Engineered genetic bioaugmentation vectors and pathways for bioremediation

Lead Research Organisation: University of Manchester
Department Name: Chemistry


Anthropogenic impact upon the environment is the biggest existential threat to humanity. Contamination of the natural environment with xenobiotics causes significant challenges in terms of containment and remediation. In these polluted environments microbial communities have been shown to evolve and adapt to grow in the presence of xenobiotics by resistance, decomposition and/or assimilation of the foreign substance. Indeed, these organisms can also provide a rich source of degradative and catabolic biosynthetic genes and pathways for use in engineered biosynthetic pathways and hosts for bioremediation.

This project will seek to use Synthetic Biology approaches to develop and optimise plasmid-based bioaugmentation strategies for bioremediation of contaminated environments. Specifically, by engineering plasmid-encoded degradative and catabolic biosynthetic pathways, for example to remove heavy metals and assimilation of plastics. This will provide novel approaches for decontamination and also provide circular economy opportunities. Alternative strategies will be employed including Adaptive Laboratory Evolution and use of Engineered Plasmids and Pathways. The evolved/engineered plasmids will then be transferred back into the indigenous bacterial community by conjugation and the impact of the modified plasmids will be studied at both the metabolic and the genetic levels. In parallel plasmid dispersal amongst the indigenous bacterial community will be studied to assess uptake, spread (horizontal genetic transfer) and longevity using genomic profiling approaches. In addition to the scientific research a key part of this PhD project will be to engage with Responsible Research and Innovation (RRI) colleagues and external stakeholders such as national and inter-governmental regulatory authorities, NGOs, and environmental pressure groups.

This PhD project will provide training in the conceptual approaches, skills and techniques of synthetic biology, plus in broad aspects of biotechnology, microbial gene expression regulation, evolutionary and environmental microbiology, molecular biology and bio-analytical methods. This project would suit individuals interested in future careers in modern environmental biotechnology, and the sustainable bioeconomy.

Planned Impact

The 2016 UK Roadmap Bio-design for the Bio-economy highlighted the substantial impact that synthetic biology can bring to the UK and global economies by developing: frontier science and technology; establishing a healthy innovation pipeline; a highly skilled workforce and an environment in which innovative science and businesses can thrive. Synthetic biology promises to transform the UK Bio-economy landscape, bringing bio-sustainable and affordable manufacturing routes to all industrial sectors and will ensure society can tackle many contemporary global Grand Challenges including: Sustainable Manufacturing, Environmental Sustainability Energy, Global Healthcare, and Urban Development. Whilst synthetic biology is burgeoning in the UK, we now need to build on the investments made and take a further lead in training next generation scientists to ensure sustained growth of a capable workforce to underpin the science base development and growth in an advanced UK bio-economy.
This training provided by this CDT will give students from diverse backgrounds a unique synthesis of computational, biomolecular and cellular engineering skills, a peer-to-peer and industrial network, and unique entrepreneurial insight. In so doing, it will address key EPSRC priority areas and Bioeconomy strategic priorities including: Next-generation therapeutics; Engineered biomaterials; Renewable alternatives for fuels, chemicals and other small molecules; Reliable, predictable, and scalable bioprocesses; Sustainable future; Lifelong health & wellbeing.
Advances created by our BioDesign Engineering approach will address major societal challenges by delivering new routes for chemical/pharma/materials manufacture through to sustainable energy, whilst providing clean growth and reductions in energy use, greenhouse gas emissions and carbon footprints. Increased industry awareness of bio-options with better civic understanding will drive end-user demand to create market pull for products. The CDT benefits from unrivalled existing academic-industry frameworks at the host institutions, which will provide direct links to industrial partners and a direct pathway to early economic and industrial impact.

This CDT will develop 80-100 next-generation scientists and technologists (via the funded cohort and wider integration of aligned students at the three institutions) as adept scientists and engineers, instilled with technical leadership, who as broadly trained individuals will fill key skills gaps and could be expected to impact internationally through leadership roles in the medium term. Importantly the CDT addresses key skill-gaps identified with industry, which are urgently required to create and support high value jobs that will enable the UK to compete in global markets. Commercialisation and entrepreneurship training will equip the next generation of visionaries and leaders needed to accelerate and support the creation of new innovative companies to exploit these new technologies and opportunities.

The UK government identified Synthetic Biology as one of the "Eight Great Technologies" that could be a key enabler to economic and societal development. This CDT will be at the forefront of research that will accelerate the clean growth agenda and the development of a resilient circular bioeconomy, and will align with key EPSRC prosperity outcomes including a productive, healthy and resilient nation. To foster wider societal impact, the CDT will expect all students to contribute to public outreach and engagement activities including: open days, schools visits, and science festival events: students will participate in an outreach programme, with special focus on widening participation.

This CDT will contribute to the development of industrial strategy through the Synthetic Biology Leadership Council (SBLC), Industrial Biotechnology Leadership Forum (IBLF), and wider Networks in Industrial Biotechnology and Bioenergy and Professional Institutes.


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Studentship Projects

Project Reference Relationship Related To Start End Student Name
EP/S022856/1 31/03/2019 29/09/2027
2602516 Studentship EP/S022856/1 03/10/2021 29/09/2025 Alejandro Marquiegui