Bernice & Crystal: Research Proposal
Brief Project Overview
We plan to develop and use genetically modified phage (M13 or other, if found more appropriate) as a source of environmental bioremediation to catabolically degrade hydrocarbons in areas devastated by oil spills.
Finding sustainable and eco-friendly solutions to clean up contaminated environments has become increasingly important as we learn more and more about the harmful costs of degrading our habitats. Harnessing and manipulating the varied and inherent capabilities of living organisms to help in recovery efforts is a natural step towards achieving this sustainability.
Researchers have recently found a way to use synthetic biological design to re-engineer the T7 phage so that it is capable of degrading a variety of harmful biofilms. The authors of the paper note that their approach can be easily exploited to target other substances and other types of bacteria as well.
Lu T Collins J. Dispersing biofilms with engineered enzymatic bacteriophage. PNAS 104(27): 11197-11202(2007) 
Using the principles behind their work, we would like to identify an enzyme or nitrate producing gene that can be incorporated into phage that are endogenous to marine environments to aid in the remediation of oil spills and leaks.
Statement of Research Problem & Goals
Current methods of bioremediation in oil spills often requires the introduction of exogenous bacteria, which an upset the balance of delicate marine microcosms. We plan to modify a phage that is endogenous to the environment it is in, so that is then able to infect its normal hosts, enabling them to produce compounds such as nitrates, sulfates, and ferric irons to bio-degrade hydrocarbons. The use of phage, as opposed to widespread dumping of these substances in affected areas, is self sustaining, less severe on the environment, and facilitates efforts in areas that may be unaccessible to prolonged human activity. We will also carefully monitor any side-effects of introducing the re-engineered phage to experimental microcosms.
Project Details & Methods
Lovley, DR (2003). "Cleaning up with genomics: applying molecular biology to bioremediation". NATURE REVIEWS. MICROBIOLOGY. 1 (1): 35 – 44.
Gives overview of the current progress and challenges in efforts to use bioremediation (employing both molecular biological analysis as well as overall evaluations of ecosystems) as a way to restore contaminated environments inexpensively yet effectively. Sees much potential in the field, and advocates expansion of similar efforts.
Brim H, McFarlan SC, Fredrickson JK, Minton KW, Zhai M, Wackett LP, Daly MJ (2000). "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments". NATURE BIOTECHNOLOGY 18 (1): 85 – 90. 
Details how one strain of bacteria was re-engineered to offset the harmful effects of radioactive waste.
Chen YD, Barker JF, Gui L. A strategy for aromatic hydrocarbon bioremediation under anaerobic conditions and the impacts of ethanol: A microcosm study. J Contam Hydrol. 2007 Sep 29; [Epub ahead of print]
Good information about the type of environment (chemicals, PH, contents of various ions) that is optimal for the remediation of aromatic hydrocarbons.
Head IM, Jones DM, Röling WF. Marine microorganisms make a meal of oil. Nat Rev Microbiol. 2006 Mar;4(3):173-82. 
How microorganisms exploit hydrocarbons as a source of energy
Antić MP, Jovancićević BS, Ilić M, Vrvić MM, Schwarzbauer J. Petroleum pollutant degradation by surface water microorganisms. Environ Sci Pollut Res Int. 2006 Sep;13(5):320-7.