Evidence for the microbial metabolism of hydrocarbons is routinely identified in diverse habitats, but particularly those associated with the production, processing, storage and use of petroleum. In these environments, microbial activity can have enormous environmental and financial consequences including oil reservoir souring, biocorrosion of the steel infrastructure, and the accidental release of hydrocarbons to undesired locations. My studies were designed to specifically examine the ecological role of microorganisms in a major oil processing facility experiencing aggressive corrosion, in seawater compensated fuel ballast tanks aboard naval surface warfare vessels and to contribute to fundamental knowledge on how anaerobic microbes are able to metabolize large molecular weight paraffin molecules. An interdisciplinary approach that combined geochemical analyses, molecular microbial ecology methods, and mass spectral-based metabolomics was employed in each of these investigations. Molecular surveys of the oil processing facility revealed a systemic colonization of both dead-leg and bulk fluids by anaerobic taxa primarily affiliated with Halanaerobiales. A desalter bulk fluid was a notable exception with members of the Epsilonproteobacteria, putative microaerophiles, representing the predominant community members. Geochemical and mass spectral analyses showed steep gradients in salinity, pH, acetate and sulfate concentrations, as well as distinct low molecular weight organic constituent profiles within stratified dead-leg fluids. These gradients contrasted with the highly similar chemical properties observed in the bulk fluids that are often recirculated between the three processing modules. The presence of alkylated monoaromatic-dihydrodiols and Epsilonproetobacteria in the desalter bulk fluid, and the lack of signature anaerobic hydrocarbon biodegradation metabolites confirms that oxygen must be introduced to the resident microflora, most likely at or near the desalter unit. The findings further suggest that anaerobic microbial communities exacerbate localized corrosion by linking the metabolism of partially oxidized aerobic crude oil intermediates from the desalter module to the reduction of oxidized sulfur species. Only by examining both the dead-legs and the bulk fluids was it possible to identify the distinct microbial assemblages across small spatial distances within each module and understand their interactions that ultimately form the basis of the proposed mechanism for microbially-influenced corrosion within this facility. The selection of hydrocarbonoclastic marine microorganisms under defined ecological conditions was also pertinent to the investigation of seawater-compensated fuel ballast tanks relative to the harbor water used to augment the tanks. The examination of ships containing ballast water of different ages, revealed a pattern of succession that ranged from predominantly aerobic to largely anaerobic microbial taxa with a concomitant decrease in available dissolved oxygen and sulfate reserves. Mass spectral analysis showed the presence of signature metabolites associated with the aerobic or anaerobic activation of mono- and polynuclear aromatic hydrocarbons within the ballast tanks of ships that retained their ballast for 1 week and 32 weeks, respectively. The presence of supersaturating concentrations of dissolved alloying metals in all of the samples, along with paired metagenomic and metabolomic data, revealed that marine microorganisms typically catalyzed the biodegradation of diesel fuel components and exacerbated the biocorrosion of the carbon steel infrastructure within seawater-compensated fuel ballast tanks aboard naval vessels. While there are thousands of chemicals in petroleum mixtures, the way individual components are metabolized in the absence of oxygen is often enigmatic. Such is the case for large molecular weight alkane molecules that are solid at room temperatures. An anaerobic microbial consortium capable of the methanogenic mineralization of long-chain n-paraffins (C28-C50) was investigated using a combined metagenomic and targeted transcriptomic analyses. Experiments were desgined to determine the mechanism(s) of paraffin activation under anaerobic conditions and to elucidate the type of interactions occurring between consortial members. Several draft genomes were binned and assembled from members of the predominant orders Syntrophobacterales and Methanomicrobiales. Five genotypes of alkylsuccinate synthase A were identified within the metagenome and transcription of each was observed during cultivation of the consortium in the presence of n-octacosane as a model substrate. Based on the metabolic reconstruction of the numerically dominant draft genomes, it was proposed that high molecular weight paraffins are activated by addition to fumarate by “Smithella sp. SDB” and fermented to acetate through a syntrophic interaction with hydrogenotrophic methanogens. The subsequent mineralization of acetate was proposed to occur via syntrophic acetate oxidation and/or acetoclastic methanogenesis based on additional recovered draft genomes. This is the first report to elucidate the metabolic pathway for such a high molecular weight hydrocarbon and it biochemically implicates a Smithella as the responsible organism initiating the anaerobic attack. The surveillance of the chemical and biological components of artificial habitats associated with petroleum production and consumption revealed that the dynamics of the resident microbial assemblages were governed by the same principles documented in other natural habitats. More specifically, hydrocarbons are susceptible to biological deterioration by the resident microorganisms when in contact with marine waters under both oxic and anoxic conditions. Distinct micro-environments arise across sometimes small spatial scales within artificial habitats and ultimately select for communities of microorganisms that vary widely in membership and/or metabolic capability. These communities can interact with others through connections based on fluid movement associated with industrial processes and the resulting effects of their activities can be manifested locally or distributed throughout the system. The nature of these effects can largely be assessed a priori by examining the dominant electron-accepting processes occurring within each distinct micro-habitat. Ultimately, paired-“omics” investigations can help elucidate contributions of specific taxa to environmental processes and services occurring within such engineered systems.