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Understanding and exploiting stoichiogenomics to harness reactive nitrogen in sustainable food production systems

About This PhD Project

Project Description

Aquaculture is the fastest growing food production sector in the world, however global aquaculture needs to double in size over the next decade to keep pace with the ever-rising demand for quality protein. Nitrogen, the main constituent of protein, is one of the most critical and valuable elements globally. Current aquaculture practices are characterised by inefficiencies in nitrogen use and globally, aquaculture is contributing to net nitrogen loading to the environment, with concomitant negative impacts on the environment and human health. As aquaculture intensifies, the volume of waste produced will increase in direct proportion to aquaculture production, however presently, there are limited solutions to deal with N-rich waste.

This research will develop innovative systems, based on the recovery of valuable resources, to pioneer sustainable food production systems and catalyse a new revolution in the nitrogen cycle. Rather than promoting technologies that result in the permanent removal of nitrogen, this research will explore the potential to exploit the genomic capacity and functional potential of microbial communities within marine sediments and deposit feeder gut microbiomes to upcycle waste N into high value biomass as organic nitrogen.

Understanding and exploiting genomics and concomitantly proteomics is a fundamental theme underpinning the research. Through a close partnership with the commercial partner, Great British Prawns Ltd, an innovative company producing high value prawns in a marine recirculating aquaculture systems (RAS), the student will use discovery science and stoichiogenomics to demonstrate how genome level responses of sediment and deposit feeder microbiomes, in response to anthropogenic Nr pollution, can be manipulated and exploited to engineer low-cost systems, that provide a myriad of solutions to the current global challenges facing the agro-industry sector.

The PhD student will work within the framework of Elemental Stoichiometry to understand the structure, organisation, function and interaction of microbial communities in deposit feeder gut, soil and sediment microbiomes. A stoichioproteomic analysis of microbial communities from different environments, including agriculture, aquaculture and engineered bioremediation systems will be undertaken using annotated sequencing data from soils, sediment and bioremediation systems currently available through the Earth Microbiome Project. Long-term growth trials of the polychaete Alitta virens reared on waste from a prawn Recirculating Aquaculture System (RAS) will be coupled with integrative microbiome research to explore the role of the ‘system microbiome’ (soil, sediment and gut microbiomes of deposit feeders), and the role they play in elemental nutrient cycling and the global N budget.

The PhD student will be primarily based at the Scottish Association for Marine Science in Oban, under the supervision of UKRI Future Leaders Fellow Dr Georgina Robinson, with additional supervision from Dr Mary Doherty, University of the Highlands and Islands and Dr Katherine Duncan, University of Strathclyde and will undertake a 3-month placement with the commercial partner GBP Ltd in Balfron. The student will receive training in a novel inter-disciplinary scientific area, providing expertise in sample collection, microbiome sequencing, molecular techniques and cutting edge transcriptomics and proteomics methodologies as well as bioinformatics and modelling.

Funding Notes

Funded by NERC Studentships awarded to the SUPER Doctoral Training Partnership. The SUPER DTP partner Universities are St Andrews University, Aberdeen University, Edinburgh Napier University, Heriot-Watt University, the University of the Highlands and Islands, Stirling University, University of Strathclyde and the University of the West of Scotland. Underpinning these research partners, providing additional training and projects are Marine Scotland, Scottish Natural Heritage, and the James Hutton Institute, among a total of 40 stakeholder organisations including industry and government agencies and international collaborators.

The start date of this project is: 5th October 2020

The 3½ year studentships cover:
• Tuition fees each year (for 2019/20 this is currently £4,327 for full-time study)
• A maintenance grant each of around £15,000 per annum (for full-time study)
• Funding for research training
• Part-time study is an option, with a minimum of 50% of full-time effort being required.

Applicants should normally have, or be studying for:
• A postgraduate Master’s degree from a degree-awarding body recognised by the UK government, or equivalent, or
• A first or upper second class honours degree from a degree awarding body recognised by the UK government, or equivalent, or
• Other qualifications or experience that affords sufficient evidence of an applicant’s ability to work at the academic level associated with doctoral study.

Project specific enquiries:

General enquiries: Graduate School Office

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