Rice Bacterial Endophytes: Isolation of a Collection, Identification of Beneficial Strains and Microbiome Analysis

Environ Microbiol Rep. 2016 Jun;8(3):388-98. doi: 10.1111/1758-2229.12403. Epub 2016 May 11.


Endophytes are harmless or beneficial microorganisms that live inside plants between cells. The relationship they develop with the plant as well as their potential role in plant health is at large unexplored and it is believed that the opportunity to find new and interesting endophytes among the large variety of plants is great. Here, we present the isolation and analysis of a large collection of endophytes from one cultivar of rice grown in Italy. A total 1318 putative endophytes were isolated from roots, leaves and stems from rice grown in submerged and dry conditions and a working collection of 229 isolates was created. Among these, several isolates were confirmed to be endophytes and a few displayed the trait of plant growth promotion. A cultivation independent analysis via 16S rDNA amplicons of the bacterial community of the endosphere was also performed providing information on bacterial diversity in the rice endopshere.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / classification*
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics
  • DNA, Ribosomal / chemistry
  • DNA, Ribosomal / genetics
  • Endophytes / classification*
  • Endophytes / genetics
  • Endophytes / isolation & purification*
  • Italy
  • Microbiota*
  • Oryza / microbiology*
  • Plant Leaves / microbiology
  • Plant Roots / microbiology
  • Plant Stems / microbiology
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA


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