Research Studentships

PhD Studentship

Unveiling the natural sulphur potential of biological nitrogen fixation in faba bean

Supervisory Team: Dr Ravi Valluru

This PhD aims to understand the potential nature of sulphur on biological nitrogen fixation in faba beans. Sulphur is an essential mineral nutrient for plant growth and development; important for primary and specialized plant metabolites that are crucial for biotic and abiotic interactions. Sulphur also plays a crucial role in biological nitrogen fixation, a natural process belonging to legumes that symbiosis with bacteria through root nodules to fix atmospheric nitrogen. Root nodules have a high demand for sulphur. In nodulated legumes, biological nitrogen fixation is more sensitive to sulphur deficiency than nitrate uptake. However, the natural sources of gypsum-mine-derived sulphur-containing by-product’s effect on plant growth, development and biological nitrogen fixation is largely unexplored. This 3.5-year project will unveil the functional relationship between sulphur nutrition and biological nitrogen fixation in faba beans using 15N stable isotopes.

Training and Development

The successful candidate will receive comprehensive research training including technical, personal, and professional skills. All researchers at University of Lincoln are part of the Doctoral College and College of Health and Science wider postgraduate community, which provides support with high quality training and career development opportunities.

Funding

This PhD studentship is fully funded and covers University fees for 3.5 years.

Entry requirements for applicants to PhD

A Master’s (honours) degree in a relevant discipline/subject area with a minimum mark of 60% in the project element (or equivalent), and the potential to engage in innovative research, and to complete the PhD within 3.5 years.

How to Apply

To find out more about the project, please contact Dr Ravi Valluru (rvalluru@lincoln.ac.uk).

Applications will require a two-page CV and a 2000-word supporting statement, showing how the applicant's expertise and interests are relevant to the project. 

Automated Robotic Rapid evaporative ionisation mass spectrometry Meat Sampling

Supervisory team: Dr Athanasios Polydoros, University of Lincoln; Dr Nick Birse, Queen's University Belfast; Professor Mark Swainson, University of Lincoln.

Meat remains a primary source of protein for much of the public, but as the public becomes increasingly aware of the environmental impacts around meat production, consumers are looking for meat that is not only of high quality but also has lower environmental impacts and higher ethical standards. Therefore, automated quality control is of high importance for meeting consumers’ requirements while minimising the environmental impact and maximising production.

Therefore, the project Automated Robotic Rapid Evaporative Ionization Mass Spectrometry Meat Sampling (AR2MS), will develop and apply Machine Learning methods for computer vision, robot control and analysis of rapid mass spectrometry data to instantly deliver assessments on the meat quality, geographical origin, and breed. This project will deliver, in combination with a major meat producer and a provider of scientific testing solutions, a commercially viable system suitable for deployment in the business of that major meat producer. Therefore, the key research areas of the project are on Machine learning methods for robot perception and control, AI data analysis and decision-making from rapid mass spectrometry data.

During the project, the successful candidate will have close collaboration with a multidisciplinary team of experts in AI, robotics, mass spectrometry and food manufacturing. Moreover, they will collaborate with the R&D team of Cranswick, a major meat producer, and they will be supported by the scientific testing provider in the development of the computational modelling needed to deliver a proof of concept for the quality control system. The successful candidate is expected to have experience in machine learning with additional experience in robotics and/or rapid mass spectrometry considered as a plus. The candidate will gain skills in computer vision, robotics, digital modelling, data management, systems integration and to a lesser extent, exposure to analytical systems used in food production systems. 

Eligibility: Due to funder restrictions, this project is currently accepting applications from home applicants only.

Application Deadline: 12pm on Friday 6 June 2025

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Trade-offs in land use: Utilising argumentation theory and dialogue to optimise for net-benefits

Supervisory team: Dr Daniel Magnone, University of Lincoln; Professor Nir Oren, University of Aberdeen; Professor Nir Oren, University of Aberdeen

The UK’s land use can be considered a complex, multiobjective optimisation problem, balancing economic yield, biodiversity enhancement, and carbon storage. With the recent introduction of the Environmental Land Management Scheme (ELMS), the need for a decisionsupport system to help stakeholders understand the impacts and trade-offs of land parcel allocation is clear and timely. 

This PhD project will utilise advances in formal argumentation theory and dialogue to encode, reason, and explain the behaviour of multi-objective optimisation algorithms. The research will focus on optimising carbon storage, biodiversity enhancement, and economic yield from agriculture. The project aims to develop an optimisation model for land use, scale the model from catchment to national levels, quantify regional or national biodiversity, carbon storage, and yield profitability within the UK, and develop the model into a package potentially suitable for commercialisation.

The student will gain a comprehensive understanding of sustainable landscapes within the UK and the necessary subsidy frameworks to achieve optimal conditions. They will review literature to understand the constraints around land parcel allocation and the objectives of different stakeholders, learn how different multi-objective optimisation techniques work, undertake research into formal argumentation, develop dialogical techniques to present reasoning to stakeholders, evaluate the effectiveness of explanations on stakeholder understanding and decision-making, and apply the model to a real-world problem. This project offers a unique opportunity to contribute to a vital area of environmental research and develop a wide range of skills in optimisation, argumentation theory, and stakeholder engagement.

Eligibility: Due to funder restrictions, this project is currently accepting applications from home applicants only.

Application deadline: 12pm on Friday 6 June 2025

This project is currently awaiting final confirmation of industry funding with confirmation expected mid-April. If the CDT has not secured funding, this project may be withdrawn. In this case we will update the status promptly and inform all applicants.

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PhD Studentship

Phylogenetic resolution and a new evolutionary timescale for Temnospondyli (Tetrapoda: Amphibia)

Project Description:

Applications are invited for a full-time PhD position at the University of Lincoln's School of Natural Sciences to work with Dr Marcello Ruta (Principal Investigator) on phylogenetic, macroevolutionary, and macroecological aspects of the origin and diversification of tetrapods (the limbed vertebrates) with a main focus on temnospondyl amphibians, the largest radiation of early tetrapods. This post is funded by a Leverhulme Trust Research Project Grant to Dr Marcello Ruta, entitled “Key Innovations as Evolutionary Drivers of the Fish-Tetrapod Transition”, and is in partnership with the Universities of Bath (Co-Investigator Professor Matthew Wills) and Uppsala (Co-Investigator Professor Per Ahlberg)

Supervisory Team:

Dr Marcello Ruta, University of Lincoln, UK; Professor Matthew Wills, University of Bath, UK; Professor Per Ahlberg, University of Uppsala, Sweden.

Project Background:

Context - Temnospondyli are the most speciose, geologically most widespread, and ecologically most diverse group of early tetrapods (limbed vertebrates), with a fossil record ranging from Lower Carboniferous, ~336 million years ago, to uppermost Lower Cretaceous, ~100 Ma. Over 350 species are known, and several new discoveries occur at a steady pace. Temnospondyls are distinguished from other early tetrapods by a set of unique skeletal features, notably a pair of large openings on the palate separated by an elongate, strut-like anterior process of the braincase. In addition, this group is of remarkable zoological interest as it is implicated in the enduring debate on the ancestry of amphibians. Given their sheer diversity and abundance, temnospondyls provide a rich source of data for investigating life-history traits, ontogenetic changes, and functional specializations. Crucially, however, tempo and mode of morphological evolution and lineage diversification within the group lag. To address these themes, an all-encompassing and robust phylogeny is needed.

Rationale – Most major groups of temnospondyls are sufficiently well diagnosed, but their interrelationships are in a state of flux. Published phylogenies reveal substantial conflict involving the placement of some problematic species, the sequence of branching events within certain groups, and the mutual relationships between major lineages. Factors responsible for this conflict include character and species selection across different studies, discrepancies in character description, formulation, and coding, and methodologies for reconstructing phylogenies. The impact of different character/species samples and character coding on phylogenetic resolution is especially vexing and requires in-depth scrutiny. Only a handful of temnospondyl datasets have been subjected to extensive revision. Therefore, additional effort in this area is critical.

Main Objectives – The project has three integrated objectives: (1) resolution of outstanding areas of uncertainty in temnospondyl phylogeny; (2) production of a new phylogeny-based timescale for temnospondyl diversification; (3) quantification of morphological evolution, with emphasis on skull shape and dimensions, and driven trends.

Research Questions – (1) Did temnospondyls experience an early burst of morphological diversification? (2) Did evolutionary changes show directionality? (3) Was speciation linked to the origin of specific traits?

Methods – Published phylogenetic datasets will be augmented through character and species inclusion and checked for consistency in character formulation and coding. First-hand specimen observations will assist in gleaning additional information for a representative sample of temnospondyls from all major groups. The resulting comprehensive dataset will be subjected to phylogenetic analyses using different methods. Phylogenies will be time-calibrated using fossil ages and a variety of sampling, origination, and extinction rates. Such phylogenies will subsequently be employed to evaluate the direction, magnitude, and distribution (temporal and groupwise) of evolutionary rates, and to establish how morphological diversity of species was partitioned through time, by groups, and in the aftermath of major faunal turnovers, including two extinction events. Alongside analyses of disparity using differences in phylogenetic trait coding, the project will explore complex morphological features of the skull using coordinates of geometric points digitised on cranial structures of interest.

Project Roles:

The successful candidate will primarily undertake research on temnospondyl amphibians, the most diverse group of early tetrapods. They will work closely with all personnel on the grant to assist with data collections. The successful candidate will be first author on all publications stemming from their dissertation, but will also co-author additional papers with the PA, RA, and co-applicants, in particular publications that tackle similar research themes, such as group expansion and decline, shape disparity, and evolutionary trends. Publications will primarily include peer-reviewed research papers, based upon individual thesis chapters. There will also be scope for producing descriptive monographs of selected temnospondyls species.

Applicant Profile:

We are seeking a driven individual working primarily under the remits of the project's chief objectives. Trained by all team members, they will primarily undertake independent research, but also assist with data collection, curation, and databasing, processing and interpretation of phylogenetic and morphological datasets, assisting with preparation of manuscripts and conference presentations, and contributing to outreach and impact activities. The applicant will have prime opportunities to interact with international specialists in the research areas covered by the proposal, acquire transferable and discipline-specific skills, and engage in networking activities, facilitating career progression.

This project will ideally suit candidates with at least a BSc (2:1) honours degree in Zoology or Palaeontology. The successful applicant will also demonstrate a good knowledge of vertebrate morphology and evolution and at least basic analytical and statistical skills

Training:

We have a strong track record of providing first-class training in our institutions, attracting able and motivated individuals and producing talented undergraduates and postgraduates. Under the project supervisory team’s guidance, the student can receive solid training in macroevolutionary analysis and deliver work of publishable standards in high-profile, peer-reviewed journals. They can acquire discipline-specific skills, including, but not limited to: shape analysis, from data collection and processing to interpretation of results; comparative phylogenetic methods, designed to quantify tempo and mode of morphological evolution; advanced statistical methods in quantitative macroevolutionary analysis, such as trait correlations, rates and shift of change, and evolutionary trends. In addition, they can master transferable skills, such as: time management and planning;  experimental design, from conception to delivery; poster presentation; academic writing; verbal communication; and critical evaluation of results. The student will be supported through in-person and online meetings (at least once a week), through provision of scripts with accompanying explanatory notes for running analyses and tests, guidance through the most recent literature on the subject covered by the studentship, and recording (e.g., via TEAMS) of software use demonstrations.

Funding:

This studentship is fully funded for 3 years (start date: 1 July 2025), covers all fees, and provides an annual stipend paid in monthly instalments. For 2024/25, this is £19,237 with slight increases each year at the rate set by UKRI.

There are several opportunities for both national and international collaborations, as well as attendance at scientific conferences.

Eligibility:

Due to funder restrictions, we can only accept applications from home applicants.

Applicant Profile:

We are seeking a driven individual working primarily under the remits of the project's chief objectives. Trained by all team members, they will primarily undertake independent research, but also assist with data collection, curation, and databasing, processing and interpretation of phylogenetic and morphological datasets, assisting with preparation of manuscripts and conference presentations, and contributing to outreach and impact activities. The applicant will have prime opportunities to interact with international specialists in the research areas covered by the proposal, acquire transferable and discipline-specific skills, and engage in networking activities, facilitating career progression.

This project will ideally suit candidates with at least a BSc (2:1) honours degree in Zoology or Palaeontology. The successful applicant will also demonstrate a good knowledge of vertebrate morphology and evolution and at least basic analytical and statistical skills

How to Apply

To apply for this position, please email cohsstudentships@lincoln.ac.uk, providing the following documents: a copy of your updated CV;  a cover letter (max 2000 words) that includes a supporting statement explaining your interest in the advertised position, the relevance of your expertise to the project, and your vision for the development of the project’s research areas; and two recent reference letters.

Deadline for Application:

The deadline for applications is Monday, 19 May 2025. Applications will be considered as they are received. We anticipate completion of the shortlisting on Wednesday, 21 May 2025. Interviews are currently scheduled to take place on Friday, 30 May 2025.

For enquiries about the project please contact Dr Marcello Ruta (mruta@lincoln.ac.uk).

Studentship One

Using AI to Manage Multi-species Grassland for Livestock Farming

Project No: FBS25-73-Parsons-lr

Supervisory Team: Professor Simon Parsons, University of Lincoln; Dr Zoe Barker, University of Reading; Professor Elizabeth Sklar, University of Lincoln

Producing plant matter for animal food is important for livestock farming, both for grazing and for 
making silage. This is typically done by growing fields of rye grass. Switching to a range of species, typically including 
other grasses, legumes like clover, and herbaceous plants like wildflowers, has benefits for the ecosystem and for the animals. The benefits for the ecosystem include improving soil quality, drought tolerance, and biodiversity. The benefits 
for animals include better health and less methane emissions. However, farmers are wary of growing multi-species 
grasslands because they do not understand how best to manage them. This project will gather evidence on management 
practice from ongoing work with multi-species grasslands, and use AI to analyse this evidence and present it farmers to 
help them manage their land.

Training Opportunities

The successful applicant will receive training in AI techniques, the use of the robotic and drone-based technologies which can be deployed in the field to obtain data on grassland, on field work elements like quadrat 
sampling and species identification, and on laboratory analysis. They will also undertake training in the responsible and 
ethical uses of AI.

Project Supervision

An online meeting with the entire supervisory team will be held once a month, and the lead supervisor will meet with the student weekly. These will be one-to-one in the sense that the DTP student will be the only student in those meetings (they will not be lab group meetings). Additional meetings with the wider supervisory group may be scheduled when appropriate (for example for planning field work during the growing season) and the student will participate in lab/group meetings where that is helpful for them. The lead supervisor has a longstanding policy of providing feedback on student paper drafts within 48 hours (in practice the turnaround is typically less). A schedule for feedback on thesis drafts (and sections thereof) varies depending on what exactly is being reviewed, but a schedule is agreed in advance.

Student Profile

This project will be of interest to candidates with either a background in agriculture or agricultural 
technology who are interested in artificial intelligence/machine learning, or to candidates with a background in artificial
intelligence/machine learning who are interested in agriculture. 

Stipend (Salary)

FoodBioSystems DTP students receive an annual tax free stipend (salary) that is paid in instalments throughout the year. 
For 2024/25 this is £19,237 and it will increase slightly each year at rate set by UKRI.

Equity, Diversity, and Inclusion

The FoodBioSystems DTP is committed to equity, diversity, and inclusion (EDI), to building a doctoral researcher (DR) and 
staff body that reflects the diversity of society, and to encourage applications from under-represented and disadvantaged groups. Our actions to promote diversity and inclusion are detailed on the FoodBioSystems DTP website and include:

• Offering reasonable adjustments at interview for shortlisted candidates who have disclosed a disability or 
specific learning difference.
• Guaranteed interview and applicant mentoring schemes for applicants, with UK home fees status, from eligible
under-represented ethnic groups. 

These are opt-in processes. 

Our studentships are offered on a part time basis in addition to full time registration. The minimum registration is 50% FT 
and the studentship end date will be extended to reflect the part-time registration.

For up to date information on funding eligibility, studentship rates and part time registration, please visit the 
FoodBioSystems website.

Applications for this opportunity are by online application form, and full details can be found on the FoodBioSystems website.

Studentship Two

ValueWaste: Revealing the Potential of Organo-Mineral Fertilisers to Enhance Crop Productivity, as Well as Improve Soil Health and Sustainability

Supervisory Team: Dr Leonidas Rempelos, University of Lincoln; Professor Ruben Sakrabani, Cranfield University; Dr Iain Gould, University of Lincoln

The UK imports a significant amount of unsustainably-mined phosphorus, with low deployment efficiency leading to environmental issues like eutrophication. Organic waste streams (e.g., manure, sewage sludge) offer potential for sustainable phosphorus use but are challenging to transport and apply. In addition, issues such as variability  in recovered phosphorus fertiliser nutrient content and stability, low micronutrient absorption in plants, and insufficient assessment of environmental impacts have led to low end-user uptake.

This exciting PhD project aims to develop a groundbreaking solution by using blends of organic waste residues as carriers for the creation of pelleted Organo-Mineral Fertilizers (OMFs) to enhance crop growth, yield, and quality, as well as improve soil health and sustainability, reducing the carbon footprint of crop production. The project will involve the development of a range of pelleted OMFs by blending different combinations/ proportions of organic waste, with varying  levels of mineral macro-micronutrient supplementation and the use of state-of-the-art sensor technologies to compare OMFs nutrient release/availability patterns and assess the potential of multiple wheat genotypes to grow with OMFs. Outputs will be scaled/validated on field trials, where the influence of OMFs accompanied by microbial biostimulants and nutrient-efficient wheat genotypes on enhancing soil health/nutrient dynamics will also be evaluated.

Training Opportunities

The project offers training covering cross-disciplinary technical and transferable skills. Training would be provided via both partners for the use of (1) various multispectral 3D scanners for canopy/root phenotyping, and image analysis to visualize plant growth and calculate a wide variety of morphological/physiological parameters, and (2) AAS, ICP-MS for heavy metal analysis, Elementar analysers for carbon, segmental flow analyser for nitrate, and spectrophotometer for phosphorus analysis. Other training opportunities include the attendance on MSc modules in areas such as soil science, plant genetics, and food quality or image/data processing, data mining, data programming in R/Python. The student will also benefit from the University of Lincoln’s Graduate School training on research skills, scientific writing, and personal development.

Project Supervision

The student will be supported by a lead supervisor and two co-supervisors representing different disciplines. The lead supervisor will be providing overall guidance and feedback, while the other members of the team will be offering specialised support/ additional feedback. In weekly one-to-one supervision and monthly full supervision team meetings progress, challenges, review of experimental results, and plan next steps will be discussed. Written feedback will be provided within two weeks of submission while oral feedback will be given during meetings. To effectively student track progress, clear action items/deadlines will be assigned, ensuring accountability and timely completion of tasks. Decisions made, actions, and follow-up points will be minuted and shared with all participants for reference. The student will also be providing regular progress reports summarizing completed tasks, ongoing work, and challenges faced.

Student Profile

This project is ideal for candidates with at least BSc (2:1) honours degree in Agricultural Sciences and Technology, Agronomy, Plant Science, Soil Science, Environmental and Biological Science, Geography, or Chemistry. Candidates from disciplines which are not directly related to the project research area should demonstrate their ability to learn and apply new concepts and skills. 

Stipend (Salary)

FoodBioSystems DTP students receive an annual tax free stipend (salary) that is paid in instalments throughout the year. For 2024/25 this is £19,237 and it will increase slightly each year at rate set by UKRI.

Equity, Diversity, and Inclusion

The FoodBioSystems DTP is committed to equity, diversity, and inclusion (EDI), to building a doctoral researcher (DR) and staff body that reflects the diversity of society, and to encourage applications from under-represented and disadvantaged groups. Our actions to promote diversity and inclusion are detailed on the FoodBioSystems DTP website and include:

• Offering reasonable adjustments at interview for shortlisted candidates who have disclosed a disability or 
specific learning difference.
• Guaranteed interview and applicant mentoring schemes for applicants, with UK home fees status, from eligible
under-represented ethnic groups. 

These are opt-in processes. 

Our studentships are offered on a part time basis in addition to full time registration. The minimum registration is 50% FT 
and the studentship end date will be extended to reflect the part-time registration.

For up to date information on funding eligibility, studentship rates and part time registration, please visit the 
FoodBioSystems website.

Applications for this opportunity are by online application form, and full details can be found on the FoodBioSystems website.