol 6:1–9CrossRefGoogle Scholar
  21. Pei C, Mi C, Sun L et al (2017) Diversity of endophytic bacteria of Dendrobium officinale based on culture-dependent and culture-independent methods. Biotechnol Biotechnol Equip 31:112–119CrossRefGoogle Scholar
  22. Pereira P, Ibáñez F, Rosenblueth M et al (2011) Analysis of the bacterial diversity associated with the roots of maize (Zea mays L.) through culture-dependent and culture-independent methods. ISRN Ecol 2011:1–10CrossRefGoogle Scholar
  23. Puri RR, Dangi SR, Dhungana SA et al (2018a) Diversity and plant growth promoting ability of culturable endophytic bacteria in Nepalese sweet potato. Adv Microbiol 8:734–761CrossRefGoogle Scholar
  24. Puri RR, Adachi F, Omichi M et al (2018b) Culture-dependent analysis of endophytic bacterial community of sweet potato (Ipomoea batatas) in different soils and climates. J Adv Microbiol 13:1–12CrossRefGoogle Scholar
  25. Rediers H, Bonnecarrère V, Rainey PB et al (2003) Development and application of a dapB-based in vivo expression technology system to study colonization of rice by the endophytic nitrogen-fixing bacterium Pseudomonas stutzeri A15. Appl Environ Microbiol 69:6864–6874CrossRefGoogle Scholar
  26. Ryan RP, Germaine K, Franks A et al (2008) Bacterial endophytes: recent developments and applications. FEMS Microbiol Lett 278:1–9CrossRefGoogle Scholar
  27. Sato T, Matsumoto K, Okumura T et al (2008) Isolation of lactate-utilizing butyrate-producing bacteria from human feces and in vivo administration of Anaerostipes caccae strain L2 and galacto-oligosaccharides in a rat model. FEMS Microbiol Ecol 66:528–536CrossRefGoogle Scholar
  28. Shen SY, Fulthorpe R (2015) Seasonal variation of bacterial endophytes in urban trees. Front Microbiol 6:1–13Google Scholar
  29. Shi Y, Yang H, Zhang T et al (2014) Illumina-based analysis of endophytic bacterial diversity and space-time dynamics in sugar beet on the north slope of Tianshan mountain. Appl Microbiol Biotechnol 98:6375–6385CrossRefGoogle Scholar
  30. Soil Survey Staff (1999) Soil taxonomy—a basic system of soil classification for making and interpreting soil surveys. USDA Agriculture Handbook No. 436. U.S. Government Publishing Office, Washington DC, pp 1–754Google Scholar
  31. Subramanian P, Mageswari A, Kim K et al (2015) Psychrotolerant endophytic Pseudomonas sp. strains OB155 and OS261 induced chilling resistance in tomato plants (Solanum lycopersicum Mill.) by activation of their antioxidant capacity. Mol Plant Microbe Interact 28:1073–1081CrossRefGoogle Scholar
  32. Taghavi S, Garafola C, Monchy S et al (2009) Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees. Appl Environ Microbiol 75:748–757CrossRefGoogle Scholar
  33. Tian B, Zhang C, Ye Y et al (2017) Beneficial traits of bacterial endophytes belonging to the core communities of the tomato root microbiome. Agric Ecosyst Environ 247:149–156CrossRefGoogle Scholar
  34. Torsvik V, Salte K, Sørheim R R et al (1990) Comparison of phenotypic diversity and DNA hererogeneity in a population of soil bacteria. Appl Environ Microbiol 56:776–781PubMedPubMedCentralGoogle Scholar
  35. Weisburg WG, Barns SM, Pelletier DA et al (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703CrossRefGoogle Scholar
  36. Xia Y, DeBolt S, Dreyer J et al (2015) Characterization of culturable bacterial endophytes and their capacity to promote plant growth from plants grown using organic or conventional practices. Front Plant Sci 6:1–10CrossRefGoogle Scholar
  37. Yang R, Liu P, Ye W (2017) Illumina-based analysis of endophytic bacterial diversity of tree peony (Paeonia Sect. Moutan) roots and leaves. Braz J Microbiol 48:695–705CrossRefGoogle Scholar

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

Personalised recommendations