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

World J Microbiol Biotechnol. 2019 Oct 31;35(11):176. doi: 10.1007/s11274-019-2754-2.


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: Endophytic bacteria; Locked nucleic acid; Metagenomics; Microbial community; Sweet potato.

MeSH terms

  • Bacteria / classification*
  • Bacteria / genetics
  • Bacteria / metabolism*
  • Base Sequence
  • Biodiversity
  • Climate*
  • DNA, Bacterial / analysis
  • DNA, Mitochondrial / analysis
  • Endophytes / classification*
  • Endophytes / genetics
  • Ipomoea batatas / microbiology*
  • Metagenome*
  • Microbiota* / genetics
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Soil / chemistry*
  • Soil Microbiology


  • DNA, Bacterial
  • DNA, Mitochondrial
  • RNA, Ribosomal, 16S
  • Soil