Midlands Integrative Biosciences Training Partnership (MIBTP)

Non-academic partner: Alltech UK Ltd

Secondary Supervisor(s): Dr Jules Pickard (Alltech UK Ltd), Dr James McCaughern, Dr Helen Warren, Dr Kate LeCoq

Project Outline: Unpredictable weather patterns, including drought, heat and rainfall, are placing pressure on UK forage production systems, reducing their yield and nutritional quality and impairing animal health and performance (Hart et al., 2022). Concurrently, volatile feed costs are increasing the requirement for high-quality home-grown forages. Developing resilient forage systems capable of maintaining productivity in a changing climate is therefore a priority.

Ensiling is used to preserve forages through fermentation and ensure a year-round feed supply with grass silage being the most common forage fed in the UK (Defra, 2025). Understanding and controlling the microbial and biochemical process involved in ensiling grass silage is therefore critical. The inoculation of grass at harvest with bacteria that promote a hetero or homofermentative fermentation presents an opportunity to more predictably control the ensiling process and improve forage quality. However, under certain conditions fungal growth can occur within silage and at feed out leading to the production of mycotoxins which is predicted to increase due to climate change (Kos et al., 2023). Mycotoxins are secondary fungal metabolites that can impair animal health, fertility and productivity and may enter the human food chain through milk and meat products. Most mycotoxin research has focused on maize silage with limited information available on grass silage or their effects on digestion, dairy cow health and productivity (Manni et al., 2023).

The aims of this studentship will be to investigate the effects of manipulating the fermentation of grass silage on the nutritive value and mycotoxin contamination of silage, and determine the subsequent impact on animal health and performance. Mini scale silos will be used to investigate the effects of fermentation pathways on silage quality and mycotoxin production. This will be followed by in vitro fermentation studies to investigate the effects on digestion to identify key treatments and mitigation strategies that will then be used in dairy cow performance studies.

Non-academic partner: Elsoms Seeds Ltd

Secondary Supervisor(s): Dr Justin Roberts (Elsoms Seeds Ltd), Professor James Monaghan, Dr Rodrigo Echegoyen-Nava (Elsoms Seeds Ltd), Dr Lauren Chappell

Project Outline: Plant diseases place a serious constraint on global crop production. Combined with environmental stress, they represent a significant threat to food security. The loss of protectant agrochemicals places increased reliance on crop resistance to combat disease. Therefore, new sources of disease resistance need to be identified and incorporated into novel commercial crop varieties. This requires researchers and crop breeders to identify plants with heightened resistance for use in breeding schemes and to understand the biological basis of such resistance.

This project brings together academia and industry to identify new sources of resistance to crop disease. You will use resources provided by one of the UK’s leading plant breeding companies to devise and use approaches to locate novel disease resistance with the supervisory help of crop resistance experts.

The target disease is parsnip root canker, a common but under-studied disease and a major constraint to production of this in-demand crop. It discolours the top of the root, leading to rotting, crop rejection and financial loss. Root canker is caused by a range of plant pathogenic fungi. but we know very little about the basis of plant resistance to these organisms.

You will establish a screening system that can detect parsnip resistance to root canker in developing plants. Earlier seedling and detached-root methods provided insights but do not correlate well with either each other or field observations meaning new assessment methods are required. You will then use this to search for resistance in parsnip lines provided by the industry partner and employ genetic and gene expression analysis to examine the underlying basis of resistance and determine genes contributing to beneficial traits. This will help increase crop quality and yield to help safeguard food provision for the future.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare, Plant and Crop Science

Lead Supervisor: Professor Nicola P Randall, Agriculture and Environment

Secondary Supervisor: Dr John Reade, Agriculture and Environment. Additional supervision provided by: Dr James McCaughen

Project Outline: Climate change is increasing the need for forage systems that are environmentally sustainable & resilient to changing conditions. Sainfoin (Onobrychis viciifolia) is a perennial forage legume with potential benefits including nitrogen fixation, drought tolerance, pollinator support & high nutritional value. Its tannins may also reduce methane emissions & bloating in ruminants, improve protein utilisation & disrupt some parasitic worm lifecycles.

In the UK, sainfoin is currently used mainly on thin alkaline soils in southern England. However, preliminary reviews & experiments at Harper Adams suggest it may establish across a wider range of soil types, although water availability may be limiting.

This PhD will investigate the potential for sainfoin to diversify UK forage systems, improve animal health & performance, & support environmental sustainability.

The project will:

• investigate opportunities & limitations for wider sainfoin establishment using glasshouse & field experiments examining soil type, water availability, temperature, variety & sward composition;
• determine how sainfoin can best be used in ruminant diets using proximate analysis & dietary formulation modelling to predict animal performance, production costs & emissions intensity;
• compare the economic & environmental performance of sainfoin with other forage crops using experimental data, desk research & expert elicitation;
• translate findings into practical recommendations for farmers, policy makers & industry.

The project will inform forage diversification, reduced fertiliser dependence, improved drought resilience & forage quality, lower methane emissions & more resilient regenerative farming systems.

Research Theme: Sustainable Agriculture and Food, Plant and Crop Science, Soil Science, Systems Biology

Lead Supervisor: Dr Paula Misiewicz, Agriculture and Environment / Engineering

Secondary Supervisor: Dr Leticia Chico-Santamarta, Global Impact Division. Additional supervision provided by: Peter Barnes, Engineering Department

Project Outline: Agricultural machinery traffic and tillage have major and lasting effects on soil structure and function. By altering soil density, pore space, aeration and water availability, they can influence soil carbon cycling, greenhouse-gas emissions and crop productivity. These long-term soil and crop responses contribute to the environmental sustainability of agricultural production but are often poorly represented in conventional life-cycle assessments, which frequently rely on generic emission factors and short-term assumptions.

This project will use the unique long-term Traffic and Tillage experiment established at Harper Adams University in 2011, which combines contrasting machinery traffic systems, including controlled and random traffic at different tyre inflation pressures, with deep, shallow and zero tillage. Previous research has generated long-term datasets on soil physical properties, soil carbon, greenhouse-gas emissions and crop performance, providing a unique opportunity to investigate how changes in soil functioning influence the environmental performance of agricultural management systems.

The research will quantify long-term relationships between traffic and tillage management, soil carbon dynamics, soil-derived greenhouse-gas emissions and crop productivity. These experimentally measured responses will then be integrated with data on machinery operations, fuel, fertiliser and other production inputs to develop a soil-informed life-cycle assessment framework. Conventional LCA approaches based on standard emission factors will be compared with assessments incorporating measured long-term soil and crop responses.

The project will determine whether accounting for changes in soil functioning alters conclusions about the environmental sustainability of contrasting traffic and tillage systems. It will provide a new systems-level understanding of the relationship between agricultural mechanisation, soil functioning and environmental performance.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare, Immunology, Microbiology

Lead Supervisor: Dr Tharangani Herath, Animal Health, Behaviour and Welfare

Secondary Supervisor: Dr Robert Mukiibi, Animal Health, Behaviour and Welfare

Project Outline: Yersinia ruckeri (YR), the causative agent of Enteric Redmouth Disease (ERM), is a major bacterial pathogen affecting salmonid aquaculture. Current bacterin vaccines, largely based on O1a strains, provide limited protection against emerging antigenically diverse variants, including O1b and non-motile biotype 2. Recurrent vaccine failures highlight the need for next-generation vaccines capable of providing broader cross-protection, improving fish health and welfare while reducing economic losses and antimicrobial use. 

This project aims to engineer an immunoinformatics-derived multi-epitope vaccine against YR and establish wax moth (Galleria mellonella) larvae (WML) as an ethical and rapid in vivo platform for early-stage vaccine screening. Reverse vaccinology and immunoinformatics will be used to identify conserved and immunogenic YR epitopes suitable for multi-epitope vaccine design. The selected vaccine construct will then be synthesised, recombinantly expressed, purified and characterised in vitro. In parallel, a reproducible WML infection model will be developed by optimising YR infection conditions and assessing survival and innate immune responses. Vaccine efficacy will subsequently be evaluated in immunised WML following YR challenge using survival, bacterial burden and immune-response measures as key outcomes.

By combining computational vaccine design, recombinant vaccine production and alternative in vivo screening, this project will accelerate the development of a broadly protective YR vaccine while supporting the 3R principles and reducing reliance on higher animal models during early-stage research. The project has the potential to improve disease prevention, animal health and welfare, support sustainable salmonid production and reduce dependence on antimicrobial treatments.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare, Immunology, Microbiology, Structural Biology, Regenerative Biology

Lead Supervisor: Dr Tharangani Herath, Animal Health, Behaviour and Welfare

Secondary Supervisor: Dr Emma Bleach, Agriculture and Environment. Additional supervision provided by: Dr Joe Roberts

Project Outline: Lameness is a major welfare and productivity challenge in dairy cattle in the UK and beyond. Current approaches, including mobility scoring, assess the clinical and functional consequences of disease, providing limited insight into biological processes within joints. There is a need for complementary tools to characterise joint health at a molecular level.

Synovial fluid (SF) provides a direct window into the joint, containing metabolites and proteins associated with inflammation, tissue injury, cartilage turnover and degeneration. 

This project will use synovial-fluid metabolomics and targeted protein analysis, integrated with clinical and pathology data, to develop a toolkit for characterising joint disease in dairy cattle. The samples will include SF and joint tissue collected from dairy cattle at abattoirs, alongside relevant animal information. The SF metabolome will be characterised using high-resolution mass spectrometry, while inflammatory and degenerative proteins will be quantified using biomarker assays. Molecular findings will be integrated with mobility and clinical information where available, pathology, histology and immunohistochemistry to investigate relationships between molecular changes and tissue pathology.

Metabolomic and protein data will be analysed to identify molecular features and pathways associated with inflammation, tissue degeneration, energy metabolism, lipid and amino-acid metabolism and oxidative stress. Relevant metabolites and proteins will be evaluated in additional samples where available, and combinations investigated as candidate signatures of lameness.

The project will develop a molecular toolkit for characterising joint disease, providing information on disease phenotype, biological activity and tissue pathology beyond conventional lameness assessment. In the longer term, identified markers could be investigated in blood and milk to support non-invasive disease detection.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare

Lead Supervisor: Dr Gemma Charlton, Animal Health, Behaviour and Welfare

Secondary Supervisor: Professor Jonathan Statham, Harper and Keele Veterinary School. Additional supervision provided by: Dr Pedro Machado 

Project Outline: Precision livestock farming is transforming how animal health and welfare are monitored on farms. However, many current monitoring systems rely primarily on visual, activity or production-based measures, meaning important behavioural and physiological signals may be missed. Sound within livestock environments contains a wealth of information about animal behaviour, health and affective state, yet remains relatively under-utilised in commercial dairy systems.

This PhD will investigate how bioacoustics and artificial intelligence can be combined to develop automated, non-invasive approaches for assessing dairy cattle welfare. The project will explore how acoustic information generated by cattle and their surrounding environment can be analysed to identify patterns associated with behaviour, health status and welfare-related states, and how these can be detected under realistic dairy-farm conditions.

The research will involve collecting and annotating acoustic data from dairy housing environments, conducting temporal and spectral signal analysis, and linking acoustic patterns to behavioural and health indicators. Computational models will be developed to recognise meaningful welfare-related patterns, and acoustic information will be integrated with behavioural, environmental and farm-management data to develop robust multimodal indicators of cattle welfare.

The successful candidate will undertake structured training in programming, signal processing, data analysis, computational modelling, animal behaviour and welfare science. Interdisciplinary training will span bioacoustics, precision livestock technologies and data-driven welfare assessment, providing the skills required to develop practical approaches for earlier and more objective detection of changes in dairy cattle welfare.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare

Lead Supervisor: Dr Juliana Garcia Alvarez, Animal Health, Behaviour and Welfare

Secondary Supervisor: Dr Gemma Charlton, Animal Health, Behaviour and Welfare. Additional supervision provided by: Dr Emma Bleach 

Project Outline: Premature loss of replacement heifers is an important welfare, economic and sustainability challenge for the dairy industry. The transition into first lactation is particularly demanding: heifers experience calving, onset of lactation, dietary and management changes, adaptation to milking and, commonly, integration with unfamiliar multiparous cows within a short period. Primiparous cows are still growing, are generally subordinate to mature cows and may experience greater competition and displacement from resources. Social stress at this physiologically demanding stage could therefore affect welfare, energy balance, health, fertility and productive longevity.

This project will investigate whether delaying social integration with multiparous cows until later in first lactation improves the welfare and biological resilience of primiparous cows, while minimising disruption to resident mature cows. Replacement heifers will experience contrasting social management strategies and will be followed longitudinally through the transition into first lactation and integration with the mature herd.

Behavioural and social responses will include agonistic and affiliative interactions, displacement, feeding and lying behaviour, rumination and activity. These will be integrated with physiological indicators of stress and energy balance, health, milk production, reproductive performance and retention. Intensive measurements around integration will characterise acute responses, while longer term monitoring will determine whether integration timing influences subsequent health, fertility, productivity and retention. The project will establish whether delaying integration offers a practical management strategy to improve welfare and productive longevity in dairy cattle.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare, Immunology, Systems Biology

Lead Supervisor: Dr Robert Mukiibi, Animal Health, Behaviour and Welfare

Secondary Supervisor: Dr Tharangani Herath, Animal Health, Behaviour and Welfare

Project Outline: Proliferative Kidney Disease (PKD), caused by the myxozoan parasite Tetracapsuloides bryosalmonae, is a pathogen affecting salmonid spp.  It is a major re-emerging disease threat, especially for Rainbow trout (Oncorhynchus mykiss) aquaculture production in the UK, Europe, and North America. In the UK, PKD causes annual losses of £2.5 million to the rainbow trout farming industry, highlighting the economic importance of the disease. 

The disease leads to severe kidney inflammation, reduced growth rates, and high mortality, thus lowering aquaculture output. The recent emergence and associated impacts of the disease predominantly occur in the summer months and are augmented by increased water temperatures. The heritability estimate for resistance to PKD in rainbow trout has been reported to be ~0.19, indicating the possibility of improving resistance to disease through selective breeding. Despite the widespread impact of the disease on the Rainbow trout aquaculture industry, the molecular mechanisms underlying the host’s response or resistance to this disease infection remain largely unknown. 

This proposed study aims to utilize epigenomic and transcriptomic analysis between PKD-resistant and susceptible fish to identify functional genomic signatures associated with PKD resistance. Next-generation sequencing data (epigenetic& transcriptomic) will be generated from three immune organs (gills, head kidney and spleen) from susceptible and resistant Rainbow trout fish from a commercial farm. These datasets will be analysed to identify functional genomic regions/ genes associated with susceptibility to PKD. Additionally, integrated biomarker analyses will be performed to identify stable biomarkers (epigenomic and transcriptomic) for resistance to PKD in farmed rainbow trout.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare

Lead Supervisor: Dr Emma Bleach, Agriculture and Environment

Secondary Supervisor: Dr Joe Roberts, Agriculture and Environment. Additional supervision provided by: Dr Juliana Garcia Alvarez

Project Outline: Resilient replacement heifers are critical to the productivity, profitability and sustainability of dairy systems. Achieving growth, health and fertility targets improve lifetime performance. However, substantial variation in performance exists even among cattle managed under similar conditions, suggesting that the biological origins of resilience to early-life challenges may begin before birth.

Despite extensive research into the impacts of late gestation, birth and neonatal management, marked variation in calf outcomes remains. Evidence from other species demonstrates that foetal development can have lasting effects on offspring health and performance, yet the influence of maternal physiological and production status throughout gestation remains poorly understood in cattle.

Replacement dairy heifers are born to growing nulliparous heifers, lactating primiparous heifers and multiparous cows conceiving at different stages of lactation and energy balance. These contrasting physiological states may alter the resources available to the foetus and influence development before birth.

This PhD will investigate whether variation in maternal physiological and production status during gestation contributes to differences in neonatal viability, resilience to early-life challenges and subsequent health, welfare and production. Samples associated with prenatal developmental conditions, including meconium, placenta and hair will be collected at birth to identify biomarkers associated with foetal development and gestational experience. These biomarkers, together with maternal physiological and production data, will be related to subsequent indicators of resilience, including vigour, health, growth, survival and performance. Findings will determine whether maternal characteristics contribute to offspring resilience, informing future selection and management strategies for cows used to breed replacements, with potential benefits for calf health, welfare and lifetime performance.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare

Lead Supervisor: Dr Gemma Charlton, Animal Health, Behaviour and Welfare

Secondary Supervisor: Dr Emma Bleach, Agriculture and Environment. Additional supervision provided by: Dr Holly Vickery

Project Outline: Dairy heifers experience substantial changes during the rearing period before they enter the milking herd, including changes in housing, diet and social groups, followed by calving and the onset of lactation. These challenges can affect health, welfare and performance, with consequences that may last into subsequent herd life. Despite the importance of dairy heifers, the period between weaning and first calving remains relatively neglected in dairy cattle welfare research.

Environmental enrichment (EE) provides opportunities to perform species-relevant behaviours, including exploration, foraging, play and social interaction, with potential benefits for positive welfare. While brushes are increasingly provided to enrich cattle environments, little is known about the welfare value of other forms of enrichment for growing heifers or whether benefits persist beyond the period of provision.

This PhD will investigate how EE can improve heifer welfare during rearing and whether enriched heifers cope better with the challenges of late pregnancy, first calving and entry into the milking herd. It will evaluate enrichment beyond brushes, including manipulable, exploratory and foraging-based resources, and quantify how heifers interact with different enrichment types.

Heifers will be followed longitudinally from rearing through first calving and early lactation. Behavioural observations and precision livestock technologies will quantify enrichment use, behavioural time budgets, social behaviour and activity, alongside responses to key life-stage transitions. These data will be combined with measures of health, physiology and production to determine both the immediate and longer-term welfare impacts of enrichment.

The project will provide evidence to inform practical recommendations for EE during dairy heifer rearing and determine whether improving the rearing environment can support welfare during subsequent life-stage challenges.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare

Lead Supervisor: Dr Gemma Charlton, Animal Health, Behaviour and Welfare

Secondary Supervisor: Dr Emma Bleach, Agriculture and Environment. Additional supervision provided by: Professor Mark Rutter                

Project Outline: Access to pasture provides dairy cows with opportunities to graze, explore, exercise and express a wide range of natural behaviours. Research has demonstrated that cows are motivated to access pasture and will choose between pasture and housing depending on factors such as time of day, feed availability and weather. However, simply providing pasture access does not necessarily ensure that cows experience the same welfare benefits. We still know relatively little about what makes pasture valuable to individual cows, including how much access is needed, when it should be available and how factors such as space allowance, environmental conditions access to shade, production level and individual cow characteristics influence motivation to use pasture.  

This PhD will investigate how the duration, timing and conditions of pasture access influence dairy cow behaviour, preferences and welfare. The project will examine factors such as the duration and timing of access, space allowance and environmental conditions, including the availability of shade. It will also investigate individual variation in pasture use to understand why some cows may value or use pasture differently from others.

A combination of controlled experiments and observational studies will be used. Behavioural observations will be integrated with precision livestock technologies, such as wearable activity sensors and automated location monitoring, alongside animal-level and environmental data. Environmental factors will include weather conditions and resources available within the pasture and indoor environments, such as space, shade and shelter. These data will be used to investigate the factors influencing pasture use and individual responses to pasture access.

The research will advance understanding of how access to different environments influences animal behaviour and welfare, while providing evidence to inform the design of pasture-based management systems and future welfare recommendations.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare, Immunology, Systems Biology

Lead Supervisor: Dr Robert Mukiibi, Animal Health, Behaviour and Welfare

Secondary Supervisor: Dr Tharangani Herath, Animal Health, Behaviour and Welfare

Project Outline: Despite the steady growth of the Atlantic salmon aquaculture industry, there are major challenges, especially infectious diseases that cause significant levels of losses to producers due to mortality and retarded growth. Cardiomyopathy Syndrome (CMS) is an economically important viral disease in the salmon industry, affecting adult fish and resulting in sudden deaths of infected fish. 

Despite the economic impact of the disease, controlling it remains a challenge as there are no efficient vaccines or therapeutics against the disease, and currently managed through biosecurity measures and selective breeding. Currently, there are efforts to decipher the molecular background of resistance and response to CMS via genome-wide association studies and transcriptomic studies that have identified potential genetic elements associated with the disease. Understanding the molecular background of resistance and response to CMS offers an opportunity to refine and enhance selective breeding for resistance to CMS and also avails opportunity for the development of therapeutics against the disease. The epigenome is an important component, contributing to phenotypic variation of complex traits such as disease resistance via modulation of gene expression. Hence, understanding the epigenetic background of response and resistance to CMS could contribute improvement the current selective breeding tools as well as the development of more effective vaccines and therapeutics against the disease. 

In the current study, we aim to identify epigenetic signatures associated with response and resistance to CMS in farmed salmon. The study will profile chromatin accessibility and DNA methylation alterations in key immune tissues and the heart, as a response to CMS infection in fish from a challenge study from a commercial breeding population. Finally, we will perform transcriptome profiling on the same tissues to relate the impact of epigenomic alterations to transcriptome changes.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare, Plant and Crop Science, Microbiology

Lead Supervisor: Dr Ben Clunie, Entomology / Agriculture and Environment

Secondary Supervisor: Dr Joseph Roberts, Agriculture and Environment. Additional supervision provided by: Professor Tom Pope

Project Outline: Honeybees are essential pollinators, but their health is threatened by various parasites, including Varroa destructor mites, which feed on bees and transmit damaging viruses. Control currently depends on a limited range of acaricides, and resistance is reducing the reliability of some treatments. Sustainable control therefore requires an integrated approach that combines accurate monitoring with chemical, biotechnical and biological methods.

This project will develop monitoring-led strategies for integrated Varroa management. First, the student will test whether volatile organic compounds released within hives, together with smart-hive measurements such as weight, temperature, humidity and sound, can provide early indicators of mite infestation. Second, laboratory studies will screen entomopathogenic fungi for activity against Varroa while assessing safety to honeybees. The student will investigate whether fungal infection changes mite feeding, transmission of deformed wing virus, and grooming or hygienic behaviour by worker bees. Chemical attractants will also be evaluated as a way to increase mite contact with fungal treatments and any other identified biological controls. 

Promising approaches will then be tested in replicated field trials alongside established methods such as brood interruption and organic-acid treatments. Mite numbers, virus prevalence, brood recovery, foraging, colony growth, honey yield and overwinter survival will be measured. By combining chemical ecology, insect pathology, molecular biology, behaviour and quantitative analysis, the project will deliver practical evidence for more sustainable Varroa control and healthier honeybee colonies.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare

Lead Supervisor: Dr Juliana Garcia Alvarez, Animal Health, Behaviour and Welfare

Secondary Supervisor: Dr Gemma Charlton, Animal Health, Behaviour and Welfare. Additional supervision provided by: Dr Sarah Icely

Project Outline: Early life is a critical period in pig production, during which animals experience multiple environmental, nutritional and social challenges. Weaning is particularly demanding, combining maternal separation and dietary change with relocation and mixing with unfamiliar animals. These concurrent stressors can affect behaviour, physiology, gastrointestinal health, feed intake and growth, and increase susceptibility to post-weaning diarrhoea.

Resilience, the ability to cope with and recover from challenges, is therefore important for pig health, welfare and sustainable production. The synthetic analogue of the natural Maternal Swine Appeasing Substance (mSAS), represents a non-invasive approach that may support pigs during stressful transitions. While effects of the product have been investigated, the biological mechanisms and recovery trajectories underlying resilience remain poorly understood.

This PhD will investigate behavioural, physiological, health and performance components of resilience in weaner and nursery pigs, and determine whether these can be modified using a porcine appeasing pheromone. Through controlled longitudinal studies, pigs will be evaluated during key early life challenges using measures of behaviour, physiological stress, health, post weaning diarrhoea and associated antimicrobial treatments, feed intake, growth and feed efficiency. Integration of these longitudinal datasets will quantify responses to and recovery from early life stressors and determine whether these trajectories are altered by pheromone treatment. The project will provide new insight into resilience in young pigs while evaluating a practical approach to improving welfare, health and robustness during a critical production period.

Research Theme: Sustainable Agriculture and Food, Plant and Crop Science, Microbiology, Soil Science

Lead Supervisor: Dr Paula Misiewicz, Agriculture and Environment

Secondary Supervisor: Professor Simon Jeffery, Agriculture and Environment. Additional supervision provided by colleagues from the University of Warwick (TBC)

Project Outline: Agricultural machinery traffic and tillage have major and lasting effects on soil structure and function. By changing soil density, pore space, aeration and water availability, they can influence the biological processes that control the cycling and storage of carbon and the production of greenhouse gases. However, the biological mechanisms linking long-term traffic and tillage management with soil carbon dynamics and greenhouse gas emissions remain poorly understood.

This project will use a unique long-term Traffic and Tillage experiment established at Harper Adams University in 2011. The experiment combines contrasting machinery traffic systems, including controlled and random traffic, with deep, shallow and zero tillage. Previous research has identified differences between these systems in soil physical properties, carbon dynamics and greenhouse gas emissions. The project will build on these findings to investigate the biological mechanisms underlying these responses.

The research will determine how long-term traffic and tillage affect soil microbial communities, their diversity and biological activity, and establish how these responses are related to the physical soil environment. Methods will combine field sampling with measurements of microbial biomass, soil respiration and enzyme activity, alongside DNA-based profiling of bacterial and fungal communities. These new biological data will be integrated with existing long-term datasets on soil physical properties, carbon and greenhouse gas emissions using statistical and multivariate approaches.

The project will provide new understanding of how agricultural management shapes the physical and biological soil environment and how these interactions regulate carbon cycling and greenhouse gas emissions, helping identify management practices that support productive, resilient and climate-smart agricultural soils.

Research Theme: Sustainable Agriculture and Food, Plant and Crop Science

Lead Supervisor: Dr Edward Dickin, Agriculture and Environment

Secondary Supervisor: Professor Jim Monaghan, Agriculture and Environment

Project Outline: Intercropping or polyculture is the traditional practice of growing more than one crop in the same place at the same time, with the Three Sisters of corn, beans and squash grown by Native Americans being the most famous example. As agriculture has mechanised, intercropping has been replaced by monoculture systems with greater reliance on fertilisers and pesticides. Agricultural vehicles have got larger, heavier and much more expensive, compacting soils and increasing costs.

The Hands Free Hectare project started at Harper Adams University in 2017, and uses small, light autonomous vehicles to reverse the trend and protect soils. In 2023 the vehicles were programmed to sow crops in 2m strips, the world’s first robot strip intercropping, and the system has been refined in following seasons. Strip intercropping allows each crop to be managed independently with sowing and harvesting at the optimal times and inputs applied at the optimal rates. As crops develop at different times (relay cropping), the demands for resources such as light are at different times, known as temporal complementarity and so edge rows of each strip benefit from edge effects. Our experiments show that cereal grain yields of edge rows are consistently around 150% of centre rows, so that a 10-row wide strip gives the yield of 11 rows.

The experiment was established on its current site in autumn 2024 and will be compared to the other long-term field experiments at HAU, the traffic and tillage since 2011 and regenerative agriculture since 2023.

The overall aim is to support the development of robot strip intercropping as a sustainable and productive system of agriculture. Objectives are to investigate crop physiology and how neighbouring rows interact both above and below ground, measure soil health metrics (e.g. penetrometer resistance, earthworm counts), and resilience to biotic and abiotic stresses, in comparison to the other long-term trials managed as monocultures with conventional machinery.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare

Lead Supervisor: Dr James McCaughern, Agriculture and Environment

Secondary Supervisor: Professor Liam Sinclair, Agriculture and Environment. Additional supervision provided by: Dr Joe Roberts & Dr Sandy Mackenzie

Project Outline: Metabolomics is a technique that utilises advanced analytical chemistry to provide researchers with a picture of the animal’s biochemical phenotype (Taylor et al., 2022). One area where the technique may serve to improve animal health, welfare and performance is the dietary supplementation of copper (Cu) to dairy cattle. Historically, deficiency of the element was of primary concern (Suttle et al., 2022). However, there is now substantial evidence of a significant over-supply of Cu to dairy cattle within various production systems across the globe, thereby, increasing the likelihood of poisoning (Sinclair and Atkins, 2015). 

Reasons for this over-feeding on farm are unclear but may result from a perception within the industry that “more is better,” coupled with the lack of a reliable diagnostic tests for poisoning. Recent evidence from Harper Adams University has also demonstrated sub-clinical consequences due to the over-feeding Cu. For example, McCaughern et al. (2024) reported both a decline in fertility, coupled with negative effects on liver function when dairy heifers were over-fed Cu, whilst Marsh et al. (2025) identified the boundaries above which Cu altered performance and liver function in these animals. Metabolomics can add further weight to these arguments by identifying key biological pathways responsible for these changes, as well as identifying novel biomarkers that can be used to test for Cu poisoning.   

Objectives:

1. To profile the metabolic changes which occur in dairy cattle fed excess Cu;

2. To identify novel biomarkers of Cu poisoning within ruminant animals;

3. To cross-validate potential biomarkers across a range of conditions.  

Methodology: 

Six dairy cattle studies have been undertaken at Harper Adams University in the last 15 years examining the factors influencing Cu metabolism in dairy cattle. These biobanked samples and associated recorded performance will be used for metabolomics analysis (objectives 1, 2 & 3).

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare

Lead Supervisor: Dr Laura Vickers, Agriculture and Environment

Secondary Supervisor: Dr Stephen Mansbridge, Agriculture and Environment

Project Outline: Black soldier fly larvae (BSFL) are a promising alternative protein source for livestock feed because they can convert low value organic materials into nutrient rich biomass. However, substrate composition strongly influences both larval growth and the nutritional quality of the resulting larvae (Barragan-Fonseca et al., 2018; Beniers and Graham, 2019; Gold et al., 2020; Spranghers et al., 2017). Current research has focused mainly on crude protein, carbohydrate, lipid and fibre content, with studies showing that balanced protein and carbohydrate supply improves growth, biomass production and conversion efficiency (Cammack and Tomberlin, 2017; Barragan-Fonseca et al., 2019; Gold et al., 2020).

What remains poorly understood is how the amino acid composition of the dietary substrate influences larval growth, nutrient conversion and the amino acid profile of the resulting larval biomass. The value of BSFL as a livestock feed depends not only on total crude protein, but on the quality and balance of amino acids available to the animal.

This project will formulate waste derived diets with amino acid supplementation to determine the effects of amino acid composition on BSFL growth, feed conversion and resulting larval nutritional composition. HPLC will be used for amino acid profiling, alongside LECO protein analysis, ICP-MS elemental analysis and determination of fibre, lipid, carbohydrate and ash. The project will identify how dietary amino acid supply can be manipulated to improve both insect production and the nutritional quality of BSFL as a sustainable livestock feed.

Research Theme: Sustainable Agriculture and Food, Diet and Health

Lead Supervisor: Dr Claire Munialo, Harper Food Innovation

Secondary Supervisor: Dr Eze Emekwuru, Engineering. Additional supervision provided by: Dr Jon Bentley & Dr Eric Siqueiros

Project Outline: The growing global demand for dietary protein presents a major challenge for sustainable food production. Animal proteins provide high nutritional quality and useful functional properties, but their production can have a substantial environmental impact. Plant proteins are more sustainable, but individual sources can have limitations in amino acid composition, digestibility and functionality. 

This project will investigate whether proteins recovered from brewery side streams can be combined with plant proteins to create sustainable, nutritionally valuable and functional ingredients for structured foods. 

Brewing produces large quantities of brewer's spent grain and spent yeast, both of which contain valuable proteins. However, their potential as components of tailored protein blends is poorly understood. The project will recover proteins from these side streams using food compatible extraction methods, including isoelectric precipitation. 

The recovered proteins will be characterised for yield, purity, amino acid composition, solubility and molecular properties. Their functional properties, including water holding, emulsification, rheology and gelation, will then be assessed. Proteins from brewery side streams will be combined with selected plant proteins, such as soy and lupine, to investigate whether complementary properties can overcome the limitations of individual protein sources. The effects of blend composition and concentration on protein interactions, rheological behaviour and gel formation will be studied to establish relationships between protein composition, structure and function. 

Optimised protein systems will then be evaluated using extrusion based 3D food printing as a model for structured food production. This will allow the links between protein functionality, rheology, printability and final food structure to be investigated. Products will be assessed for physicochemical and textural properties, with sensory acceptance and protein digestibility.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare

Lead Supervisor: Dr Simon Segar, Agriculture and Environment

Secondary Supervisor: Professor Tom Pope, Agriculture and Environment. Additional supervision provided by: Professor Michael Lee & Dr Joe Roberts

Project Outline: Bluetongue virus has re-emerged as a major threat to UK livestock, yet we still lack a predictive understanding of how farm environment, vector ecology and midge-associated microbes combine to determine local transmission risk. National surveillance identifies broad patterns of Culicoides activity, but farms contain highly heterogeneous habitats and microclimates that may strongly influence vector abundance, host contact and infection.

This project will investigate how farm habitat, microclimate and livestock management shape Culicoides communities and bluetongue risk. It will address three objectives: (1) quantify spatial and seasonal variation in Culicoides abundance and species composition within and among livestock farms; (2) identify environmental and management factors associated with vector hotspots and livestock exposure; and (3) determine whether variation in midge species, microbiome composition and endosymbionts is associated with bluetongue infection. As part of our work we will seek to develop effective lure-based trapping.

Repeated field sampling will combine Culicoides trapping with microclimate monitoring, habitat mapping and livestock-management data. Morphological and molecular identification will be complemented by targeted high-throughput sequencing of selected midges to characterise species identity, bacterial associates including Wolbachia and Cardinium, and viral diversity, with RNA-based methods used for bluetongue detection and strain characterisation. Hierarchical and spatial models will integrate ecological, environmental and molecular data to identify the strongest predictors of vector activity and infection.

The project will deliver a mechanistic, farm-scale understanding of bluetongue vector risk and identify opportunities for sustainable disease-risk reduction. It will provide interdisciplinary training in entomology, molecular ecology, genomics, bioinformatics and quantitative disease ecology.

Research Theme: Sustainable Agriculture and Food, Plant and Crop Science

Lead Supervisor: Professor Tom Pope, Agriculture and Environment

Secondary Supervisor: Dr Joe Roberts, Agriculture and Environment. Additional supervision provided by: Dr Ben Clunie

Project Outline: Background - The cabbage stem flea beetle (CSFB) is an economically important pest of oilseed rape (OSR) crops responsible for large economic losses and reduced crop area. Development of effective and sustainable solutions for the management of this pest are urgently needed. However, progress has been hindered by a lack of knowledge of the biology of this species in relation to the influence of temperature on development and abundance and how CSFB adults respond to plant species used as cover crops and whether these responses are influenced by the volatile organic compounds (VOCs) produced by host and non-host plants. Finally, few studies have previously investigated responses of female and male CSFB to conspecifics and the role of VOCs in mate location.

The aim of this project is to improve management of CSFB through improved understanding of the biology of this species.

Objectives:
1. Investigate the influence of temperature on development of CSFB life stages.

2. Investigate the physiochemical cues that determine the timing of CSFB egg hatch.

3. Record behavioural responses of adult CSFB to host and non-host plants, including those species widely used as cover crops by farmers.

4. Record the behavioural responses of female and male CSFB adults associated with mating.

5. Identify VOCs associated with behavioural responses to host/non-host plants and conspecifics.

Methods: 
The influence of temperature on CSFB development (O1) will be investigated under laboratory conditions using constant and fluctuating temperatures. Each developmental stage of the CSFB life cycle will be studied. Physiochemical cues determining timing of egg hatch (O2) will be investigated through analysis of root exudates.  Behavioural responses of adult CSFB (O3 & O4) will be recorded using olfactometer experiments recorded using an Ethovision XT system. Identification of VOCs associated with behavioural responses of CSFB adults (O5) will be done through use of air entrainments.

Research Theme: Sustainable Agriculture and Food, Plant and Crop Science

Lead Supervisor: Professor Karl Behrendt, Harper Adams Business School

Secondary Supervisor: Dr Kanthu Joseph Mhango, Agriculture and Environment. Additional supervision will be provided by a subject specialist in pastures and grazing.

Project Outline: UK grazing livestock systems are increasingly exposed to drought, heat, waterlogging and changing pasture-growing seasons. Their resilience depends on anticipating pasture quantity and quality, yet prediction is difficult because weather, soils, sward condition, fertilisation, liming and grazing interact dynamically. Process-based models represent these mechanisms but contain structural and parameter uncertainty. Machine-learning models can identify complex relationships, but may require large datasets, violate biological constraints and extrapolate poorly to climatic extremes.

This project will develop a Knowledge-Guided Machine Learning (KGML) framework for forecasting UK pasture growth and quality under climate uncertainty. Mechanistic knowledge and simulated states from the established Sustainable Grasslands Model (SGM) (Behrendt et al, 2020) will guide learning from weather, soil, pasture, management and remote-sensing observations. An initial data-readiness assessment will establish whether available datasets provide adequate temporal, spatial and management coverage, and identify priority gaps.

Process-based, conventional machine-learning and KGML models will be compared using validation across withheld sites, years and extreme climatic periods. KGML methods may include process-model residual correction, biologically informed predictors, and constraints on biomass accumulation, grazing removal and regrowth. Performance will be assessed through accuracy, uncertainty, biological consistency and transferability between upland and lowland systems.

The best-performing pasture model will be integrated within the SGM. Stochastic simulation and bioeconomic optimisation will evaluate grazing, fertilisation, liming and supplementary-feeding strategies. The project will test whether better real-time forecasts reduce feed deficits and downside financial risk, improving the resilience and profitability of UK livestock farms under climate and market uncertainty.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare

Lead Supervisor: Dr Malgorzata Behnke, Animal Health, Behaviour and Welfare

Secondary Supervisor: Dr Holly Vickery, Animal Health, Behaviour and Welfare. Additional supervision provided by: Dr Gillian Tabor

Project Outline: Stereotypical behaviours (ex. crib biting, wind sucking, weaving and box walking) are prevalent within Thoroughbred racehorse populations and are increasingly recognised as indicators of compromised welfare. Although these behaviours are generally considered to arise from interactions between environmental, management and individual factors, increasing concern exists regarding their potential implications for musculoskeletal health. 

Veterinary physiotherapy is increasingly incorporated into the management and rehabilitation of racehorses. However, despite widespread clinical application, objective evidence supporting its use in managing secondary musculoskeletal consequences associated with stereotypical behaviours is lacking. Using a combination of behavioural observation, quantitative assessment of musculoskeletal function, and structured welfare evaluation, the student will investigate whether targeted interventions can influence behavioural expression or physical outcomes. 

The overarching aim is to generate evidence that supports improved equine welfare and informs best practice in training, management and rehabilitation.  

The objectives are to: 
1) Establish associations between stereotypical behaviour and musculoskeletal status in racehorses. 

2) Evaluate the effect of veterinary physiotherapy on stereotypical behaviour frequency and duration compared with untreated controls. 

3) Quantify longitudinal changes in musculoskeletal parameters following veterinary physiotherapy intervention compared with baseline and control groups. 

4) Determine associations between changes in stereotypical behaviour, musculoskeletal status, and training load to inform evidence-based approaches to equine welfare and management. 

This project offers scope for interdisciplinary development, quantitative analysis, and engagement with industry stakeholders, while allowing the student to shape the specific research questions within the broader theme.

Research Theme: Sustainable Agriculture and Food, Plant and Crop Science, Systems Biology

Lead Supervisor: Dr Joe Roberts, Agriculture and Environment

Secondary Supervisor: Professor Tom Pope,  Agriculture and Environment. Additional supervision provided by: Dr Ben Clunie

Project Outline: Background: Aphid parasitoids develop inside living hosts and eventually transform them into protective mummies. During final infection, parasitised aphids may leave feeding sites and die elsewhere on the plant. This is often labelled parasite manipulation, but it is unresolved whether the developing wasp controls movement, whether destination choice is plastic, and whether it improves parasitoid fitness. This project tests the hypothesis that parasitoids manipulate host behaviour to construct a favourable thermal and hydric niche for pupation.

If this is the case, terminal movements should track available fine-scale microclimates, vary among parasitoid families and place mummies where survival and reproductive performance improve under heat and drought. The project will distinguish adaptive manipulation from host pathology, fixed aphid preferences and passive differential survival through three key objectives:

1) Determine how parasitised aphids alter pre-mummification movement across plant microclimates under heat and drought.

2) Test whether naturally selected mummy locations causally improve parasitoid survival and adult performance.

3) Partition host, parasitoid-family and environmental contributions to final location and fitness.

Methods: Using Ephedrus cerasicola and peach potato aphid, synchronised parasitism and whole-plant video will reconstruct movement during the 48 hours before mummification. Temperature, relative humidity and vapour-pressure deficit will be mapped at leaf scale under independently controlled heat and humidity treatments and engineered microclimate mosaics. Causality will be tested by relocating age-matched mummies between selected and avoided sites, with sham-handled controls, and replaying corresponding profiles in environmental chambers. Emergence, development, sex ratio, adult size, longevity, egg load and subsequent parasitism will be measured.

Research Theme: Sustainable Agriculture and Food, Plant and Crop Science

Lead Supervisor: Dr Joe Roberts, Agriculture and Environment

Secondary Supervisor: Professor Tom Pope, Agriculture and Environment. Additional supervision provided by: Dr Joseph Mhango

Project Outline: Background: Farmers and crop advisers usually discover aphid outbreaks only after numbers have increased. Yet colonies may change how they feed, move and respond to danger days before abundance changes. Whether these transitions constitute repeatable biological states, and whether they forecast population growth, dispersal or decline, remains unknown. This project tests behaviour as a mechanistic early-warning signal rather than merely a correlate of pest density.

The central hypothesis is that plant quality, temperature, crowding and natural-enemy cues move colonies among a small number of measurable behavioural states, and that state transitions contain predictive information not captured by current aphid counts or environmental measurements. The project will address three key objectives:

1) Quantify behavioural and feeding-state responses to plant quality, temperature, colony density and natural-enemy cues.

2) Determine whether behavioural-state transitions forecast subsequent population growth, dispersal or decline beyond current abundance and environmental measurements.

3) Test transferability across aphid genotypes and in a cereal aphid–wheat system.

Methods: Peach-potato aphids on brassica plants will be exposed to independently varied plant quality, temperature, colony density and natural-enemy cues in randomised, replicated experiments. High-resolution macro-video will be synchronised with electrical penetration graph recordings and 7–14-day measurements of survival, reproduction and winged-morph production. Explainable computer-vision models will track individuals and quantify feeding, walking, resting and alarm behaviour. Hidden semi-Markov and Bayesian state-space models will identify states and test whether transitions improve forecasts beyond baseline counts and environment. Randomly timed perturbations will strengthen causal inference. Models will be validated prospectively on held-out runs, unseen aphid clones and a cereal aphid on wheat.

Research Theme: Sustainable Agriculture and Food, Plant and Crop Science

Lead Supervisor: Professor Simon Jeffery, Agriculture and Environment

Secondary Supervisor: Professor Tom Pope, Agriculture and Environment. Additional supervision provided by: Dr Joe Roberts

Project Outline: Agriculture faces increasing pressure to produce food while protecting environmental health. This has driven growing interest in alternative approaches, including regenerative agriculture. Regenerative agriculture seeks to improve soil health by minimising soil disturbance and working with soil organisms to harness the ecosystem services they provide. Although interest is increasing, less than 5% of UK arable land is currently managed using regenerative approaches.

Interactions between organisms above and belowground are important drivers of ecosystem function. Changes in soil biological communities can influence plant health and interactions with insects, including pollination, natural pest control and herbivore feeding. Understanding these links could help reveal how regenerative agriculture influences wider ecosystem processes.

Arbuscular mycorrhizal (AM) fungi form beneficial associations with plant roots, improving plant access to nutrients and water. They are often more abundant where soil disturbance is minimised, but their effects on aboveground plant-insect interactions remain poorly understood, particularly under UK field conditions.

This project will investigate how regenerative and conventional agricultural management influence interactions between crops and AM fungi, and how these belowground relationships affect plant-insect interactions aboveground. It will use established, long-term, systems-level field experiments, combining field measurements with analysis of plant, AM fungal and insect responses. Particular emphasis will be placed on how AM fungi influence chemically mediated interactions between plants and insects.

The project will improve understanding of links between soil biology, plant health and aboveground biodiversity, helping identify how regenerative agriculture can harness beneficial soil-plant-insect interactions to support sustainable crop production.

Research Theme: Sustainable Agriculture and Food, Plant and Crop Science, Plant Science

Lead Supervisor: Professor Jim Monaghan, Agriculture and Environment

Secondary Supervisor: Professor Miriam Gifford, School of Life Sciences - University of Warwick. Additional supervision provided by: Dr Andrew Beacham 

Project Outline: Breeding crops which are resilient to climate change is becoming increasingly essential, and plants that quickly establish root systems have the potential for faster establishment, improved tolerance to abiotic stresses and decreased reliance on inputs such as fertilisers (Roberts et al. Annals of Applied Biology 2020). Hence, root traits are a key area of interest in respect to sustainable intensification of production systems.

This project investigates newly isolated CRISPR rapid rooting lines in lettuce (Lactuca sativa) that originate from previous PhD research carried out in collaboration between the supervisory team. 

The project has three aims which can be pursued in parallel, maximising the chance of student success:

1) Characterisation of rapid rooting lettuce lines, using plant genotypes that are available from a recent PhD project. This will involve confirming CRISPR edits then carrying out preliminary phenotypic and molecular analysis to characterise the mechanism of beneficial effects on lettuce growth and yield.

2) Phenotypic analysis of rapid rooting lettuce lines in greenhouse and commercial growing conditions (including hydroponics) in order to document full-cycle performance in hydroponic systems used by growers.

3) Determine the impact of rapid rooting on other traits including drought resilience and nutrient stress conditions. Bioassays that lead to detrimental stress effects in wild-type plants will be run for rapid rooting lines to test for additional beneficial effects. 

The project benefits from having access to both the excellent crop research facilities and growth techniques (Wharton et al. Plant Methods 2025) and links to industry partners at Harper Adams University, as well as the bioinformatics and molecular expertise at the University of Warwick.

Overall, the work will validate the agronomic benefits of affecting rapid rooting expression on lettuce yield, and assess impacts on drought tolerance and nutrient uptake

Research Theme: Sustainable Agriculture and Food, Plant and Crop Science

Lead Supervisor: Dr Andrew M Beacham, Agriculture and Environment

Secondary Supervisor: Professor Dawn Arnold, Professor and Associate Pro-Vice Chancellor (Research and Research Culture). Additional supervision provided by: Becky Howard, Processors and Growers Research Organisation (PGRO)

Project Outline: Sustainable production of sufficient food during the current climate requires consideration of what we eat and how we grow it. Plants represent sustainable dietary protein alternatives to meat. Legume crops, such as peas and beans, are not only protein-rich, but thanks to their relationship with nitrogen-fixing bacteria, offer soil health benefits, reduce agricultural inputs and improve environmental stewardship. However, like all crops, legumes suffer from challenges of pests and environment. 

Peas are a prime legume crop, worth £71M in the UK alone. A key disease of peas is leaf and pod spot, which causes plant death, yield and quality loss. Current control options are limited due to poor resistance in commercial pea cultivars and reduced chemical protection options. Novel control options for this disease are therefore needed.

Naturally occurring soil fungi can reduce crop disease. However, these ‘biocontrol’ agents have not been evaluated against leaf and pod spot in peas. Antitranspirants, coatings applied to plant surfaces to reduce water loss and drought stress, can also reduce disease. These, similarly, have not been tested against pea leaf and pod spot.

In this project, you will investigate fungi and antitranspirants as control options for leaf and pod spot. Diverse pea varieties will first be screened for resistance to the disease. Selected pea varieties will then be used to examine the effect of fungi and antitranspirants on disease control. Examination of the biology of the interaction between pathogens and control products will provide understanding of underlying control mechanisms. 

This work will provide valuable data regarding the influence of pea genetics on leaf and pod spot resistance and reveal potential novel control options to help combat this disease. They are of key importance to the agriculture industry in driving the durability and sustainability of dietary protein provision and agricultural sustainability.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare

Lead Supervisor: Dr Holly, Animal Behaviour, Health, and Welfare

Secondary Supervisor: Dr Ellen Williams, Animal Health, Behaviour and Welfare. Additional supervision provided by: Helen Braid, Senior Lecturer in Equine Practice, University of Liverpool

Project Outline: Animals are routinely used to teach clinical skills to veterinary students (McGreevy et al. 2007) yet there is a lack of legislation in relation to their use and little research quantifying welfare impacts. Within veterinary education (VE), requirements differ across accrediting bodies however providers are required to have animal use policies in place (AVMA, 2025; RCVS, 2023). Consultations with VE colleagues highlighted a lack of guidance on creating animal-use policies. Animals in VE are routinely exposed to a range of handling from potentially positive (e.g. light muscular palpation) to more aversive practicals (e.g. rectal examinations). Preliminary work undertaken by the project team has shown behavioural changes in companion and farm animals (Sadler et al., 2024). Students demonstrate a preference for teaching ith live animals over the use of non-animal alternatives (Elcoro et al., 2013) and the practical nature of the activities is able to meet the needs of different learning styles (Vemulapalli et al., 2017). However, benefits for students must be weighed against animal welfare. There is an urgent need to quantify the impact of veterinary education provision on animals and to understand the impact of non-animal alternatives on students.

Objectives and methods 

Determine current animal use and perceived impacts of VE on animals through a delphi consultation with colleagues in veterinary education. Consultation will focus on animal use, monitoring protocols and perceived areas of welfare compromise.  

Quantify the impacts of current VE practicals on animals used in VE through cross-disciplinary experiments. Analysis will focus on interactions between animal personality, health and practical type and animal responses 

Understand the impacts of animal models in VE provision through assessing student experiences and skills development when using non-animal model alternatives 

Evidence-based best practice guidelines for animal use in VE will be developed

Research Theme: Sustainable Agriculture and Foo, Animal Health and Welfare

Lead Supervisor: Dr Holly Vickery, Animal Behaviour, Health, and Welfare

Secondary Supervisor: Dr Ellen Williams, Animal Health, Behaviour and Welfare

Project Outline: Across both further and higher education farm animals are routinely used to teach students (McGreevy et al., 2007). In the UK, there are approximately 130 school farms used to support teaching (Cooke, personal communication). Farm animal teaching activities vary from observational (e.g. gait assessments, behavioural monitoring), to routine husbandry (foot trimming, health checking) or more invasive clinical skills (ex. pregnancy diagnosis via rectal examinations). Live animal use in education is considered essential for developing the required familiarity and proficiency expected of graduates (Vemulapalli et al., 2017). Whilst evidence demonstrates varied effects of human-animal-interactions on farmed animals (Mota-Rojas et al., 2020), literature in relation to the specific context of educational use is lacking. There is an urgent need to collect an evidence base quantifying the impact of educational training sessions on farmed animals, to inform welfare-friendly educational guidelines which support student learning without compromising animal welfare.  

Objectives:

Quantify current farmed animal use in education with consideration of species, production cycle stage and skills taught. Consult with farm staff and academics to understand perceived welfare impacts and barriers to improved welfare.  

Quantify the welfare impacts (short and longer term) of current educational use on farmed animals on animal behaviour (activity budgets, qualitative behavioural assessment) and health data (locomotion, milk yield etc.), with consideration of species-specifics impacts and animal individuality. 

Develop evidence-based best practice guidelines for animal-welfare monitoring protocols for farmed animals in education.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare, Plant and Crop Science, Plant Science

Lead Supervisor: Dr Matthew J. Hill, Agriculture and Environment

Secondary Supervisor: Dr Simon Segar, Agriculture and Environment. Additional supervision provided by: Dr Alexander Watson-Lazowski, Professor Jan Axmacher, University College London

Project Outline: Globally, ~75% of crops are reliant on insect pollination, yet even for plants with obligate insect pollination there is concern regarding over reliance on honeybees, and a recognition that functional diversity of pollinators is vital. Ponds are widely recognised for their ecosystem services within agricultural landscapes, however these habitats are seldom considered as a provider of pollination and pest control services. 

This PhD project will address core knowledge gaps in our understanding of the relationship between ponds, pollination and pest management. First, studies that have considered the contribution of ponds to pollination have focussed on soft fruit yield and on broad faunal groups. Furthermore, it is not clear how the pollination services provided by ponds compare to other semi-natural habitats. This PhD will examine the impact of ponds on the taxonomic and functional diversity of pollinator species and will assess oil seed rape and soft fruit yield in areas where ponds are present, where other semi natural habitats are present, and where there is only cropland. Second, previous research has failed to consider how many ponds may be required to contribute to crop yield, where the ponds should be situated across the landscape, and if pond restoration increases pollinator services. 

This PhD will identify the effect of pond restoration on pollinators and crop yield, and the structure of pond networks to increase crop productivity at a landscape scale. Finally, minimal have assessed the importance of ponds for natural pest management. This PhD will examine the relationship between pond habitats and pest management among oilseed rape and soft fruit crops. Specifically, this PhD will identify which pest predators are benefitting from the presence of ponds and the relationship between pond habitat and pest abundance on proximal crops. Opportunities for the integration of pond networks into existing integrated pest management (IPM) plans will also be explored.

Research Theme: Sustainable Agriculture and Food, Animal Health and Welfare

Lead Supervisor: Dr Kirstie Pickles, Harper and Keele Veterinary School

Secondary Supervisor: Dr Emily Craven, Harper and Keele Veterinary School. Additional supervision provided by: Dr Veronica Roberts, University of Bristol

Project Outline: Trigeminal-mediated headshaking (TMHS) is an equine neuropathic facial pain syndrome characterised by violent, repetitive, predominantly vertical movements of the head and signs of nasal irritation. The trigeminal nerve is ten times more sensitive in TMHS horses than in control horses, and this is thought to result in neuropathic facial pain. Some horses are seasonally affected and there is a complex interaction with environmental triggers e.g. pollen or wind. Although TMHS can occur at rest, episodes are more severe at exercise. Recently facial pain scores have shown that severely affected horses experience pain in between, as well as during, clinical episodes. As there is currently no cure, management is aimed at reducing triggers and controlling clinical signs. If clinical signs cannot be managed, euthanasia may be necessary on welfare, and/or safety grounds, or because horses are unable to perform to their intended level. As such, TMHS has a significant impact on equine welfare, horse-owner interactions and economics. The impacts of the condition have not been quantified, meaning decision making for both horse and the affected stakeholders using the one welfare approach are hard to determine.

Aim: To quantify the daily welfare impact of equine trigeminal-mediated headshaking (TMHS)

Objectives: 
1. To explore welfare assessment in TMHS using validated quality-of-life measures and use of qualitative behavioural assessment scores at rest and exercise
2. To develop and validate computational methods for automated detection and classification of TMHS-associated head movements from continuous accelerometer data and/or video recording algorithms collected during normal activity
3. To investigate daily behaviours and time budgets of TMHS horses using quantitative and qualitative assessments
4. To design and validate a quality-of-life measure for TMHS 
5. To explore the emotional burden of management of TMHS horses in owners and caregivers

Research Theme: Renewable Resources and Clean Growth, Industrial Biotechnology, Microbiology, Soil Science

Lead Supervisor: Dr Lucy Crockford, Agriculture and Environment

Secondary Supervisor: Dr Simon Cooper, Engineering. Additional supervision provided by: Dr Paula Misiewicz 

Project Outline: Land drainage has been a key factor in realising the production potential of agricultural land for food production but has wider environmental impacts.

This project proposes to investigate the use of bio-based materials, including woodchip, biochar, and other biodegradable carbon-rich media, within unlined subsurface drainage channels to promote denitrification of nitrate-enriched waters. Such systems have the potential to combine effective drainage with in-situ nutrient attenuation, carbon storage, and enhanced soil ecological function, providing a sustainable alternative to conventional drainage infrastructure.

Methodology
The project will evaluate the hydraulic, biogeochemical, and environmental performance of biological drainage media through a combination of laboratory experiments, field trials, and numerical modelling.

Using an established research protocol, this project will characterise a range of candidate materials (e.g. hardwood and softwood chips, biochar, and other organic media) for hydraulic conductivity, structural stability, decomposition rate, nutrient retention, and carbon release. Experimental field-scale bioreactors and drainage trenches will be established to compare drainage performance, nutrient removal efficiency, greenhouse gas emissions, and operational longevity under varying soil and climatic conditions.

Monitoring will include soil moisture, water table dynamics, drainage flow, nitrate, phosphorus, dissolved organic carbon, and microbial community development. Finally, modelling will be used to optimise system design and evaluate the economic benefits of the novel systems.

Expected Outcomes
The project will establish the scientific and engineering basis for bio-based subsurface drainage systems capable of delivering effective land drainage while simultaneously reducing nutrient losses, improving soil ecological function, and lowering the environmental footprint of agricultural drainage infrastructure.

Research Theme: Renewable Resources and Clean Growth, Industrial Biotechnology

Lead Supervisor: Dr Marie Kirby, Agriculture and Environment

Secondary Supervisor: Professor Simon Jeffery, Agriculture and Environment

Project Outline: Modern agriculture is required to produce ever increasing quantities of food, both for humans and livestock, from a reducing land area. To maximise crop production, agriculture relies on nutrient inputs, sourced from internationally traded artificially made fertilisers and through the re-use of locally available animal excreta (slurries and anaerobic digestates). The manufacture of artificial fertilisers requires a significant amount of fossil fuel and mined rock phosphorus, increasing the carbon footprint of the food we eat. Their continued use is now considered unsustainable.

A considerable proportion of the phosphorus and nitrogen fertiliser nutrients applied to soils are captured in animal slurries and anaerobic digestates. Legislation dictates when and how they can be applied to soil for crop growth, but their land application is time-consuming, increases soil compaction and if applied incorrectly, can result in the loss of nutrients to the environment. Slurry and anaerobic digestates are applied to meet the crop's nitrogen requirement, causing an overapplication of phosphorus. To overcome this, phosphorus and nitrogen can be removed from animal slurries and anaerobic digestates prior to soil application. Previous research at HAU has demonstrated that >98% of phosphorus can be removed from animal slurry using a novel electrocoagulation technology, with the recovered phosphorus remaining bioavailable for future crop use. 

This PhD project will develop this research, concentrating on the recovery of phosphorus and nitrogen from slurries and digestates, leaving only water for further reuse. The project will explore the optimisation of this novel technology and the further use of these recovered nutrients for crop utilisation to offset artificial fertiliser use. The potential environmental impacts and associated carbon footprints from these recovered nutrients will be explored in comparison with other current nutrient application approaches.

Research Theme: Renewable Resources and Clean Growth, Plant and Crop Science, Bio-energy, Plant Science

Lead Supervisor: Dr Simon Segar, Agriculture and Environment

Secondary Supervisor: Dr Joe Roberts, Agriculture and Environment. Additional supervision provided by: Dr Martin Volf, Department of Ecology, Czech Academy of Sciences

Project Outline: Willow short-rotation coppice (SRC) is an important renewable biomass crop, but insect herbivory can reduce productivity and threaten the sustainability of low-input bioenergy systems. The blue willow beetle Phratora vulgatissima is a major UK pest and shows strong preferences among willow genotypes, yet the chemical mechanisms underlying resistance, host choice and pest movement through genetically diverse plantations remain poorly understood. Recent work shows that SRC willow genotypes differ markedly in metabolomic profiles and that neighbourhood composition can alter both plant chemistry and herbivory. Willow species and hybrids also differ in constitutive and herbivore-induced volatile organic compounds (VOCs). However, these strands have not been integrated to identify the chemical traits that make bioenergy willows resistant or attractive to pests.

This project will determine how constitutive and herbivore-induced chemistry shapes pest resistance in bioenergy willow. It will (1) quantify beetle preference, feeding, oviposition and performance across contrasting commercial and experimental willow genotypes; (2) characterise leaf metabolites and VOCs before and after herbivory using untargeted metabolomics and volatilomics; (3) test candidate chemical cues using behavioural assays and, where appropriate, electrophysiology; and (4) determine whether mixtures of chemically contrasting genotypes disrupt host finding or generate associational resistance.

Multivariate and machine-learning approaches will integrate chemical fingerprints with insect behaviour and plant damage to identify predictive markers of resistance. The project will connect mechanistic chemical ecology with crop protection and bioenergy production, providing principles for breeding and deploying pest-resilient willow cultivars and mixtures while reducing reliance on insecticides.

Research Theme: Understanding the Rules of Life, Immunology, Neuroscience and Behaviour, Systems Biology

Lead Supervisor: Dr Tharangani Herath, Animal Health, Behaviour and Welfare

Secondary Supervisor: Dr Robert Mukiibi, Animal Health, Behaviour and Welfare. Additional supervision provided by: Dr Ellen Williams 

Project Outline: Environmental enrichment can improve fish welfare by providing opportunities for exploration, shelter and natural behaviours. However, we do not know whether long-term enrichment causes persistent biological changes beyond immediate behavioural and physiological responses. In particular, it is unclear whether enrichment alters DNA methylation in breeding fish and whether these changes are detectable in their gametes and offspring.

This project will determine whether long-term environmental enrichment alters welfare, stress and immune function in common carp and whether these responses are associated with DNA methylation changes detectable in the germline and offspring. To test our hypothesis, adult carp from a common breeding population will be maintained in either standard, structurally simple aquaria or enriched aquaria providing greater physical and spatial complexity. The fish husbandry conditions will be controlled between treatments. Behavioural, physiological and immune indicators will be measured over time to assess welfare. DNA methylation will be compared between treatments in adults, sperm and eggs to identify enrichment-associated changes and determine whether they occur in the germline. To test whether the enrichment-associated DNA methylation changes occur in the germline and remain detectable in developing offspring, embryos and offspring will be reared under identical common-garden conditions and sampled at defined developmental stages. DNA methylation will be compared across parents, gametes and offspring, alongside offspring behavioural and physiological measures.

The project will establish whether environmental enrichment influences the germline epigenome and associated changes persist into offspring. By linking captive environment, welfare and epigenetic responses, the findings will advance understanding of environmental effects on fish biology and provide evidence to improve captive fish welfare, husbandry and environmental design.

Research Theme: Understanding the Rules of Life, Plant and Crop Science, Soil Science

Lead Supervisor: Dr Samuel Eze, Agriculture and Environment

Secondary Supervisor: Professor Simon Jeffery, Agriculture and Environment

Project Outline: Soil health is typically evaluated by combining physical, chemical and biological measurements. Earthworms are among the most practical biological indicators because they are relatively simple and inexpensive to survey and respond to changes in land management. Measures of earthworm abundance and community composition provide valuable evidence of soil condition. Nevertheless, such measures provide a snapshot of the biological community and offer limited insight into how an intact soil system operates when environmental conditions change.

This study proposes to examine soil health through dynamic biological responses rather than presence alone. Earthworms will be used as responsive biological probes within intact soil, with their behaviour monitored as the soil is subjected to defined and repeatable perturbations. Controlled changes in e.g., moisture and mechanical conditions will provide standardised challenges, while continuous observations of earthworm activity will be combined with measurements of associated physical, chemical and biological changes in the soil. Established soil-health measurements will be collected in parallel to determine whether behavioural responses capture functional information that conventional indicators do not reveal.

The research will address a fundamental question: Can the dynamic response of soil organisms to a standardised perturbation reveal a measurable dimension of soil function that is not captured by conventional soil-health indicators? If demonstrated, this would extend the role of earthworms beyond their established use as indicators of biological condition. Rather than simply asking how many organisms are present, the approach would examine how a living soil system responds when deliberately challenged. This will help to establish a functional soil-health assessment framework that retains the accessibility of biological indicators while adding a dynamic measure of soil-system behaviour

Research Theme: Understanding the Rules of Life, Animal Health and Welfare, Neuroscience and Behaviour

Lead Supervisor: Dr Ellen Williams, Animal Health, Behaviour and Welfare

Secondary Supervisor: Dr Jack Bamber, Agriculture and Environment. Additional supervision provided by: Dr Kat Hamill, Nottingham Trent University

Project Outline: Red squirrels (Sciurus vulgaris) are an important native species maintained in zoos across the UK as part of regulated, conservation breeding programmes. They are housed in a variety of enclosures that differ in design, complexity, social composition and management. Zoos represent a novel, highly variable environment in which animals must adapt to social, physical and management conditions that differ from the wild. Understanding how individual characteristics interact with environmental conditions within these systems can provide valuable insights into behavioural development and plasticity, which can shape animal management from the perspective of welfare and conservation. This PhD aims to investigate the development and expression of behavioural phenotypes in zoo-housed red squirrels, with a particular focus on interactions between individual traits, developmental history, and environmental conditions across life stages.

Objectives/methods:

1) Characterise behavioural phenotypes (at species and individual level) in zoo-housed red squirrels through multiple measures of personality and behaviour, including responses to novelty, exploratory behaviour, activity patterns and keeper questionnaires

2) Understand how individual characteristics (e.g. age, sex, personality and developmental history) influence behavioural variation through longitudinal behavioural monitoring. Where feasible, assessments will focus on the emergence and development of behavioural phenotypes in kittens from early life through maturation 

3) Quantify the influence of environmental conditions on behaviour and welfare through multi-zoo comparisons and targeted observational studies

4) Develop evidence-based recommendations for in-situ and ex-situ red squirrel management to promote positive behavioural outcomes and support conservation breeding programmes, based on behavioural, environmental and welfare data collected across a suite of zoological collections