Genome analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management

PLoS One. 2014 Aug 13;9(8):e104651. doi: 10.1371/journal.pone.0104651. eCollection 2014.


The Bacillus amyloliquefaciens subsp. plantarum strain UCMB5113 is a Gram-positive rhizobacterium that can colonize plant roots and stimulate plant growth and defense based on unknown mechanisms. This reinforcement of plants may provide protection to various forms of biotic and abiotic stress. To determine the genetic traits involved in the mechanism of plant-bacteria association, the genome sequence of UCMB5113 was obtained by assembling paired-end Illumina reads. The assembled chromosome of 3,889,532 bp was predicted to encode 3,656 proteins. Genes that potentially contribute to plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis and siderophore production were identified. Moreover, annotation identified putative genes responsible for non-ribosomal synthesis of secondary metabolites and genes supporting environment fitness of UCMB5113 including drug and metal resistance. A large number of genes encoding a diverse set of secretory proteins, enzymes of primary and secondary metabolism and carbohydrate active enzymes were found which reflect a high capacity to degrade various rhizosphere macromolecules. Additionally, many predicted membrane transporters provides the bacterium with efficient uptake capabilities of several nutrients. Although, UCMB5113 has the possibility to produce antibiotics and biosurfactants, the protective effect of plants to pathogens seems to be indirect and due to priming of plant induced systemic resistance. The availability of the genome enables identification of genes and their function underpinning beneficial interactions of UCMB5113 with plants.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / growth & development
  • Arabidopsis / microbiology*
  • Bacillus / genetics*
  • Bacterial Proteins / genetics*
  • Base Sequence
  • Biofilms / growth & development
  • Brassica napus / growth & development
  • Brassica napus / microbiology*
  • Cluster Analysis
  • Computational Biology
  • Genome, Bacterial / genetics*
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Phylogeny*
  • Plant Roots / microbiology*
  • Sequence Analysis, DNA
  • Species Specificity


  • Bacterial Proteins

Associated data

  • GENBANK/HG328254

Grant support

This work was supported by the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS), Carl Tryggers Stiftelse, Nilsson-Ehle Stiftelsen, Helge-Ax:son Johnsons Stiftelse, the Swedish University of Agricultural Sciences (SLU) and the Higher Education Commission of Pakistan (HEC). Funding for plant growth facilities were provided in part by KFI-VR. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.