Hydrocarbon Degradation Potential in Free-Living and Micro-Aggregate Bacterial Structures in the Waters of the Gulf of Mexico

Abstract

Crude oil is a heterogenous complex mixture composed of hydrocarbons with different structures, bioavailability, and chemical properties. Due to the various components of crude oil, it is crucial to understand how and when hydrocarbon-degrading microbial communities respond to each crude oil component during degradation. Here, I used culture-independent DNA analytical approaches to monitor structural and functional changes in natural marine microbial communities from northwest Gulf of Mexico over weeks to months after exposure to added oil and chemically dispersed oil in two different experiments, one using mesopelagic waters and the other using coastal surface waters. The first experiment, described in Chapter II, is an investigation of the impact of crude oil or dispersed oil exposure in different concentrations on mesopelagic microbial community abundance and composition as examined via microscopy and 16S rRNA amplicon analysis and biodegradation of oil, assessed via hydrocarbon chemistry. The second experiment, presented in Chapters III and IV, simulated an oil spill in coastal waters. Metagenomics was used to determine taxonomic and functional profiles of free-living and oil-droplet associated (BOMA) microbial communities analyzed based on comparing their Metagenome-Assembled Genomes (MAGs). The work presented in Chapter II showed that the concentration of spilled oil substantially affects the microbial response more than the presence of dispersant - higher concentrations of oil, regardless of the presence of dispersant, resulted in higher concentrations of BOMA and similar microbial communities. In addition, the relative abundance of the most abundant putative hydrocarbon degrader detected, Marinobacter, was not influenced by dispersant when oil was present. Data in Chapter III showed that the selective pressure of hydrocarbons led to the enrichment of certain species that are metabolically adapted to hydrocarbon degradation, shifting the microbial communities into more specialized taxa, and changing the overall community structure, which offers more niches to occupy. The microbial community structure of free-living and BOMA size fractions was different, especially between control and Oiled treatments. At the end of the experiment, overall reduced biodiversity was observed, which indicates enhanced hydrocarbon degradation. In Chapter IV, the results suggested that BOMA contains exclusive genes that weren’t detected in Free-living Oiled microbial communities. This includes genes encoding chemotaxis and heavy metal transport, suggesting that the microorganisms living in micro-aggregate communities appear to be more specialized. While genes involved in aromatic hydrocarbon degradation pathways were detected more frequently in free-living microbial metagenomes, indicating that the Free-living fraction is more proficient in overall hydrocarbon degradation.