Integrated strain isolation, comparative genomics, and microbial community analysis reveal metabolic versatility and adaptive strategies of facultative anaerobic PAH-degrading Pseudomonas

Abstract

Remediation of PAH-contaminated soils is often limited by oxygen delivery, highlighting the importance of organisms that maintain PAH degradation under anoxic conditions. We isolated three Pseudomonas/Stutzerimonas strains on pyrene with nitrate as electron acceptor and confirmed their rapid nitrate-reducing removal of phenanthrene (up to ~90% in 4 d) and benzo[a]pyrene (up to ~95% in 5 d), expanding pure-culture evidence for high-molecular-weight PAH degradation under nitrate respiration. Combined with six previously reported facultative anaerobic PAH-degrading Pseudomonas strains, we analyzed nine genomes representing the presently verifiable phenotype-defined subset. Comparative genomics showed an accessory-dominated pan-genome with a strict core (0.07% of 30101 orthogroups), coexistence of diverse aerobic ring-hydroxylation and anaerobic-associated activation (including carboxylation- and methylation- related) genes. Notably, stress resistance genes were present at significantly elevated copy numbers compared to other genes, reflecting adaptive genomic plasticity. The finding that Pseudomonas was the only genus consistently detected across all 17 petroleum-contaminated soils aligns well with the metabolic flexibility and stress-tolerance potential revealed by our phenotypic and genomic analyses. These findings provide a genomic and ecological framework for understanding facultative anaerobic PAH-degrading Pseudomonas strains and support their application in complex, contaminated environments.

Graphical abstract

Keywords

Pseudomonas / Facultative anaerobic bacteria / PAH degradation / Comparative genomics analysis / Environmental adaptability / Bioremediation

Highlight

	● Three new strains removed ~90% phenanthrene and ~95% BaP with sole nitrate.
	● Aerobic and anaerobic associated PAH-degrading genes co-occur with redundancy.
	● Stress adaptation genes show significantly elevated copy numbers.
	● Pseudomonas is the only genus detected in all 17 petroleum-contaminated soils.

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