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Open Access Research article

Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation

Han Ming Gan15, André O Hudson2, Ahmad Yamin Abdul Rahman3, Kok Gan Chan4 and Michael A Savka2*

Author Affiliations

1 Science Vision SB, Shah Alam, Selangor, Malaysia

2 The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology (RIT), Rochester, New York, USA

3 Bio Easy SB, Shah Alam, Selangor, Malaysia

4 Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaysia, 50603 Kuala Lumpur, Malaysia

5 School of Science, Monash University, Sunway Campus, Bandar Sunway, Selangor, Malaysia

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BMC Genomics 2013, 14:431  doi:10.1186/1471-2164-14-431

Published: 28 June 2013

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.

Keywords:
Novosphingobium; Marine adaptation genes; Quorum sensing; Aromatic ring hydroxylating dioxygenase