Unveiling the Hydrocarbon-Degrading Potential of Bacillus Cereus BY-16: A Multi-Omics, Proteomics and Biogenic Nanoparticle Profiling-Driven Investigation

Petroleum hydrocarbon contamination poses a serious threat to environment and public health due to the persistence of toxic compounds like alkanes, aromatics, and polycyclic aromatic hydrocarbons (PAHs). This research explores isolation and detailed characterization of a novel hydrocarbon-degrading bacterium, Bacillus cereus BY-16, from petroleum-contaminated soil. Among five isolates, BY-16 demonstrated highest hydrocarbon utilization on Bushnell Haas Agar amended with 1% petrol, confirmed through modified DCPIP assays. Unique feature of this study is the integrated application of multi-omics, proteomics and advanced spectroscopic tools. GC-MS and FTIR confirmed the efficient degradation of 105 hydrocarbon compounds into only 29 less-toxic intermediates (e.g., phenol, ethanol, butanoic acid, dihydroxybenzaldehyde and agaricic acid) within 20 days. Raman spectral analysis revealed that BY-16 co-expresses multiple metabolite classes—biosurfactants, siderophores, phenazines, and peptide antibiotics—within the same system. Complementary XRD data identified biogenic FeTiO₃, TiO₂, and chromite nanoparticles, marking the first report of their microbial formation. These nanomaterials, along with biosurfactants, likely enhanced hydrocarbon bioavailability, detoxification, and emulsification. Proteomic profiling (LC-MS/MS) revealed 241 hydrocarbon-responsive proteins, including alkane monooxygenases, cytochrome P450s, ABC transporters, and efflux pumps, showcasing the strain’s metabolic and adaptive versatility. FESEM, EDS and HRTEM analyses further demonstrated biofilm formation, intracellular adaptation, and elemental responses under hydrocarbon stress. This study highlights B. cereus BY-16 as a highly adaptable, nanoparticle-synthesizing bacterium with robust hydrocarbon degradation potential, offering a powerful biological tool for eco-friendly bioremediation of petroleum-contaminated environments. Further experiments in the current study validated the performance of strain BY-16 under field conditions using petroleum contaminated soil.