Abstract
BackgroundBacteria 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.ResultsThe 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.ConclusionsThe 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.
Highlights
Bacteria belonging to the genus Novosphingobium are known to be metabolically versatile and occupy different ecological niches
This study reveals that the quorum sensing system that utilizes the acylhomoserine lactones (AHL) class of signals is not universally present in the genus Novosphingobium
General features of the sequenced Novosphingobium strains and their correlation with phylogenomic classification Tables 1 and 2 present the general and genomic features respectively of the strains used in this study
Summary
Bacteria belonging to the genus Novosphingobium are known to be metabolically versatile and occupy different ecological niches. Bacteria belonging to the genus Novosphingobium are often associated with the biodegradation of aromatic compounds such as phenol, aniline, nitrobenzene, 4-chlorobenzene, phenanthrene, pyrene, carbofuran, dibenzofuran and estrogen [2,3,4,5,6,7,8,9,10]. Given their extensive bioremediation properties these bacteria are frequently isolated from estuarine sediment, coastal sediment and marine aquatic environments that have been exposed to high level of anthropogenic activities. AP12 has been isolated from the rhizosphere of Populus deltoides as part of the initiatives to understand the metabolic interactions between plants and bacteria belonging to this genus [12]
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