Postgraduate research study
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PhD project: Controlling bacteria aggregation for environmental remediation and biotechnological applications

Project description

Bacteria commonly exist in aggregated communities of cells that can be freely suspended in liquid (flocs) or attached to surfaces (biofilms).  In these aggregated microbial communities, the cells produce extracellular polymers (EPS) such as polysaccharides, proteins, and nucleic acids that mediate cell-cell cohesion and adhesion to surfaces. Although these communities are detrimental in  many industrial (e.g., pipe corrosion) and clinical settings (e.g., cystic fibrosis infections), they are also crucial for many environmental and biotechnological applications. For example in wastewater treatment, aggregating bacteria cells clean the sewage water whilst forming flocs that subsequently settle under gravity allowing for clean effluent to be returned to the water cycle. 

In this project, the student will investigate ways to control bacteria aggregation for biotechnological and/or environmental remediation purposes. This work will explore 1 of 3 potential strands depending on the student's interest:

  1.  There has been growing concern about microplastics (MPs) in recent years, not least, because they are linked with a plethora of health problems such as cancer, breathing disorders, and cardiovascular disease. MPs also pervade and negatively impact many of our ecosystems, with alarming incidence in many aquatic environments. Indeed, MPs constitute a significant fraction of the plastic waste found in many of the world's river basins, and are also thought to dominate the plastic count in the oceans. A promising strategy to help tackle MP pollution in aqueous environments is to use microbes for bioremediation. In many cases, this involves harnessing the adhesive nature of polymers associated with biofilm- and aggregate-forming bacteria. In these aggregated microbial communities, the cells produce extracellular polymers (EPS) such as polysaccharides, proteins, and nucleic acids that mediate cell-cell cohesion and adhesion to surfaces. These interactions can be exploited to capture the MPs into bacterial aggregates and thus separate the suspended MPs from the aqueous environment. The underpinning science that describes the interactions between microplastics, the bacteria, and EPS lies in domains of soft matter and biological physics. Optimising the bacteria-MP interactions for efficient capture, however, also requires an engineering biology approach to facilitate system design from the bottom-up. In this project, we will adopt an interdisciplinary approach to probe the ability of biofilm/aggregate-forming bacteria and genetically engineered bacteria to explore and characterise their ability to capture a variety of MPs (e.g., types, shape, and size) from aqueous suspensions; 

  2. Therapeutic proteins (TPs) are produced by microbes in fermenters and must then be purified. When the TP is produced intracellularly, downstream processing involves: a) harvesting the microbes from the culture medium (typically via centrifugation); b) resuspending and lysing cells to release the TP; c) TP collection via centrifugation or filtration. In the second step, homogenisation can give rise to a complex lysate, rich in cell debris, membranes, and nucleic acids that make protein separation with high yields difficult. Thus, energy-intensive and expensive techniques such as centrifugation and filtration are used. Furthermore, the high viscosity of the complex lysate can hamper further downstream separation steps and slow down processing times. As a more sustainable and simpler alternative for protein separation during steps b and c, we propose to engineer downstream separation steps into the microbes. Here, the student will engineer the cells to express produce proteins that can aggregate cells and cell debris together in a tunable manner. We anticipate that these Engineering Biology (EB) approaches will pave the way for high yields, short processing times, decreased energy usage, less waste, and reduced costs; 

  3.  Nitrous oxide, N2O, is the 3rd most important greenhouse gas (GHG) after carbon dioxide (CO2) and methane (CH4). A strong GHG, N2O is ~300 times more potent per mass than CO2, and its average concentration in the atmosphere has increased 2% per decade over the last 150 years (with the rate doubling over the last 30 years). It is also the main contributor to the depletion of the ozone layer. N2O is generated by the nitrification and denitrification activity of microorganisms in variety of different environments ranging from soil ecosystems to the wastewater treatment (WWT) process. In WWT, for example bacteria degrade dissolved pollutants in the wastewater whilst forming compact flocs (or aggregates), which are then subsequently separated from the liquid under gravity (settling). When oxygen is low, some bacteria can then use alternative electron acceptors (e.g., NO3, NO2) for respiration, producing N2O as a result. We have developed a systematic understanding of denitrification and N2O generation in well-mixed suspensions of non-aggregated WWT bacteria when subjected to different oxygen conditions. In this project, we will extend this research to explore this behaviour in more spatially structured environments such as biofilms and suspended aggregates, and assess how denitrification and N2O are influenced by the emerging concentration gradients of O2; 

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