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A synthetic microbiome approach to develop new CO2 bioconversion solutions

   Department of Earth and Environmental Sciences

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  Dr Sophie Nixon, Prof E Takano, Dr Katharine Coyte, Prof R Breitling  No more applications being accepted  Funded PhD Project (UK Students Only)

About the Project

In recognition of the growing climate emergency, nations have committed to net zero CO2 emissions by 2050 or earlier. These ambitious targets call for direct removal of emissions from the atmosphere. While geological storage has the potential to remove vast quantities of CO2 emissions in the long term, utilisation offers a means to up-cycle humankind's largest waste-stream in the shorter term, helping achieve a decarbonised future built on a circular carbon economy. Not only is utilisation an attractive option for generating wealth from waste; it can also mitigate the storage burden through costly injection into the deep subsurface.

Value-added products made from CO2 utilisation include feedstock chemicals methanol and acetate (used in polymers synthesis) and alternative fuels such as ethanol. Enzymatic pathways that mediate the conversion of CO2 into organic compounds are prolific in the biosphere, and represent some of the most ancient metabolic pathways known in the prokaryotic world. Furthermore, microorganisms produce a myriad of secondary metabolites of high value to humankind ('natural products'), including antibiotics, anticancers, surfactants, pigments and flavours. As such, biological utilisation of CO2 holds significant potential to turn waste into wealth whilst contributing significantly to net zero emissions.

The genomic revolution has highlighted that biogeochemical cycles in the environment are driven by complex networks of metabolic interactions within microbial communities, where waste compounds from one organism serve as food for another. Traditional microbiological and biotechnological approaches focus on isolating and harnessing the traits of individual microorganisms. However, microorganisms have evolved not to exist in isolation but in multi-species interdependent consortia.

In this PhD project you will design, build, test and learn from synthetic communities of microorganisms that can harness numerous interlinked metabolic pathways to produce value-added products from CO2, independently of photosynthetic pathways. The design of these communities will be guided by energetic and kinetic predictions, as well as published reports of metabolic function of candidate strains. Multi-omic (genomic, transcriptomic, metabolomic and proteomics) approaches will be used to track metabolism, characterise microbe-microbe interactions, and ultimately trace the anabolic metabolism of CO2 into value-added organics. In the process, you will characterise the ecological and metabolic interactions at play using a combination of modelling and sequencing approaches. Crucially, you will not only target the 'high yield, low value' primary metabolic products, but also 'low yield, high value' secondary metabolites that are expected to be produced via ecological interactions of community members. Synthetic biology approaches will then be applied to augment desirable processes and increase yields of and promising value-added products at the community scale.

In this muti-disciplinary biotechnology project you will combine microbiological cultivation, genome-resolved omics, bioinformatics, energetic and ecological modelling and genome editing to develop novel and scalable ways to convert CO2 to value-added products using 'designer' microbial consortia. The project will enable a student to join a vibrant and growing research group in the Manchester Institute of Biotechnology, and benefit from training in all aspects of the research. You will be working alongside team members investigating CO2 bioconversion potential of naturally-enriched microbial communities, and will benefit from the collaborative opportunities that will arise through this complementarity. The research has significant potential to lead to new industrial-scale processes of interest to industry.



To make an application please visit - https://www.ees.manchester.ac.uk/study/postgraduate-research/how-to-apply/

Please search and select PhD Environmental Science (academic programme) and PhD Environmental Science (academic plan)

Equality, diversity and inclusion is fundamental to the success of The University of Manchester, and is at the heart of all of our activities. We know that diversity strengthens our research community, leading to enhanced research creativity, productivity and quality, and societal and economic impact. We actively encourage applicants from diverse career paths and backgrounds and from all sections of the community, regardless of age, disability, ethnicity, gender, gender expression, sexual orientation and transgender status.

We also support applications from those returning from a career break or other roles. We consider offering flexible study arrangements (including part-time: 50%, 60% or 80%, depending on the project/funder).

All appointments are made on merit.

Funding Notes

Department funded - fees and stipend provided at the current UKRI rate. Start date July 2023


1. Nixon, Bonsall and Cockell 2022. Limitations of microbial iron reduction under extreme conditions. FEMS Microbiology Reviews https://doi.org/10.1093/femsre/fuac033
This major meta-study employed thermodynamic calculations to predict limits to a microbial metabolism. Similar energetic calculations will be used in this project.
2. Connolly ... Takano and Breitling 2022. Harnessing intracellular signals to engineer the soil microbiome. Natural Product Reports 39(2):311-324.
This publication explores the potential for exploitation of natural signalling molecules - essential for microbe-microbe interactions in a microbiome - for optimised community function, such as beneficial interactions with crops. The fundamental idea - that microbe-microbe interactions are central to community function - underpins this PhD project.
3. Robinson et al ... Takano and Scrutton 2021. Prototyping of microbial chassis for the biomanufacture of high-value chemical targets. Biochem Soc Trans 49(3):1055-1063
This review draws on the Design-Build-Test-Learn pipeline approach that underpins synthetic biology, and that we will draw upon for designing and engineering synthetic communities in this project.
4. Rao, Coyte et al 2021. Multi-kingdom ecological drivers of microbiota assembly with preterm infants. Nature 591(7851):633-638.
This research showcases how absolute abundance quantification combined with experimentally validated ecological modelling can uncover interactions between community members within a microbial community assembling in preterm infant guts. These approaches will be used in this project to understand and exploit ecological interactions in synthetic and engineered microbiomes.

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