Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants of environmental concern. Bioremediation, relying on stimulation of natural microbial degradation processes, is a well-established technology to clean up PAH-contaminated soils. However, bioremediation does not necessarily lead to a reduction in soil toxicity. PAH-contaminated sites are affected by extremely complex mixtures, like coal tar or creosote, and biotransformation products or co-occurring compounds can also contribute to the overall toxicological effects of contaminated soil before and after bioremediation. Therefore, the objective of this dissertation was to use non-target analysis workflows to identify the genotoxic transformation products, important co-occurring pollutants, and the unrecognized biotransformation pathways that could contribute to explain the toxicological effects observed beyond parent PAHs.

To identify the source(s) of increased genotoxicity in bioremediated soil, we pursued a non-target analytical approach combining effect-directed analysis (EDA) and metabolite profiling to compare extracts of PAH-contaminated soil before and after bioremediation. A compound with the composition C 15H8O2 and four methylated homologues were shown to accumulate as a result of bioreactor treatment, and the C15H 8O2 compound was determined to be genotoxic. Its structure was established as a heretofore unidentified alpha,beta-unsaturated lactone, 2H-naphtho[2,1,8-def ]chromen-2-one (NCO), which was confirmed by synthesis. It also accumulated in aerobically incubated soil from two additional PAH-contaminated sites and was formed from pyrene by two pyrene-degrading bacterial cultures known to be geographically widespread, underscoring its potential environmental significance.

Azaarenes are nitrogen heterocyclic polyaromatic compounds that co-occur with PAHs but have been poorly studied in environmental systems. High resolution mass spectrometry (HRMS) and mass-defect filtering were applied to four PAH-contaminated samples to analyze the their diversity, abundance, and biodegradation behavior. The diversity, relatively high concentrations, and persistence of high-molecular-weight azaarenes were highlighted, and isomer-selective biodegradation was observed.

To help elucidate PAH biodegradation pathways and endpoints in contaminated soil, HRMS and stable isotope-assisted metabolomics (SIAM) workflows were tested and applied to a PAH-contaminated soil. Uniformly 13C-labeled fluoranthene, pyrene, or benzo[a]anthracene were spiked into the soil and incubated in microcosms. With SIAM, known and unknown metabolites such as ring-cleavage products and conjugates were detected, and the transformation pathways leading to their formation proposed.