GEOCHEMICAL AND METAGENOMIC INVESTIGATION OF MARINE HYDROCARBON BIODEGRADATION

Restricted (Penn State Only)
Author:
Nguyen, Uyen T
Graduate Program:
Geosciences
Degree:
Doctor of Philosophy
Document Type:
Dissertation
Date of Defense:
October 01, 2018
Committee Members:
  • Jennifer Macalady, Dissertation Advisor
  • Jennifer Macalady, Committee Chair
  • Katherine Haines Freeman, Committee Member
  • James Kubicki, Committee Member
  • Ming Tien, Outside Member
  • Sara Ann Lincoln, Committee Member
Keywords:
  • oil biodegradation
  • high pressure
  • gulf of mexico
  • deepwater horizon
  • hydrocarbon-degrading genes
  • coal biodegradation
Abstract:
Hydrocarbon degraders have been long suggested to be ubiquitous in the ocean and keep marine ecosystems intact from the vast volume of petroleum hydrocarbons from both natural and anthropogenic sources entering the ocean annually. They also provide significant bioremediation application wherein they help reduce the concentration and toxicity of chemical pollutants, specifically petroleum, by breaking these compounds to smaller molecules and eventually convert them to CO2. The first two chapters of this dissertation investigated the process of crude oil biodegradation by indigenous microbial communities of marine sediments in the Northern Gulf of Mexico. This study aimed to understand the oil fate in the Deepwater Horizon disaster in 2010, the first major oil spill occurring in deep waters (1500 m), at low temperature and high pressure. Sediments collected at various water depths (60–1500 m) were incubated with crude oil under simulated in-situ temperature and pressure conditions for 18 days. By comparing extents of degradation of n-alkanes and polyaromatics (PAHs), I found a mild inhibitive effect of pressure on oil biodegradation and distinction in microbial communities between deep and shallow samples. Finally, in the third chapter, I investigated potential of oil biodegradation in oceans at global scale using a metagenomic approach. I searched in publicly available marine metagenomes for genes encoding alkane hydroxylase (AlkB) and ring hydroxylating dioxygenases (RHDs). These enzymes respectively catalyze the activation of aerobic degradation of n-alkanes and aromatics, the two major groups of oil hydrocarbons. More than 80% of 770 metagenomes analyzed contained AlkB and RHDs, suggesting of their ubiquity in marine environments. Relative abundances of both genes were higher in deep waters (>1000 m) than shallow waters (< 200 m), possibly due to the higher diversity in functional processes at shallow depths (e.g., photosynthesis). Homologous sequences in marine metagnomes of both genes were extremely diverse, and many novel sequences of these genes remained undiscovered. Taxonomic affiliations of both genes displayed biogeographic variation in hydrocarbon degrading communities as there were significant difference between deep and shallow water samples, and between North Atlantic and North Pacific oceans.