Characterizing endophytic competence and plant growth promotion of bacterial endophytes inhabiting the seed endosphere of Rice

BMC Microbiol. 2017 Oct 26;17(1):209. doi: 10.1186/s12866-017-1117-0.


Background: Rice (Oryza sativa L. ssp. indica) seeds as plant microbiome present both an opportunity and a challenge to colonizing bacterial community living in close association with plants. Nevertheless, the roles and activities of bacterial endophytes remain largely unexplored and insights into plant-microbe interaction are compounded by its complexity. In this study, putative functions or physiological properties associated with bacterial endophytic nature were assessed. Also, endophytic roles in plant growth and germination that may allow them to be selectively chosen by plants were also studied.

Results: The cultivable seed endophytes were dominated by Proteobacteria particularly class Gammaproteobacteria. Highly identical type strains were isolated from the seed endosphere regardless of the rice host's physiological tolerance to salinity. Among the type strains, Flavobacterium sp., Microbacterium sp. and Xanthomonas sp. were isolated from the salt-sensitive and salt-tolerant cultivars. PCA-Biplot ordination also showed that specific type strains isolated from different rice cultivars have distinguishing similar characteristics. Flavobacterium sp. strains are phosphate solubilizers and indole-3-acetic acid producers with high tolerance to salinity and osmotic stress. Pseudomonas strains are characterized as high siderophore producers while Microbacterium sp. and Xanthomonas sp. strains have very high pectinase and cellulase activity. Among the physiological traits of the seed endophytes, bacterial pectinase and cellulase activity are positively correlated as well as salt and osmotic tolerance. Overall characterization shows that majority of the isolates could survive in 4-8% salt concentration as well as in 0.6 M and 1.2 M sucrose solution. The activities of catalase, pectinase and cellulase were also observed in almost all of the isolates indicating the importance of these characteristics for survival and colonization into the seed endosphere. Seed bacterial endophytes also showed promising plant growth promoting activities including hormone modulation, nitrogen fixation, siderophore production and phosphate solubilization.

Conclusion: Though many of the isolates possess similar PGP and endophytic physiological traits, this study shows some prominent and distinguishing traits among bacterial groups indicating key determinants for their success as endophytes in the rice seed endosphere. Rice seeds are also inhabited by bacterial endophytes that promote growth during early seedling development.

Keywords: Bacterial endophytes; Endophytic competence; Physiological characterization; Plant growth promotion; Rice seeds.

MeSH terms

  • Bacteria / classification
  • Bacteria / enzymology
  • Bacteria / isolation & purification*
  • DNA Fingerprinting
  • DNA, Bacterial / genetics
  • Endophytes / classification
  • Endophytes / enzymology
  • Endophytes / isolation & purification*
  • Endophytes / physiology*
  • Genetic Variation
  • Germination
  • Microbiota
  • Oryza / growth & development*
  • Oryza / microbiology
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Salinity
  • Seedlings / growth & development
  • Seedlings / microbiology
  • Seeds / growth & development*
  • Seeds / microbiology*


  • DNA, Bacterial
  • RNA, Ribosomal, 16S