Fishing out microorganisms for bioremediation using metagenomics: Isolation and whole-genome sequencing of the metabolically versatile Rhodococcus erythropolis LP27217 strain from oil spill lake

Abstract

Isolating microorganisms from oil spill-contaminated environments is essential for advancing bioremediation strategies and discovering novel bioprocesses for hydrocarbon degradation. In this study, we report the isolation of a novel strain, Rhodococcus erythropolis LP27217, from Pertusillo Lake (Italy) on february 2017. Water samples were collected during an oil spill event and microbial community was previously characterized using 16S rRNA gene-targeted metagenomic analysis and functional prediction. The Rhodococcus genus was identified as the dominant member of this microbiome, and functional predictive analyses guided the isolation of the R. erythropolis LP27217 strain under various growth conditions, including the presence of hydrocarbons and in Liquid Microbial Fuel Cell (L-MFC) systems. This strain exhibits a versatile hydrocarbon-degrading and transforming metabolism, effectively addressing pollutants such as crude oil, polycyclic aromatic hydrocarbons (PAHs), and dibenzothiophene (DBT), even under psychrophilic conditions. Additionally, R. erythropolis LP27217 demonstrated the ability to produce lipopeptide biosurfactants and lipophilic polymers, with the latter being associated with the formation of an electrogenic hydrocarbonoclastic biofilm at the anoxic oil-water interface. Overall, this study demonstrated that R. erythropolis LP27217 is a promising candidate for sustainable applications, including in situ bioremediation of oil spills in lake ecosystems and the biosynthesis of innovative polymers and biosurfactants for biotechnological and environmental purposes. Furthermore, its ability to operate across oxic and hypoxic conditions, at the oil-water interface and within the water column, highlights a novel microbial mechanism with significant ecological and industrial potential.

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Identifiers

DOI

10.1016/j.jhazmat.2025.139463

PubMed

40795730

Journal

Journal of Hazardous Materials

Year

2025