Pan‐Genomic and Phenotypic Characterisation of Petroleum Hydrocarbon Degradation by Pseudomonas Species

TL;DR

This study explores how different Pseudomonas bacteria break down petroleum hydrocarbons by analyzing their genomes and finding key genes involved in the process.

Contribution

The study introduces a genus-level pan-genomic analysis of Pseudomonas to reveal complementary degradation pathways for bioremediation.

Findings

Pseudomonas strains like P. citronellolis and P. putida have the highest abundance of genes related to petroleum hydrocarbon degradation.

Degradation-related genes are concentrated in the accessory genome, indicating metabolic specialization and potential synergistic interactions.

P. aeruginosa, P. luteola, and P. putida show broader genetic access to PAH degradation pathways.

Abstract

Pseudomonas, a cornerstone genus in petroleum hydrocarbon bioremediation, exhibits remarkable metabolic diversity. To systematically decipher the genetic basis of this trait, we constructed a curated collection of representative Pseudomonas strains with documented degradation capabilities through a bibliometrics‐driven approach. Comparative genomic analysis revealed that these strains possess a rich repertoire of genes linked to petroleum hydrocarbon degradation, including those encoding key enzymes such as monooxygenases, dioxygenases, alcohol dehydrogenases, cytochrome P450, ferredoxins, and regulatory proteins (e.g., LuxR, AraC, GntR). Among the strains examined,
P. citronellolis
and
P. putida
contained the highest abundance of such genes. The accessory genome size varied considerably across the 15 strains (ranging from 3290 to 5745 genes), and functional enrichment analysis indicated a significant concentration of degradation‐related genes within this component. This genomic architecture not only reflects distinct metabolic specialisations among species but also implies potential synergistic interactions, as suggested by the broader genetic accessibility to polycyclic aromatic hydrocarbon (PAH) degradation pathways observed in
P. aeruginosa, P. luteola
, and
P. putida
. Overall, this study establishes a robust genomic framework that extends beyond single‐species analysis, offering a genus‐level perspective essential for designing tailored, high‐efficiency microbial consortia for targeted bioremediation strategies.

Pseudomonas is one of the most significant bacterial genus involved in the petroleum hydrocarbon bioremediation. Innovatively, through pan‐genomic analysis at the genus level, we found that different Pseudomonas strains have excellent complementarity at the nodes of the degradation pathway of petroleum hydrocarbons.

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