Abstract
Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7 ± 19.1 and 36.5 ± 10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and ‘open’ state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.
Highlights
Devosia comprises a group of motile, gram-negative bacteria within the class Alphaproteobacteria and family Hyphomicrobiaceae[1]
The genomic repertoire adapted for utilization of organic sulfur, phosphorus and aromatic compounds are presumed to enable the members of the genus Devosia to survive in harsh sites
Genome analysis of twenty seven strains of the genus Devosia showed >96% completeness establishing the reliability of the datasets for comparative analyses
Summary
Devosia comprises a group of motile, gram-negative bacteria within the class Alphaproteobacteria and family Hyphomicrobiaceae[1]. Previous studies have aimed to characterize their metabolic routes of detoxification[20] In spite of their abundance in culture collections and public repositories, the genetic repertoire that enables them to survive in harsh environments have not been elucidated. The study revealed that the genomes harbor a large diversity of transporters involved in uptake of di- and oligo-peptides from the environment. These peptide transport systems enable bacteria to take up short peptides of different amino-acid composition for satisfying nutritional demands and have been extensively studied in species of Lactococcus and Staphylococcus[21,22]. The presence of toxin-antitoxin (TA) loci within their genomes provided evidence of enhanced genome plasticity for maintaining a wide range of biological functions including stress response
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
