Complete genome sequence analysis of Pseudomonas aeruginosa N002 reveals its genetic adaptation for crude oil degradation

Abstract

The present research work reports the whole genome sequence analysis of Pseudomonas aeruginosa strain N002 isolated from crude oil contaminated soil of Assam, India having high crude oil degradation ability. The whole genome of the strain N002 was sequenced by shotgun sequencing using Ion Torrent method and complete genome sequence analysis was done. It was found that the strain N002 revealed versatility for degradation, emulsification and metabolizing of crude oil. Analysis of cluster of orthologous group (COG) revealed that N002 has significantly higher gene abundance for cell motility, lipid transport and metabolism, intracellular trafficking, secretion and vesicular transport, secondary metabolite biosynthesis, transport and catabolism, signal transduction mechanism and transcription than average levels found in other genome sequences of the same bacterial species. However, lower gene abundance for carbohydrate transport and metabolism, replication, recombination and repair, translation, ribosomal structure, biogenesis was observed in N002 than average levels of other bacterial species.

Biological Treatment of Synthetic Oilfield-Produced Water in Activated Sludge Using a Consortium of Endogenous Bacteria Isolated from A Tropical Area

“…Furthermore, it is well known that these strains can synthesize bioemulsifiers, which can enhance the bioavailability of hydrocarbon as a carbon source [26,27]. Strains that have genes involved in bioemulsifier synthesis and regulation are versatile for the degradation, emulsification, and metabolizing of hydrocarbons [28].…”

Complete genome sequence of a versatile hydrocarbon degrader, Pseudomonas aeruginosa DN1 isolated from petroleum-contaminated soil

“…Subsequently, protocatechuic acid and catechol are degraded by ortho-cleavage and meta-cleavage pathways, respectively (Mishra et al, 2014). Across the genome of the strain DN1, plenty of genes and gene clusters could contribute to the degradation of aromatic compounds, such as catA (catechol 1, 2 dioxygenase, orf02054), pcaG (protocatechuate 3,4-dioxygenase subunit beta, orf00224) and pcaH (protocatechuate 3,4-dioxygenase alpha subunit, or f00226) (Mishra et al, 2014), homogentisate 1,2-dioxygenase (hmgA, orf01281), 2,4′-dihydroxyacetophenone dioxygenase (dad, orf04509), homoprotocatechuate 2,3-dioxygenase (hpcB, orf04547), benzoate/toluate 1,2-dioxygenase (orf01400, orf02068, orf02070, orf02071), gentisate 1,2-dioxygenase (orf01281, orf02001, orf06111), 4-hydroxyphenylpyruvate dioxygenase (orf06272), 4-hydroxyphenylacetate 3-monooxygenase(hpaA, hpaC, orf04505, orf04506), 4-hydroxybenzoate 3-monooxygenase (pobA, orf00357) (Gibson and Parales, 2000;Cao et al, 2015;Das et al, 2015). Moreover, many other genes were predicted to encode other enzymes involving in degradation of alkane and alkene, such as alkane 1-monooxygenase (alkB1, alkB2, orf02163, orf05286), polyhydroxyalkanoate synthesis protein (phaF, orf07819), 2-oxo-hepta-3-ene-1,7-dioic cid hydratase (hpcG, orf04550), 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (hpaI, orf04551), 2-nitropropane dioxygenase (orf06032) (Smits et al, 2002;Beilen et al, 2003;Hamme et al, 2003;Beilen and Funhoff, 2007 degradation of alkane, alkene and aromatic compounds were identified in genome of strain DN1 with comparative genomic analysis of other bacterial genome from NCBI database (Table 2).…”

Genome annotation of Poly(lactic acid) degradingPseudomonas aeruginosaandSphingobacterium sp.

“…Both Sphingobacterium sp . and P. aeruginosa had been documented before to have a role in the degradation of different environmental pollutants such as mixed plastic waste, PAHs, oil, and dyes and pesticides, P. aeruginosa has also been reported to have potential to degrade PLA nano-composites [19, 26, 28, 91, 92]. In our previous study we characterized the degradation of PLA by our isolates [12].…”