Using a synthetic biology approach to engineer urban water system biofilms

Lead Research Organisation: University of Sheffield
Department Name: Chemical & Biological Engineering

Abstract

"Synthetic biology aims to design and engineer biologically based parts, novel devices and systems as well as redesigning existing, natural biological systems" (The Royal Academy of Engineering (2009) Synthetic Biology: scope, applications and implications. ISBN:1-903496-44-6). This exciting and emerging technology is largely directed at providing solutions for challenges within the manufacturing, healthcare and energy sectors. Synthetic biology offers exciting and new possibilities that have the potential to transform the water industry by offering new biologically based solutions to address global water challenges. However little attention has been directed at developing synthetic biology solutions to address urban water systems challenges such as increased performance, enhanced water quality and energy saving. Current synthetic biology activities in the water arena tend to address specific research challenges (e.g. biosensors, biodesalination, microbial fuel cells) and are yet to be translated to application beyond the laboratory scale. What is missing is a demonstrated synthetic biology led solution that not only addresses the technical challenges of deploying such a solution within the urban water environment, but also engages the appropriate stakeholders to address and debate concerns over governance, acceptability and risk. The bright IDEA is to provide such an example. Here, a synthetic biology approach is used to design and engineer urban water system biofilms, transforming their current negative image into a positive resource. More specifically, an engineered biofilm will be designed and tested to reduce frictional losses and repair wall defects to increase hydraulic capacity and reduce in/ex filtration within sewers. This will be achieved within a controlled urban water environment at different engineering scales. As well as addressing the technical challenges of engineering biofilms with desired characteristics, within a complex environment, the social issues and implications will also be discussed through various stakeholder engagements and a focused workshop. This project will therefore provide a synthetic biology led solution for increasing performance within sewer networks, and provide the basis to investigate the translation and implementation challenges for deploying the solution within the urban water environment. This project will also provide the foundation for UK based research centre focused on urban water challenges that ensures effective engagement and communication with the appropriate stakeholders to set the research priorities and deliver synthetic biology solutions both now and in the future.

Planned Impact

The UK water industry invests over £4B annually with steady growth projected for the foreseeable future (www.innovateuk.org/sustainabilityktn). The global water technology market is estimated at £231.5 B (Global Water Intelligence). Therefore, the potential market for technologies that are more reliable and cost effective than current technology ranks on the order millions of pounds per year. Process improvement and infrastructure performance enhancement technologies that reduce resource usage, save energy and minimize costs will have significant future markets and economic impact. The specific example addressed here will impact directly on the UK's public sewer system, which has an estimated replacement asset value of £104B. Synthetic biology led solutions that are able to address global water challenges both now and in the future therefore have the potential for major wealth creation via the generation of new science, new solutions, new technologies and products and improved efficiencies and performance.

The impact on the water Industry and its future competitiveness is not only limited to the provision of new technical solutions, but the bright IDEA presented here also offers a transformative shift in attitude. Using synthetic biology led solutions to address urban water challenges demonstrates the positive potential of the biological community, rather than a negative entity that needs to be avoided and removed. The stakeholder engagements will also address attitudes surrounding the deployment of synthetic biology systems within the urban water system context. This research will therefore have impact on the policy arena and the wider public as new understandings and tools are development to address water challenges with the societal issues of high importance. The research will also impact on research funding and policy through the development of a roadmap that sets out the priorities for UK research excellence, technology needs, barriers to innovation afuture opportunities.

The long term academic impact is the development of a research centre that focuses the UK research capability and expertise to address synthetic biology solutions for urban water systems. Through demonstrated examples, this centre will provide the focal point for future research activities offering a framework to successfully integrate and demonstrate synthetic biology led solutions for global water challenges with genuine and long term stakeholder engagement.

Publications

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Jensen H (2016) The importance of sewer biofilms The importance of sewer biofilms in Wiley Interdisciplinary Reviews: Water

 
Description The aim of this project was to engineer bacteria to form biofilms of a specific characteristic or design. The application was for biofilms in sewers, but the approach could be applied more widely. To start the project we needed to understand the baseline biofilm forming characteristics of our chosen bacterium, Acinetobacter baylyi ADP1. We looked at its ability to form biofilms on tissue culture-treated polystyrene and stainless steel as well as on sewer-relevant materials such as high density polyethylene and concrete. Biofilms formed best on tissue culture-treated polystyrene. We then used a systematic synthetic biology approach to increase the ability of Acinetobacter baylyi to attach to a variety of surfaces. To achieve this, two separate strands of investigations were followed.
(1) Express a strong and durable underwater adhesive protein from the Mediterranean mussel (Mytilus galloprovincialis) on the surface of Acinetobacter baylyi ADP1.
(2) Engineering polyphosphate production and utilisation in Acinetobacter baylyi ADP1 to control production of extracellular polymeric substances which aid in biofilm development.

It was discovered that expression of adhesin protein alone did not increase the biofilm formation ability of Acinetobacter baylyi. Co-expression of an extracellular tyrosine kinase was required to modify the tyrosine residues on the adhesive protein to L-dopamine to confer adhesive behaviour. Tyrosine kinase expressing mutants were created, however secretion of this enzyme was a bottleneck. The 24 months were completed before this bottleneck could be overcome.

The increased utilisation of polyphosphate increased the aggregation of Acinetobacter baylyi in suspension. However, this did not increase biofilm formation on tissue-culture treated polystyrene. Going forward, engineering increased polyphosphate utilisation as well as production of mussel adhesive protein and secreted tyrosine kinase in the same strain would allow biofilm formation by Acinetobacter baylyi ADP1 on a variety of surfaces. The inability to obtain such an engineered strain within the 24 month time frame precluded the demonstration of the survival of the engineered strain within a microbial community and at the pilot scale.

Two different off-the-shelf biofilm bioreactors - the Centres for Disease Control bioreactor and the biofilm annular reactor - were procured for use in the project in order to test the engineered strains under different shear flows that will be encountered in the sewer networks. Good biofilm formation was obtained by the unengineered organism on polystyrene coupons on the CDC reactor. However, this observation could not be replicated in the biofilm annular reactor. It was discovered that this was because of Acinetobacter baylyi was an obligate aerobe and inability to aerate the contents of the biofilm annular reactor resulted in insufficient dissolved oxygen levels in the reactor to sustain the organism in the reactor long enough to establish biofilms.
Exploitation Route Further exploratory funding via RCUK, but more likely through a water company sponsored PhD to allow the time and freedom to be more blue sky. After further demonstration, then it may be possible to explore avenues of talking with water companies about demonstration projects
Sectors Energy,Environment,Manufacturing, including Industrial Biotechology

 
Description TWENTY 65: Tailored Water Solutions for Positive Impact
Amount £3,962,860 (GBP)
Funding ID EP/N010124/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start 01/2016 
End 01/2021
 
Description Fear of the unseen - Engineering good bacteria 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact The event was called "Fear of the unseen - Engineering good bacteria". It was part of the Festival of Mind activities in 2016. The event took place in Sheffield on 19th September. The event was organised by the CBMNet centre manager, Jen Vanderhovan.

During the event, Dr Esther Karunakaran (PDRA on the project) was part of a panel of researchers talking about how we are employing bacteria for beneficial activities and we had a question and answer session. She spoke about quorum sensing, biofilm formation and how we are employing the social behaviour of bacteria for bioremediation and enhancing the performance of water distribution networks. The panel answered questions from the public about genetic engineering.
Year(s) Of Engagement Activity 2016
 
Description PWG industrial advisory board 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact presented our work to the PWG industrial advisory board. They welcomed the technology and acknowledged its benefits. We discussed barriers to implementation, which revolved mostly around regulatory hurdles to employing GM organisms in the environment. The Yorkshire water representative mentioned that a framework focusing on GMO use in environmental engineering was recently drawn up. We also discussed the need for devoting more time and resources for testing the technology at the pilot scale before employing it in the field. The industry representatives were quite keen on this.
Year(s) Of Engagement Activity 2016
 
Description Presentation about research outcomes at Newcastle University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Presentation to new Professors at Newcastle University about my research interests
Year(s) Of Engagement Activity 2019
 
Description Research Seminar - overview of activities 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Invited research seminar to School of Engineering, Newcastle University, where I gave an overview of my research activities with the aim of future collaborations
Year(s) Of Engagement Activity 2018