In situ interrogation of microorganisms mediating hydrocarbon degradation

Abstract

Microbially mediated hydrocarbon biodegradation is a cornerstone of natural attenuation and engineered bioremediation, yet the in situ mechanisms and key microbial players remain incompletely resolved due to the historical reliance on cultivation-based approaches. Recent advances in cultivation-independent tools, particularly metagenomics, stable isotope probing (SIP), and single-cell techniques, now enable more effective identification of active microbial populations, their functional genes, and metabolic networks directly mediating hydrocarbon degradation in situ. These studies have unveiled a far greater phylogenetic and functional diversity than previously recognized, including the unexpected co-existence of alkane-oxidizing archaea and bacteria in similar environments. The underlying microbial actors exploit distinctive enzymes to initialize hydrocarbon oxidation under oxic and anoxic conditions and achieve complete degradation through complex ecological networks that involve cooperative and/or competitive interactions with other community members such as viruses. These findings offer better insights into the functioning of the microorganisms that control the fate of hydrocarbons in situ and, as a final outcome, help tailor bioremediation strategies for better performance.