Anaerobic pyrene biodegradation coupled to nitrate reduction by a Paracoccus versutus strain PYRN-PV

The investigation of anaerobic pyrene biodegradation by nitrate-reducing microorganisms, particularly the identification of responsible species and elucidation of associated metabolic pathways, had remained in its nascent stages. In this study, a nitrate-reducing bacterium, designated strain PYRN-PV, was identified, which showed the closest phylogenetic relationship to Paracoccus versutus. This strain was newly found to biodegrade 99.6 % of pyrene within 20 days while simultaneously reducing nitrate to nitrogen gas. Through comprehensive metabolite and isotopic-metabolite analyses, coupled with genomic and RT‒qPCR analyses, the metabolic pathways involved in anaerobic pyrene biodegradation by strain PYRN-PV were elucidated. Pyrene was initially activated through carboxylation and methylation, yielding pyrene-2-carboxylic acid and 2-methylpyrene, respectively. Notably, the methylation step was proposed as a novel mechanism for anaerobic pyrene biodegradation. Subsequently, 2-methylpyrene was transformed to pyrene-2-carboxylic acid through direct oxidation. CoA ligation and ring reduction through hydrogenation were identified as midstream steps. Finally, ring cracking to produce substituent benzene, ring reduction to produce substituent cyclohexanone, and ring cleavage and mineralization to produce short-chain fatty acids and carbon dioxide were identified as downstream steps. Additionally, strain PYRN-PV was capable of utilizing other aromatic hydrocarbons, including benzene, naphthalene, anthracene, phenanthrene, and benz[a]anthracene, as carbon sources, achieving over 99 % degradation efficiency. This study provided valuable insights into the mechanisms underlying anaerobic pyrene biodegradation under nitrate-reducing conditions and offered practical guidance for the bioremediation of polycyclic aromatic hydrocarbon contaminants in anaerobic environments.