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

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-acylhomoserine 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.

Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics

“…This phylogenomic tree showed that three strains isolated from the copper mine (namely, ZJ, DX, and ZBY) were clustered together (group 2 in Figure 2 ). Similarly, an earlier study reported that taxonomic clustering of six strains belonging to the genus Novosphingobium was generally influenced by their respective source of isolation (Gan et al, 2013). Further inspection revealed that the geographic distribution of strain ZBY was distinctively differed from those of the other two strains (ZJ and DX), and the genome-content-based distance matrix implied a slight evolutionary divergence ( Figure 2 ).…”

Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes

“…This broad range of genome sizes is reflected in the diversity of gene repertoires: only a tiny minority of prokaryotic genes are (nearly) universal whereas the great majority are present in small subsets of genomes [6,10,11]. Substantial differences in genome size and gene content are often evident between species within the same genus [12][13][14] and even between strains of the same species [15][16][17].…”

Hydrolyzed Organic Fish Fertilizer and Poultry Litter Influence Yield and Rhizosphere Ecology of Sweetpotato

“…Statistical significance from analysis of variance of fertilizer amendments, cultivar and fertilizer amendments · cultivar interaction for soil pH, organic carbon, and enzyme activities. recently, this group has been discovered in plant-associated habitats such as the internal stem of Gossypium hirsutum (K€ ampfer et al, 2015), the rhizosphere of Arabidopsis thaliana (Gan et al, 2013), and surface of a crown gall tumor on grapevine (Lin et al, 2014). One suggestion for Novosphingobium association with plants in the rhizosphere is the presence of xenobiotic aromatic compounds.…”