| Summary: | A slightly and two severely biodegraded crude oils with the same origin were analysed using negative-ion electrospray ionization Orbitrap mass spectrometry (ESI Orbitrap MS), gas chromatography-nitrogen chemiluminescence detector (GC-NCD), and GC-sulfur chemiluminescence detector (GC-SCD) to investigate the composition of heteroatomic compounds and their fate during severe biodegradation and to provide insights into biodegradation pathway of hopanes, nitrogen- and sulfur-containing compounds. Twelve heteroatomic compound classes, including O<sub>1</sub>–O<sub>5</sub>, N<sub>1</sub>, N<sub>2</sub>, N<sub>1</sub>O<sub>1</sub>–N<sub>1</sub>O<sub>3</sub>, N<sub>1</sub>S<sub>1</sub> and O<sub>3</sub>S<sub>1</sub>, were detected and assigned unambiguous molecular formulae. The O<sub>1</sub> species are likely phenols with additional naphthenic and/or aromatic rings. Carboxylic acids (O<sub>2</sub> species) are originated from oxidation of hydrocarbons, and the tricyclic naphthenic acids are the most resistant, followed by bicyclics. Hopanes could be biodegraded by demethylation or by unstable hopanoic acids as intermediates to yield 25-norhopanes. The N<sub>1</sub> species are pyrrolic compounds with naphthenic and/or aromatic rings and are dominated by carbazole analogues. Carbazoles with more aromatic rings are more resistant to biodegradation. The N<sub>1</sub> species could be converted to N<sub>1</sub>O<sub>1</sub> and N<sub>1</sub>O<sub>2</sub> compounds via ring-opening and hydroxylation pathways. The N<sub>1</sub>S<sub>1</sub> species contain a pyrrolic and cyclic sulfide structure, which are highly recalcitrant to biodegradation. Benzothiophenes and dibenzothiophenes might be biodegraded via the complete pathway or the sulfur-specific pathway rather than by other pathways to yield acidic oxygenated sulfur compounds.
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