Whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut

PLoS One. 2014 Aug 27;9(8):e104259. doi: 10.1371/journal.pone.0104259. eCollection 2014.


Coconut, cocoa and arecanut are commercial plantation crops that play a vital role in the Indian economy while sustaining the livelihood of more than 10 million Indians. According to 2012 Food and Agricultural organization's report, India is the third largest producer of coconut and it dominates the production of arecanut worldwide. In this study, three Plant Growth Promoting Rhizobacteria (PGPR) from coconut (CPCRI-1), cocoa (CPCRI-2) and arecanut (CPCRI-3) characterized for the PGP activities have been sequenced. The draft genome sizes were 4.7 Mb (56% GC), 5.9 Mb (63.6% GC) and 5.1 Mb (54.8% GB) for CPCRI-1, CPCRI-2, CPCRI-3, respectively. These genomes encoded 4056 (CPCRI-1), 4637 (CPCRI-2) and 4286 (CPCRI-3) protein-coding genes. Phylogenetic analysis revealed that both CPCRI-1 and CPCRI-3 belonged to Enterobacteriaceae family, while, CPCRI-2 was a Pseudomonadaceae family member. Functional annotation of the genes predicted that all three bacteria encoded genes needed for mineral phosphate solubilization, siderophores, acetoin, butanediol, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, chitinase, phenazine, 4-hydroxybenzoate, trehalose and quorum sensing molecules supportive of the plant growth promoting traits observed in the course of their isolation and characterization. Additionally, in all the three CPCRI PGPRs, we identified genes involved in synthesis of hydrogen sulfide (H2S), which recently has been proposed to aid plant growth. The PGPRs also carried genes for central carbohydrate metabolism indicating that the bacteria can efficiently utilize the root exudates and other organic materials as energy source. Genes for production of peroxidases, catalases and superoxide dismutases that confer resistance to oxidative stresses in plants were identified. Besides these, genes for heat shock tolerance, cold shock tolerance and glycine-betaine production that enable bacteria to survive abiotic stress were also identified.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antioxidants / metabolism
  • Areca / growth & development
  • Areca / metabolism
  • Areca / microbiology
  • Cacao / growth & development
  • Cacao / metabolism
  • Cacao / microbiology
  • Cocos / growth & development
  • Cocos / metabolism
  • Cocos / microbiology
  • Crops, Agricultural / growth & development
  • Crops, Agricultural / metabolism
  • Crops, Agricultural / microbiology*
  • Enterobacteriaceae / genetics
  • Enterobacteriaceae / metabolism*
  • Genome, Bacterial*
  • Hydrogen Sulfide / metabolism
  • Metabolic Networks and Pathways / genetics
  • Metabolome / genetics
  • Molecular Sequence Annotation
  • Plant Growth Regulators / biosynthesis*
  • Plant Growth Regulators / genetics
  • Plant Roots / growth & development
  • Plant Roots / metabolism
  • Plant Roots / microbiology*
  • Pseudomonadaceae / genetics
  • Pseudomonadaceae / metabolism*
  • Rhizobiaceae / genetics
  • Rhizobiaceae / metabolism*
  • Rhizosphere
  • Sequence Analysis, DNA
  • Symbiosis


  • Antioxidants
  • Plant Growth Regulators
  • Hydrogen Sulfide

Grant support

The study was internally funded by SciGenom Labs Pvt Ltd. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.