Unraveling Functional Dynamics in Synthetic Bacterial Consortia: A Metaproteomic Analysis of Complex Waste Oil Biodegradation

This thesis investigated the functional dynamics of synthetic oil-degrading bacterial consortia using a metaproteomic approach. Consortia were enriched from petroleum-contaminated soil at RAF Brize Norton using a complex mixture of industrial waste oils as the sole carbon source. Metagenomic analysis of the enriched consortia (BPS4 and BPS8) identified the predominance of Stenotrophomonas maltophilia, with BPS4 exhibiting greater diversity, including key hydrocarbon degraders such as Pseudomonas fluorescens and Delftia acidovorans. Compositional analysis of the waste oils revealed aromatics, polyaromatics, n-alkanes, and organophosphates. Bottom-up metaproteomics focused on BPS4 resolved taxonomic restructuring and functional shifts under oil exposure. Quantitative label-free analysis showed increased abundance of Delftia and Achromobacter proteins, highlighting their selective advantage under contaminant stress. Enzymatic mapping revealed significant enrichment in aliphatic and aromatic degradation pathways, with metabolic routing through catechol intermediates to the TCA cycle. This was supported by increased fold changes in oxidoreductases, dehydrogenases, and β-oxidation enzymes. Gene ontology enrichment demonstrated heightened nitrogen cycling, suggesting an adaptive response to hydrocarbon mineralisation. Artificial selection via in vitro batch-fed adaptation provided limited enhancement for recalcitrant fractions, such as branched aliphatics and organophosphates, indicating intrinsic metabolic limits. However, metaproteomic insights identified pathways for alternative energy acquisition that stabilise communities under stress. While top-down enrichment yields robust hydrocarbon degraders, further functional adaptation may require engineered strains or alternative protocols. Overall, this work demonstrates how metaproteomics can unravel the intricate metabolic and ecological mechanisms of waste oil biodegradation, providing a foundation for ecological engineering strategies.