Evaluating impact of marine hydrocarbon-degrading microorganisms and chemical dispersants in mitigating oil-spill environmental damage
Lead supervisors: Dr Benjamin Gregson, Dr Gareth Thomas and Dr Boyd McKew
Location: School of Life Sciences, University of Essex
Duration: 8 weeks
Suitable undergraduate degrees: Biology, Chemistry, Maths, Computer Science
The marine environment is highly susceptible to pollution by petroleum hydrocarbons, meaning it is important to understand how microorganisms degrade these compounds to mitigate ecosystem damage. Additionally, chemical dispersants are seen as an effective oil-spill response tool, as they reduce the interfacial tension between oil and water, producing small oil droplets that are more readily degraded by indigenous oil-degrading bacteria. However, these droplets can interact with marine snow particles in the ocean, forming marine oil snow (MOS). Sinking of MOS particles can transport toxic oil compounds to sensitive benthic ecosystems, altering redox conditions, and negatively impacting their biodiversity. Whether or not the application of dispersants enhances MOS formation is still up for debate, with contradictory studies suggesting they either enhance or inhibit these formations. Additionally, many of these studies have been scrutinised for not accurately replicating conditions in the marine environment. This project will use a combination of proteomics and DNA sequencing to further our understanding of how particular bacteria break down petroleum hydrocarbons and assess the impact of chemical dispersant application on the formation of MOS particles and the microbial community compositions within them.
Aims and objectives:
1) Identify proteins and pathways utilised by a marine aromatic hydrocarbon-degrading bacterium
In this experiment we will use shotgun proteomics to quantify changes in protein expression for Cycloclasticus zancles 78-ME, a key bacterium involved in aromatic hydrocarbon-degradation. Protein expression will be compared during growth on aromatic hydrocarbons and non-hydrocarbon controls. Differential expression analysis will be performed by the student on the generated spectral count data. The student will receive training on how to perform this analysis using R (e.g., edgeR, LIMMA, DESeq2). This will identify key proteins involved in the biodegradation of aromatic hydrocarbons and changes to the bacterium’s physiology. The student will also be trained in using a variety of bioinformatic software (e.g. BLASTP, CDD, SCOOP, CATH, I-TASSER) to further characterise the function of individual proteins that demonstrate a significant increase in abundance.
2) Evaluate the effects of chemical dispersants on marine oil snow (MOS) formation and hydrocarbon-degradation
The student will conduct an MOS formation experiment at natural in-situ conditions, replicating a North Sea marine environment, to establish the effects of chemical dispersants on MOS formation and the degradation of hydrocarbons present in the oil. MOS particles will be generated in microcosms under various treatments of oil and dispersant concentration on roller tables to simulate turbulent conditions. A high intensity lighting system will allow for the replication of light intensity observed in natural day/night cycles. The student will have the opportunity to assist in the design and running of the microcosm experiment as well as assisting in sample processing (including DNA extractions from the MOS particles, and measuring hydrocarbon-degradation through analytical chemistry techniques (e.g., GC-MS)). The student will also learn how the DNA extract will then be used for Next-Generation Sequencing and qPCR, to identify and quantify oil-degrading microbes associated with MOS.