Comparative Genomic Analysis of Six Bacteria Belonging to the Genus Novosphingobium: Insights Into Marine Adaptation, Cell-Cell Signaling and Bioremediation

BMC Genomics. 2013 Jun 28;14:431. doi: 10.1186/1471-2164-14-431.

Abstract

Background: Bacteria belonging to the genus Novosphingobium are known to be metabolically versatile and occupy different ecological niches. In the absence of genomic data and/or analysis, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. In this study, we analyzed the whole genome sequencing data of six bacteria in the Novosphingobium genus and provide evidence to show the presence of genes that are associated with salt tolerance, cell-cell signaling and aromatic compound biodegradation phenotypes. Additionally, we show the taxonomic relationship between the sequenced bacteria based on phylogenomic analysis, average amino acid identity (AAI) and genomic signatures.

Results: The taxonomic clustering of Novosphingobium strains is generally influenced by their isolation source. AAI and genomic signature provide strong support the classification of Novosphingobium sp. PP1Y as Novosphingobium pentaromaticivorans PP1Y. The identification and subsequent functional annotation of the unique core genome in the marine Novosphingobium bacteria show that ectoine synthesis may be the main contributing factor in salt water adaptation. Genes coding for the synthesis and receptor of the cell-cell signaling molecules, of the N-acyl-homoserine lactones (AHL) class are identified. Notably, a solo luxR homolog was found in strain PP1Y that may have been recently acquired via horizontal gene transfer as evident by the presence of multiple mobile elements upstream of the gene. Additionally, phylogenetic tree analysis and sequence comparison with functionally validated aromatic ring hydroxylating dioxygenases (ARDO) revealed the presence of several ARDOs (oxygenase) in Novosphingobium bacteria with the majority of them belonging to the Groups II and III of the enzyme.

Conclusions: The combination of prior knowledge on the distinctive phenotypes of Novosphingobium strains and meta-analysis of their whole genomes enables the identification of several genes that are relevant in industrial applications and bioremediation. The results from such targeted but comprehensive comparative genomics analysis have the potential to contribute to the understanding of adaptation, cell-cell communication and bioremediation properties of bacteria belonging to the genus Novosphingobium.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adaptation, Physiological / drug effects
  • Adaptation, Physiological / genetics*
  • Alphaproteobacteria / classification
  • Alphaproteobacteria / cytology*
  • Alphaproteobacteria / genetics
  • Alphaproteobacteria / physiology*
  • Amino Acid Sequence
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Biodegradation, Environmental
  • Conserved Sequence
  • Dioxygenases / genetics
  • Gene Transfer, Horizontal / genetics
  • Genes, Bacterial / genetics
  • Genomics*
  • Molecular Sequence Data
  • Oceans and Seas*
  • Phenotype
  • Phylogeny
  • Quorum Sensing / genetics
  • Salts / pharmacology
  • Sequence Homology, Nucleic Acid
  • Signal Transduction / genetics*
  • Species Specificity

Substances

  • Bacterial Proteins
  • Salts
  • Dioxygenases