PhD opportunities

Title: Testing for the occurrence of adaptive haplotypes in a wild relative of wheat

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Understanding and exploiting the genomics and genetic diversity of crop species and their wild relatives is crucial in order to develop the next generation of crops. Genomic studies of wild relatives of crop species hold a great promise to recover some or most of the functional diversity lost during domestication and further selection processes.

Although recombination is required to create and break allele combinations, recent findings show that plant adaptation requires the maintenance of successful allele combinations in the form of non recombining chromosomal regions extending several megabases [1].

This project aims at testing for the occurrence of blocks of coadapted genes (non recombining haplotypes) in Aegilops tauschii, a wild relative of wheat which contributed to the domestication of the hexaploid modern wheat (D genome). A. tauschii is diploid and its genome has been recently sequenced [2].

This PhD offers the opportunity to work with two research groups: Dr R Bergero from SRUC and Dr M Hartfield, from the Institute of Evolutionary Biology, University of Edinburgh, with complementary areas of expertise in plant genetics and evolutionary genomics (Dr. Hartfiled, University of Edinburgh).

You will learn how to generate sequencing reads from natural accessions of A. tauschii from the Mazandaran Province, Iran (covering the natural distribution of the sublineage L2E, which represents the closest ancestor of the wheat D genome [3]),  map sequencing reads to the reference genome, retrieve polymorphisms, identify non-recombining haplotypes and test for haplotypes underlying plant adaptation and ecotype differentiation.

Linkage disequilibrium analyses coupled with coalescence and phylogenetic analyses will be employed to estimate haplotype size, age and origin in genomes of this wild relative of wheat. Functional characterisation of the identified haplotypes will be carried out together with association analyses of the phenotypic diversity of A. tauschii natural accessions from Mazandaran Province (Iran). Such knowledge will aid in further characterizing the large and complicated genomes of wheat and will help identify new elite coadapted alleles for developing the next generation of wheat cultivars.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Roberta Bergero, Dr David Marshall and Dr Matthew Hartfield

[1] Todesco et al. (2020) Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature  584, 602-607.
[2] Jia et al. (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496, 91-95.
[3] Zhou et al. (2021) Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement. Nat. Plants 7, 774-786.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/RB.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Integrating trees into agricultural landscapes to enhance biodiversity and associated ecosystem services

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Tree planting is at the forefront of the current environmental agenda to mitigate climate change and the biodiversity crisis. For instance, the Scottish Government has a current target of planting 12,000 ha of trees per year, increasing to 15,000 ha from 2024. Agricultural land covers over 70% of the UK, so it is likely that a large proportion of tree cover expansion will take place on farmland.

Given the many demands we place on rural landscapes, alongside the semi-permanency of tree cover, it is crucial to determine the spatial arrangements that maximise the biodiversity and wider environmental benefits derived from trees. Trees can be planted in a range of spatial configurations along a gradient of land-sparing (like creating woodland patches) to land-sharing (such as in agroforestry systems that integrate trees with crops or livestock). Whilst both these strategies have the potential to deliver a range of biodiversity benefits, they are unlikely to be equivalent.

The aim of this studentship is to assess the relative merits of separating versus integrating trees with food production to provide the greatest benefits for biodiversity (with a focus on invertebrate communities because of their diverse ecological roles which underpin ecosystem functions and services vital to food production). Specific research questions to address include:

1. How are invertebrate communities in agricultural landscapes influenced by trees in various spatial configurations, representing a gradient of land-sparing to land-sharing management approaches?
2. How do invertebrates with varying life histories and functional traits respond to tree planting along the land sharing-sparing continuum, and what implications does this have for ecosystem service provision?
3. Are land managers more amenable to planting trees in certain spatial configurations than in others, and what implications does this have for the implementation of tree planting strategies?

To address these questions, fieldwork will be conducted in agricultural sites where trees have been planted across a range of spatial configurations encompassing a gradient of land-sparing to land-sharing. Data collection will focus on ground-dwelling predators (like carabid beetles and spiders), with the potential to also include insect pollinators (like hoverflies, bees and butterflies) to encompass a wider range of functional traits and ecosystem services.

The student will have access to an existing dataset of beetles (30,000 individuals of 130 species) and spiders (4,000 individuals of 103 species) which have been recorded at 60 woodlands planted on former agricultural land (part of the WrEN project), and to a beetle functional traits database compiled by SRUC.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr E Fuentes-Montemayor, Dr A Gathorne-Hardy, Dr L Cole and Dr John Holland.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Understanding detection and colonisation of lignocellulose by anaerobe fungi to improve agricultural waste valorisation

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

The use of lignocellulose as renewable resource for production of biofuels and biomaterials is increasingly important and sustainable processing techniques are therefore essential.

Anaerobe fungi colonise lignocellulose during ruminant digestion; motile zoospores detect plant material, attach, germinate and grow. Species differ in their responses to lignocellulose recognition and while carbohydrate recognition and uptake is expected to be critical, such as in zoospore chemotaxis, it is unknown how most anaerobe fungi initiate lignocellulose colonisation.

The project aims to generate understanding of carbohydrate recognition and uptake that drive initial colonisation of plant biomass by anaerobe fungi. This knowledge will be used to create combinations of fungi and lignocellulose with increased potential in selective lignocellulose pre-treatments for bioprocessing. Key objectives are:

1. Exploring how carbohydrate recognition and uptake drive initial colonisation of plant biomass by a panel of fungal species, and assess variation in mechanisms. Uptake of radio-labelled carbohydrates by zoospores during colonisation will be assessed and compared to their ability to induce chemotaxis, germination, and sustain growth
   
   
2. Researching variability in how inducers affect enzymatic activities generated by the fungi during degradation of plant biomass. Selecting species with distinct carbohydrate recognition profiles, effect of inducers on enzyme production is assessed via proteomics and transcriptomics and enzyme activity assays
   
   
3. Using gained knowledge to optimise fast and selective pre-treatment of renewable lignocellulose resources. Gained insights may be used to match fungal degradative capacity to bioprocessing requirements. Trials for biomaterials applications focus on generation of xylan-rich fractions from wheat-derived materials important as renewable feedstock to the UK

Together this delivers insight in how carbohydrate recognition affects fungal colonisation of plant biomass, and provides data underpinning development of fungal pre-treatments in renewables-based technology.
This project builds on experience in fungal biology, enzymology and bioprocessing at SRUC, and expertise lignocellulose biochemistry, including carbohydrate-radiolabelling at University of Edinburgh (UoE).

The student benefits from training across these disciplines and will be registered at UoE, based at SRUC in Edinburgh, working closely with Institute of Molecular Plant Sciences at this campus. The student will have the opportunity to use bioprocess facilities at SRUC's Barony campus.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Jolanda van Munster, Prof S C Fry and Dr V Gupta.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO One Health and Animal Welfare in Livestock Production: farmer-centric perspectives

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

One Health (OH) approaches are based on the principle that the health of people, animals and the environment are intimately linked. However, OH has not been commonly used in modern farms, even though there are animals and people sharing a common environment on farms. We propose to use OH approaches to explore relationships between human and animal health and wellbeing on Scottish pig farms.

Our approach is based on the principle that each farm is a dynamic system where there are many interactions between people and animals on the farm. Farmers and animals influence each other’s health through these complex interactions along complex pathways.

For example, farming is a stressful activity, stress is a determinant of physical and mental health, and farmer mental health has been linked to farmer accidents and suicide attempts. Livestock can affect farmer mental health because animal disease, production losses and animal welfare issues can increase farmer stress, not least when disease control strategies are complex and involve difficult trade-offs.

The health and welfare of animals on the farm is dependent on the farmer who cares for them. It can be expected that the level of animal care provided will vary depending on the mental and physical health of the farmer, especially when their capacity for uptake of optimal practice is affected.

The pig sector is an example of the interplay between human and animal health. There are recruitment challenges which threaten maintenance of animal health practices, and which can negatively impact the health and wellbeing of staff. Many of the staff employed in the sector do not have English as their first language, and may find animal health information and advice inaccessible, resulting in poor levels of compliance.

We propose three hypotheses:

1. Animal health and the health and wellbeing of the humans responsible for their care are linked
2. Support for human health and wellbeing will improve levels of animal health
3. The provision of animal health information and advice tailored for farmer and farm staff will contribute to reduced levels of disease in animals

The student is expected to challenge these, suggest alternatives, and contribute directly to the design of studies to test hypotheses.
We propose to conduct the project in the pig sector in Scotland. The supervisors have strong relationships with farmers, and access to SRUC health surveillance/information systems to measure outcomes and generate information.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Prof John Berezowski, Dr A Macrae, Prof George Gunn, Dr Kate Stephan and Dr Maria Costa.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: Biodiversity responses to tree planting across a land sharing-sparing gradient

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

The restoration of degraded landscapes is a global imperative to mitigate the current climate and biodiversity crises.

International commitments such as the UN’s Decade on Ecosystem Restoration 2021-30 recognise tree cover expansion as a key priority for landscape restoration, and many nations have ambitious afforestation targets. For instance, the Scottish Government has pledged to plant 12,000 ha of trees per year, increasing to 15,000 ha from 2024.

With agricultural land covering over 70% of the UK, a large proportion of tree cover expansion is likely to take place on farmland. However, there is much debate in the scientific and practitioner communities on the relative merits of alternative afforestation strategies.

Trees can be planted in a range of spatial configurations along a gradient of land-sparing (such as woodland patches) to land-sharing (such as in agroforestry systems that integrate trees with crops or livestock). Farm woodlands are a common feature of UK landscapes, but their creation often requires taking land out of agricultural production. Conversely, agroforestry systems have the potential to reduce these trade-offs in land use, resulting in calls to promote their take-up as a complementary approach to achieve the UK’s afforestation targets.

Whilst both these strategies have the potential to deliver a range of biodiversity benefits, they are unlikely to be equivalent. For example, woodland specialist species associated with more cluttered, densely-shaded environments are unlikely to utilise sparsely-wooded agroforestry areas that may in turn provide better resources for generalist species.

The overall aim of this studentship is to compare the biodiversity benefits of separating versus integrating trees with food production systems. The study will focus on vertebrate communities known to be influenced by agricultural intensification, and to respond to habitat creation fairly quickly (such as birds and bats). Biodiversity data will be collected using full-spectrum acoustic recorders (for example AudioMoths) to monitor animal vocalisations and characterise the ultrasonic and audible 'soundscapes' (which can be used to detect shifts in faunal communities).

Study sites will include woodland patches planted on former agricultural land (part of the ongoing WrEN project) and agroforestry sites (to be identified through SRUC’s close links with land managers, such as via the Agroforestry RISS group).

Additionally, a component of the study will focus on investigating land managers’ perceptions of the integration of trees into agricultural systems, to determine constraints and perceived trade-offs with food production. This work will generate empirical evidence to underpin tree cover expansion strategies that maximise the biodiversity benefits derived from trees in agricultural landscapes.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Elisa Fuentes-Montemayor, Dr Lorna Cole, Dr John Holland and Dr Alfred Gathorne-Hardy.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/EF.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: E4 A history matching with evolutionary algorithms approach to calibrating complex process based simulators

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 6 January 2022

Complex process based computer simulation models used to characterise dynamic natural phenomena such as plant growth and soil biogeochemistry can have hundreds of input parameters, multiple time series of exogenous forcing factors, and hundreds of outputs.

Lack of knowledge about the values such parameters should take undermines the utility of models for quantitative risk assessment and projection. Calibration, namely parameter selection or estimation, for such models often involves finding a single optimal combination of parameter values that minimise a specified objective function.

Such procedures are computationally challenging, and ignore uncertainty (usually a range of parameter values are plausible) leading to unwarranted certainty in projected impacts of climate change, which could lead to poor decision making.

History matching is an alternative statistical procedure that yields not a single parameter combination, instead it is an iterative procedure that sequentially reduces an initially large volume parameter space to an increasingly reduced volume plausible space. A further distinction from calibration is that the plausible space can be an empty set if no combinations are deemed acceptable, indicating that the model structure may be inadequate.

Several open questions remain about implementation of history matching including best procedures for sampling a multiple dimension space at each iteration, how to reduce the parameter space for multiple objective functions, and attaching probabilities to different parameter combinations in the plausible space.

The PhD candidate will work to find answers to each of these questions. The work would be anchored to real world applications in crop growth and soil biogeochemistry using one or more established simulators, such as STICS, and would use existing and newly collected field data from one or more locations in Scotland. The candidate is expected to undertake in-depth study of calibration/estimation methods (in both frequentist and Bayesian settings), as well as other aspects of the modelling of uncertainty in simulators (such as sensitivity analysis, emulation, forecasting).

The project will be very interdisciplinary in terms of the evaluation of developed methods and application of the methods using crop growth models selected by the supervisors from SRUC and BioSS. Research questions include:

1. What are efficient procedures for sampling the reduced multi-dimensional parameter space at successive iterations (waves) of history matching?
2. Given multiple outputs with varying levels of importance, what selection criteria should be used for screening (reducing) the parameter space at each iteration?
3. How can probabilities be attached to different regions of the plausible parameter space and how can they be used to communicate various kinds of uncertainty about model fit, output, and predictions?
4. How to interpret the relative importance of different parameters on different outputs in the plausible parameter space?

Methodology

Year 1: Review literature on history matching procedures, and other aspects of the analysis of complex simulators including sensitivity analysis, uncertainty analysis, and emulation. Gain understanding of the crop growth and soil biogeochemistry simulator as well as acquiring experience running the simulator.

Year 2: Develop and explore possible answers to the key research questions. Evaluation of and alternatives to a currently used sampling procedure based on the intersection of pairs of convex hulls is one starting point. This can include use of evolutionary algorithms and identification of the Pareto Frontier. Translate approaches into computationally efficient algorithms and test with simulated data using a crop growth and soil biogeochemistry simulator. Evaluate performance of alternative approaches.

Year 3: For the most promising answers and algorithms, carry out in depth theoretical analyses of computational efficiency and asymptotic results. Apply methods using the crop growth and soil biogeochemistry model and real data sets. Write one or more manuscripts for appropriate science and/or applied statistics journals.

Year 4: Complete algorithmic refinement and theoretical assessment. Revise and resubmit manuscripts as necessary and complete thesis.

The training programme in the Academy for PhD training in statistics includes computer intensive statistical methods, frequentist and Bayesian inference procedures, analysis of uncertainty in complex models, and other relevant courses.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Ken Newman (University of Edinburgh, BioSS), Adam  Butler (BioSS) and Kairsty Topp (SRUC).

Apply

Please visit the University of Edinburgh website for full application instructions and needed forms.

Title: A seascape approach to improving fisheries sustainability and restoration

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Numerous fish stocks in economically developed nations are harvested sustainably or are in recovery. Yet, despite more than a decade of rebuilding attempts West of Scotland finfish fisheries remain in crisis.

The destructive effects of mobile fishing gear on benthic habitats and the loss of high-quality habitat networks are likely factors contributing to the lack of recovery of these fish stocks. This is a complex and contested issue; resolution is needed to reverse biodiversity decline and support thriving coastal rural communities.

Biodiversity restoration and sustainable use of natural capital like fisheries require knowledge of the distribution and movements of exploited species across a landscape. This studentship will develop state-of-the-art understanding of fish-habitat relationships at patch and seascape scales, provide a model for incorporating habitat and landscape considerations into fisheries management and influence Scottish Government policy.

Habitat use and occupancy is often inferred by considering the immediate habitat where fish are found. However, we also recognise that different habitats confer different benefits, such as refuges from predation or feeding areas. Therefore, it is essential to not only consider the immediate habitat occupied by an animal but also the wider environment and variety of habitats available.

This PhD will adopt a novel seascape approach which understands that the spatial arrangement of marine habitats is important, and that links must be maintained to allow animals to move between them.

While previous work has shown the local abundance of juvenile gadoids to increase with increasing habitat heterogeneity, we do not know how patch size, or the arrangement of patches, influences abundances. Additionally, at broad spatial scales of <100 km ontogenetic shifts in habitat preferences are common. However, little is known about how habitat use changes at a fine spatial scale as juvenile fish grow.

Modelling the distributions of many species is possible because behavioural traits which influence their densities are often minimal. However, some species maintain constant densities and are vulnerable because they display hyperstability (for example spawning cod or grouper).

The work of this project will also develop seascape models which include species that maintain constant densities in a habitat patch and, by using wrasse as model species, explain the role played by behaviours which govern densities across seascapes.

This project will develop understanding of fish ecology and conservation, providing urgently needed information about fish habitat relationships, develop methods and a research strategy for seascape-based conservation and management to reverse biodiversity decline.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Prof Eileen Wall, Dr Neil Burns and Dr David Bailey.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/EW.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: E4 Horizontal gene transfer of cytolethal distending toxin as a potential mechanism to aid environmental transmission of pathogenic bacteria

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Cytolethal distending toxin (CDT) is a genotoxin found in a range of bacteria, many of which are human pathogens. CDT is thought to contribute to virulence during infection. It is not universal within any one species, but there is a strong association of CDT with some genotypes, which may be related to its carriage on mobile elements like bacteriophage and plasmids. The CDT gene cluster is present in some isolates that are associated with environmental hosts and habitats.

This raises the question about its role outwith warm-blooded animal hosts. It also raises public health concerns about the potential for transmission from environmental sources. This premise is supported by the presence of CDT in some notorious pathogens that can be transmitted via environmental pathways, including the Shigatoxigenic E. coli (STEC) and Salmonella enterica subsp. enterica serovar Typhi.

Since CDT has been characterised in the context of human or other animal hosts, any wider ecological role is unclear. However, the mode of action of CDT in infection implies a universal action on animal hosts, including those associated with soil and plants. We think that CDT acts as an ecological fitness factor, potentially by providing a protective role against invertebrate predators of the bacteria. In turn, this confers an advantage during any environmental phases of the pathogen lifecycle. However, what drives acquisition of CDT is unknown.

This project will assess the likelihood of horizontal transfer of CDT genes under conditions relevant to environmental hosts and habitats, including soil microcosms and nematode infections. The project will make use a set of environmental isolates of E. coli in a divergent taxonomic group (cryptic Clade-V) that encode a three-gene cluster of CDT, located within a mobile lysogenic bacteriophage. The soil and plant root isolates have persisted in the absence of large mammals and provide a comparison for STEC human/bovine isolates that also encode the CDT cluster.

The potential that horizontal gene transfer of CDT gene cluster confers an ecological fitness advantage will be tested in the following research questions:

1. How does the regulatory profile compare between STEC and environmental E. coli isolates, does soil act as an environmental cue for expression?
2. Are there differences in CDT B toxin secretion and production between STEC and environmental E. coli isolates?
3. Is the CDT bacteriophage in the environmental isolates likely to be transferred under environmental conditions?
4. Can CDT be transferred from environmental E. coli to naïve STEC or to other E. coli hosts?
5. How widespread is CDT in Gram negative bacteria of environmental origin?

The project will use a range of molecular microbiology and bioinformatics techniques, split between the Edinburgh (Roslin Institute, University of Edinburgh) and Aberdeen (SRUC). The project benefits from a CASE partner, a commercial reference laboratory for environmental and food microbes (NCIMB Ltd.), who will host a three-month internship for the student.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: David Gally (University of Edinburgh), Nicola Holden (SRUC) and Samantha Law (NCIMB Ltd)

Apply

Please visit the University of Edinburgh website for full application instructions and needed forms.

Title: EASTBIO Genetic study of dairy cattle resilience to climate change and nutrient intake variation

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

This PhD project will examine the capacity of dairy cows to respond to environmental challenges manifested in climate change and variation in the nutritional value of consumed feed. The hypothesis is that different animals respond differently to such challenges, partly due to inherent genetic factors.

The successful candidate will have the opportunity to work with data from a unique dairy cattle population raised at the SRUC research farm in Scotland. The cows are closely monitored and densely phenotyped as part of a long-running feed and genetic selection study.

Individual cow data include milk yield and composition (protein, fat, lactose), feed intake, live body weight, body condition score, reproduction, and health records. These performance data span more than 20 years and will be matched with corresponding weather data and data on the nutrient composition of feed consumed by the cows.

All data will then be jointly analysed with random regression models to derive novel phenotypes reflecting the response of animal performance to variation in weather and nutrient intake. The magnitude of this response will determine the animal’s resilience to external challenge.

The novel resilience phenotypes will subsequently be analysed together with available animal pedigree and genotypic data from genome-wide DNA arrays. These analyses will aim to genetically characterise animal resilience through variance component and genetic parameter estimation, genome-wide association studies, regional heritability mapping and calculation of genomic breeding values. Genetic and genomic associations of resilience with other cow traits (productivity, reproduction, health) will also be derived.

The project will require advanced data handling skills and aptitude in statistical, computational and genomic analysis. Relevant specialised training will be available as needed.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Prof G Banos, Prof J Newbold, Dr Bingjie Li and Dr Enrique Sanchez-Molano.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Exploring the genetic determination of aggressive behaviour in adult female pigs to improve human safety and animal welfare

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

This PhD project will explore the genetic determination of aggressive behaviour in adult female pigs (sows). Sows express aggression towards humans, piglets and other sows. Aggression risks human injury, reduces the welfare of recipient animals and likely reflects poor welfare of the aggressive sow herself.

Globally, modern genotypes of sows are becoming increasingly aggressive, especially towards humans. Aggressive behaviour by sows has been poorly studied. Selective breeding can lead to cumulative and permanent improvements in behaviour and there is a pressing need to quantify the inter-relationships between sow aggressive behaviour performed in different contexts and estimate the genetic basis to these behaviours. We also seek to confirm evidence that less aggressive sows produce more viable piglets as this would deliver further welfare, economic and sustainability benefits from reducing sow aggression.

The project will partner with SUISAG, the Swiss national pig breeding organisation. SUISAG wishes to maintain and improve Switzerland’s high standards of pig welfare by creating a selection strategy to reduce and optimise sow aggressive behaviour across contexts, improving farmer safety and pig welfare.

We aim to develop validated methods to record sow aggression and estimate the associated heritability. We also want to quantify the genetic correlations between different aggressive behaviour traits, and hence how improving one form of aggression will impact others. Furthermore we'll try to quantify the impacts of reducing aggression on reproductive and piglet welfare traits.

The student will be registered at the University of Edinburgh, based at SRUC and undertake two placements of 3-9 months duration each with SUISAG in Switzerland, with desk-based and on-farm elements. The student will join the Animal Behaviour and Welfare Team at SRUC, which is one of the largest groups of its kind with 15 academic staff and 17 PhD students. They will also become part of the research and development team within SUISAG. The student will gain training opportunities in experimental and project management, business development and communication to academic and non-academic audiences.

This multidisciplinary animal science project combines animal behaviour, welfare, quantitative genetic analysis and applied animal breeding. The supervisory team brings the necessary expertise in each of these fields and will support the student in the development of academic skills within each discipline. The combination of academic training in breeding applied to behaviour and welfare, and exposure to a progressive breeding company, is expected to be highly attractive to future employers. 

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Rick D'Eath, Dr A Wilson (Edinburgh Uni), Prof R Roehe and Dr S Turner.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Integrating genomics and machine learning technologies to improve feed efficiency in dairy cattle

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Feed accounts for the largest part of operating cost in dairy cattle production. Improving feed efficiency (FE) of dairy cattle contributes to dairy profits and reduced environmental footprint of dairy production.

Feed efficiency phenotypes are generally difficult and costly to measure in a large scale, limiting the accuracy of genetic improvement. This PhD project aims to study the possibility of improving dairy feed efficiency by integrating genomic selection and phenotype prediction for feed efficiency using data-driven technologies including machine learning.

The successful student will analyse individual cow records from the SRUC’s world-leading Langhill research herd, currently in Dumfries, Scotland. The herd has been continuously operational for nearly five decades since the 1970s, accumulating a world-leading and genetically unique database including longitudinal data for milk production, fertility, health, welfare, and feed efficiency. The research herd has won SRUC Queen's Anniversary Prize and has been widely recognized as a unique resource for dairy genetics research whose feed efficiency data will be available for the current PhD project.

Three studies are included in the PhD project:

1. Phenotype prediction for dairy FE using routinely available milk infrared spectra data together with data on milk production, milk composition, and body weight. Prediction methods of partial least square (PLS) regression and deep learning neural network (DLNN) will be used to evaluate and compare the prediction abilities
2. Genome-wide association studies for FE phenotypes at different lactation stages will be carried out to detect large-effect markers associated with FE and changes in genetic background of FE across lactation.
3. Improving genomic prediction for FE using predicted records from point 1 and genomic results from point 2. Methods of combining actual FE records and predicted records by introducing weights into prediction will be examined. The best ratio of actual records to predicted records in genomic prediction for FE will be determined. In addition, large-effect markers associated with FE from point 2 will be used as biological priors to improve prediction accuracy for FE.

The project integrates data-driven technologies (machine learning, genomic selection) into dairy genetic research. Relevant specialised training will be available.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Prof Mike Coffey, Prof G Banos, Dr Bingjie Li and Dr James Robson.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: The impact of gut fungal morphology on digestion of plant material

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Sustainable ruminant farming is required to ensure food security for the growing world population while mitigating environmental impacts. Ruminant performance, including greenhouse-gas emission, is critically impacted by activity of the microbiome.

Anaerobic rumen fungi are thought to derive their plant-biomass degradative capacity from a combination of degradative enzymes and physical force exerted by fungal cells on plant material. However, gut fungal species have been identified both with and without filamentous structures that penetrate plant biomass during its degradation, and in preliminary experiments, activity of these fungal types on model lignocellulose materials differ considerably.

This project aims to assess the impact of fungal morphologies on degradative strategies of gut fungi, and to explore if activity of either type of fungi may be used to aid digestive performance of the rumen microbiome on specific feeds.

The key objectives are

1. Assess changes brought about in (model) lignocelluloses by bulbous and filamentous fungi

Employing techniques as fibre analysis, carbohydrate epitope detection, mass spectrometry and radiolabelling, you will characterise biochemical and structural alterations in lignocellulose, and identify differences in fungal degradative mechanisms.

2. Understand effects of degradative enzymes taken into lignocellulose material by both types of fungi

You will identify soluble and fungal cell-associated enzymes via proteomics and use biochemical enzyme assays to assess functions.

3. Identify (model) lignocelluloses ideally suited for fungal degradation, and confirm fungal fermentation performance alone and in a complex rumen microbiome environment

Based on degradation capacity uncovered in point 1 and 2 you will select lignocelluloses with specific properties or composition, and assess their in vitro fermentation by bulbous and filamentous fungi alone, and in rumen microbiome co-fermentations.

This project builds on expertise in fungal biology, carbohydrate enzymology and the rumen microbiome at SRUC, and expertise lignocellulose biochemistry and carbohydrate-radiolabelling, at University of Edinburgh (UoE). You’ll benefit from training across these disciplines. The project aligns with research centres for safe and improved food and climate emergency, and with well-established program of activities around the rumen microbiome in sustainable farming, thus ensuring opportunities to collaborate.

You will be registered at The University of Edinburgh, based at SRUC in Edinburgh, and work closely with Institute of Molecular Plant Sciences at this campus. The supervisory team is committed, and expects your active contribution, to an inclusive work environment and professional development of all research team members.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Jolanda van Munster, Prof Jamie Newbold and Prof Stephen Fry at Edinburgh University.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/JM.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: E4 Unveiling the role of urban hedgerows in the mitigation of traffic-related particulate matter and metal pollution

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 6 January 2022

Road vehicles and infrastructure are among the leading sources of hazardous pollutants, such as heavy metals and fine particulate matter (PM2.5). Road traffic contamination is of particular concern in urban areas, where high pollutant concentrations and population converge. The latest reports show that roadside PM2.5 levels breached the World Health Organization guidelines in 62% of the monitored locations in the UK.

In this context, green infrastructure is receiving increasing attention for the broad array of ecosystem services it provides in urban settings, including air pollution alleviation. Hedges are particularly important because they constitute a ground-level barrier where traffic-related emissions are greater and more detrimental to residents, pedestrians, and especially children.

However, there are several knowledge gaps that need to be addressed, specifically concerning real-life scenarios, PM-linked heavy metal contamination and remediation, and how the traits of different hedge species influence PM2.5 and metal sequestration.

This doctoral project will be primarily centred on assessing the abatement of PM and metal pollution by roadside hedges in Edinburgh, where 3.7% of deaths in adults over the age of 25 are attributable to PM2.5 (ranked first in Scotland, ahead of Glasgow, Aberdeen, and Dundee). The work will gather comprehensive real-world data on PM (coarse, PM10; and fine, PM2.5) and metal concentrations in different hedge species, PM vertical and horizontal displacement, and the effect of roadside distance, traffic volume, speed limits, and meteorological parameters, amongst other factors. The following research questions will be addressed:

1. Which hedge species are more effective in mitigating particulate matter and metal pollution?
2. Which hedge traits are more desirable to ensure greater particulate matter capture?
3. What is the effect of road distance, traffic volume, street canyons, meteorology, and seasonality on particulate matter and metal accumulation in urban hedges?
4. Can urban hedgerows be used as reliable biomonitors for particulate matter and metal pollution?

Further information

For further information about the project (including methodology, training, and requirements) visit the University of Edinburgh website.

This PhD project is part a competition funded by E4 NERC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Luis Novo (SRUC), Prof Margaret Graham (School of Geosciences, University of Edinburgh), Prof Mathew Heal (School of Chemistry, University of Edinburgh) and Dr Jennifer Carfrae (SRUC).

Apply

Please visit the University of Edinburgh website for full application instructions and needed forms.

Title: EASTBIO Investigation of the holobiont of host genomics and rumen microbiome in beef cattle

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

The PhD student will carry out research on the hot topic of symbiotic relationships between host cattle and the essential nutrient providing microbial community living in their large stomach, the rumen.

Our previous research has revealed that the holobiont (the animal host and its associated microbiota) has a substantial impact on feed conversion efficiency (Lima et al., 2019, Frontiers in Genetics), animal health (Auffret et al., 2017, Microbiome) and emissions of the greenhouse gas methane (Roehe et al., 2016, PLOS Genetics) in beef cattle. In particular, the host cattle genomic interactions with the rumen microbiome are strong, so that the abundances of the microbiota or its genes are of great interest to the world’s leading beef breeding company Genus plc.

This studentship is aligned to an ongoing BBSRC LINK project entitled 'Elucidating bovine host genomic links with rumen microbial genes to improve sustainably feed conversion efficiency using unique selection criteria' a collaborative research project involving SRUC, University of Edinburgh and Genus, which will provide data, samples and expertise for this studentship.

In this PhD studentship another omics level will be added to genomic and metagenomic information, the metabolomics of the microbiota and the host based on rumen and blood samples respectively. The main aim of the project is to improve our understanding of the symbiotic links within the holobiont, based on host genomic, metagenomic and metabolomic information. Then we want to find out how to use these links for breeding of animals that emit less methane, require less feed per kg growth and have a healthy rumen microbial ecosystem.

The PhD student will have access to novel identified species of rumen microbes (Stewart et al., 2019, Nature Biotechnology) to analyse their effects on the above described environmentally and economically important traits.

Besides doctoral training at EASTBIO, SRUC and University of Edinburgh, the student will be trained in host genomics, ruminant science, rumen microbial community/genes, microbial and animal metabolism. The student will further benefit from training in microbiology, genetics, metabolomics, bioinformatics and animal nutrition.

The exposure to two academic partners, together with regular interactions with the world’s leading breeding company Genus as well as the farming and agri-food industries, will broaden the students’ horizons and place them in an excellent position for future employment in academia or industry.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Prof R Roehe, Prof M Watson and Prof R Dewhurst.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: Understanding, predicting and preventing the welfare costs of inappropriate body condition in suckler cows

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Around 6% of beef calves die early in life. Calf morbidity and mortality represents a significant economic, environmental, reputational and welfare cost. Two key determinants of failure to thrive are calving difficulty and poor calf vigour, both of which may be affected by the mother’s body condition (fat reserves) during gestation and at birth.

This project aims to understand the effect of poor body condition on cow hunger, calving ease and calf vigour. It will also test a method to predict which cows will lose too much condition and a method to prevent the worst effects of poor condition.

It is currently recommended that spring calving beef cows lose body condition during pregnancy to minimise winter feed costs, but 30% of cows lose more condition than recommended. SRUC data from 40 UK farms found a link between cow body condition and the size of the calf at birth and its subsequent growth, suggesting that condition may affect calf vigour.

The project will survey Scottish and Irish farmer uptake of condition scoring (Objective 1). It will quantify the biological effects of absolute body condition, or changes in condition over time, on cow hunger (feeding motivation) (Objective 2) and subsequent calving ease and calf vigour (Objective 3). It will also test the efficacy of predicting condition loss based on easily implemented measures of temperament previously linked to growth (Objective 4).

Lastly, reactive treatment of calves identified to have poor vigour occurs too late to prevent negative impacts on immunity and subsequent development. Non-steroidal anti-inflammatory drugs (NSAIDs) administered following calving can improve cow welfare and calf weight gain in early life. Objective 5 will test the effectiveness of targeting NSAIDs towards cows (and/or their calves) whose condition profile puts their calf at risk of poor vigour.

The project will provide basic biological understanding of the effects of inappropriate body condition and a route towards better prediction and treatment of these effects to improve animal welfare, production efficiency and the large climate impact of the beef sector. The studentship is a collaboration between SRUC, the University of Edinburgh and Teagasc in the Republic of Ireland. The project will be based at SRUC’s Edinburgh campus and will include short periods of data collection in Ireland. The student will gain first-hand experience of two farm-based and two academic teams. They will be mentored in engaging with industry and will play an active part in knowledge exchange.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr S Turner, Prof A Macrae, Dr Bernadette Earley and Dr K Rutherford

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/ST.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Can insect farming waste be utilised as a sustainable soil improver contributing to circular bioeconomy goals?

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

In recent years there has been in increase in domestic protein production to reduce the reliance on imported protein and develop more sustainable sources.

The use of insects as a protein source in animal feeds and oil within the petrochemical industry can also act as a viable waste treatment process for a number of organic wastes (such as food and distilling wastes). In addition the production of insect faeces (frass) has the potential to be upcycled as soil improving fertiliser product.

However, to date little is known about the composition of frass, in particular the effect of the dietary substrate used within the insect farming and its potential use as a biofertiliser or soil improver. If shown to be an effective soil improver frass could contribute circular bioeconomy goals in food production and provide an alternative to synthetic fertilisers and peat-based composts.

A pilot study was conducted (2019) in collaboration with Zero Waste Scotland, assessing crop growth across soil-only, soil-compost and soil-frass mixtures. Black solider fly (BSF) frass from three dietary sources were used with results showing both positive and negative implications for crop growth. Soil mixed with frass derived from pre-commercial food-waste was shown to act as a slow-release fertiliser, performing better than the soil-only and soil-compost treatments in terms of lettuce production. 

This PhD studentship will develop upon recent findings to experimentally investigate the range of insect frass available, its composition and its effectiveness as a biofertilizer, and its contribution to circular bioeconomy. Factors such as the variability in frass composition, assessing soil-frass mixtures for optimal plant/crop growth and the implications of frass use on soil health and crop composition will be investigated as well as the potential for frass to be pyrolyzed for biochar production.

In addition to investigating the practical applicability of frass material in crop production, the project will explore legal requirements (such as Waste Management Licensing (Scotland) Regulations 2011), certification (Pas100) and socio-economic implications for its use and key ethical questions to consider. This is a novel area of research with few previous studies conducted, so there is scope for the student to drive the direction of this research in many directions.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Bob Rees and Sarah Buckingham.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO The role of legumes in achieving net zero: reducing nitrogen losses and improving soil health

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

The Scottish Government has pledged to meet a net-zero target for greenhouse gas (GHG) emissions in Scotland by 2045, and the UK government by 2050. However, current agricultural practices result in high nitrogen (N) losses through nitrate leaching and emissions of GHG nitrous oxide (N₂O).

Improved agricultural practices can prevent soil health depletion and excess synthetic nitrogen fertiliser application. Implementing legumes into the crop system to capture and utilise biological forms of nitrogen provides a nature-based solution contributing to net zero targets.

Diverse plant species mixtures that include nitrogen-fixing legumes (such as red clover, black medic, lucerne) are currently being used in organic agriculture, but further development in conventional agriculture is needed, particularly understanding nitrogen cycling and soil GHG release in diverse species mixtures versus monocultures.

Evidence-based studies which directly measure nitrogen transfer-processes across contrasting agricultural systems (cover crops, grass/legume mixtures, intercropping, herbal leys) are needed to better understand plant-soil interactions and their ability to be manipulated for optimising nitrogen use efficiency and reducing GHG emissions whilst maintaining crop productivity.

An experimental programme will be developed to investigate grass-legume species diversity, composition and intercropping effects on nitrogen fixation, nitrogen pools, nitrogen uptake and ecological responses, such as soil health status and plant productivity. Implications for residue quality and incorporation will also be studied in terms of net-gains and losses for the following crop and wider legacy effects.

The project will develop grass/legume management guidance for optimal nitrogen use efficiency utilizing existing experimental field sites linked with current mob grazing, carbon sequestration potential, GHG monitoring and future RESAS research activities.

The student will be trained in a range of analytical techniques (for example continuous flow analysis, gas chromatography, isotope ratio mass spectrometry, genetic techniques/analyses) to explore nitrogen pools, GHG emissions and soil microbial community diversity. These would provide detailed information about plant-soil nitrogen interactions, which is vital for development of relationships that will be incorporated into dynamic deterministic models to improve the predictions of nitrogen cycling.

Collectively supervisors on this project have extensive PhD supervision experience (at lead and co-supervisor levels on a range of interdisciplinary topics). The lead supervisor is responsible for identifying training needs through active communication with the student and awareness of the student’s background and relevant experience. To ensure excellent training of the selected PhD student, the student’s progress and training needs are monitored throughout the PhD programme.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr P Hoebe, Dr J Cloy, Dr S Buckingham, Prof Elizabeth Baggs and Dr Francois Dussart.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: Evaluating the potential role of elicitors and biologicals in an IPM programme to manage chocolate spot (Botrytis spp.) of field beans (Vicia faba)

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Integrated pest management (IPM) is an integral component of sustainable crop production. IPM strategies employ multiple tools and techniques to reduce reliance on pesticides. Pressure to reduce fungicide use has increased over the last decade due to the loss of fungicide active ingredients through regulatory processes and the evolution of microbial resistance.

Much of the 1,804ha of field beans (Vicia faba) grown in the UK require significant pesticide inputs [1] to protect them from the fungal disease chocolate spot (Botrytis cinerea/fabae), which can result in yield losses of up to 59% [2].

Additionally, Botrytis species can quickly evolve and overcome new fungicides, therefore alternatives to fungicides, such as plant defence elicitors and microbial biocontrol agents, will likely have an increasingly significant role in the future.

Recent work conducted by SRUC has indicated that plant defence elicitors (such as compounds that can induce host defence responses) can be used in isolation and in conjunction with reduced doses of synthetic fungicides to effectively manage crop diseases.

Microbial biocontrol agents use an array of mechanisms to control crop diseases, for example induction of disease resistance, antibiosis, mycoparasitism and competition with plant pathogens. In the UK, commercially available microbial biocontrol agents include the bacteria, Bacillus subtilis (marketed as Serenade) to manage diseases including Botrytis cinerea, and the fungus Coniothyrium minitans (marketed as Contans WG) for managing Sclerotinia diseases of high value crops like carrots.

This project will investigate the potential role of elicitors and microbial biocontrol agents in an IPM programme to manage chocolate spot. Evidence gathered will ultimately allow growers to make better informed pest management decisions. Using a range of novel and commercially available microbial biocontrol and elicitor products, this project will identify the mechanism by which control is achieved by identifying activated defence pathways and changes in gene expression.

IPM field trials will be conducted at sites across Scotland and Ireland to investigate management of chocolate spot under different growing conditions. Results from field trials, glasshouse studies, and laboratory work will provide a greater understanding of the mechanisms that are responsible for control with the potential for microbial biocontrol and elicitor products to become integrated into a robust management programme.

[1] Wardlaw, J., Davis, C., Monie, C. and Reay, G. 2020. Pesticide Usage in Scotland: Outdoor Vegetable Crops 2019. National Statistics Publication for Scotland.

[2] Davidson, J.A., Pande, S., Bretag, T.W., Lindbeck, K.D. and Krishna-Kishore, G., 2007. Biology and management of Botrytis spp. in legume crops. In Botrytis: biology, pathology and control (pp. 295-318). Springer, Dordrecht.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Henry Creissen, Dr Helen Rees and Prof Gary Loake.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/HR.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Microbe-dependent trait expression in wheat

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

A recent publication in PNAS (Wagner et al. 2021) demonstrated that heterosis of root biomass and germination in maize is strongly dependent on the below ground microbial environment. Inbred lines performed as well for these traits as their F1 offspring under sterile conditions, but heterosis could be restored by inoculation with a simple community of seven bacterial strains.

Wagner et al. observed the same pattern of differences in heterotic effect between seedlings inoculated with autoclaved or live soil slurries in a growth chamber, and for plants grown in fumigated versus untreated soil in the field.

This project will test if the same phenomenon is present between wheat hybrids and their parents. It will also test for differences in response among a greater range of wheat lines, including contemporary varieties, old lines, and lines newly created from wide crosses to ancestral species (termed synthetics). There will also be opportunity to work with freely available mapping populations (such as MAGIC) for which additional trait and marker data exist.

An advantage of this project is that much of the experimental work can be done under glass or in growth chambers, so several experiments can be run per year to support field work, where relevant aspects of soil composition and crop rotation can be studied. This will include sampling of material from other projects on wheat with field trials and different growing systems.

Within SRUC and the University of Edinburgh, this project fits well with our research activities on genetics and plant breeding, the crop rhizosphere and microbiome, agricultural systems and different aspects of the 'precrop' effect (biological and/or physical and/or chemical).

The student will learn the skills required for this project, including quantitative genetics (needed for trait mapping and to evaluate the merit and methods of integration of results from this project into practical breeding programmes), together with knowledge in soil science, microbiology, and crop physiology. This will result in a well-rounded education with a unique combination of skills giving opportunities for employment in several fields, including plant breeding or research.

If successful, we hope to deliver a glasshouse screening test, either using artificially inoculated soil or live soil slurries compared to sterile soil. Similarly, quantitative trait loci (QTL) for response and/or the potential for genomic prediction can be delivered.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Prof I Mackay, Dr Rajiv Sharma and Prof Peter Doerner.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Assessing microbiome functional traits as indicators of soil health for sustainable agriculture

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Soil is a multifunctional environment upon which our food security depends. The ability of soils to maintain particular functions which contribute to ecosystem services (such as food, fibre and energy production) is compromised by soil degradation. This degradation is primarily associated with unsustainable agricultural management practices developed over the past 70 years to maintain optimum productivity of food, fibre, or energy crops.

Contrasting land management practices result in variation in soil nutrient availability and/or pH levels, over time this generates distinct microbiomes and functional properties in adjacent soil systems. Not all of these communities or functional properties will be desirable and what is desirable will be dependent on what the land is being used for.

Understanding what a healthy and well-functioning soil community looks like in the context of specific land use is of great importance not only to sectors involved in land-based production but also to policy makers driving towards net zero carbon emissions and those wishing to restore degraded land.

The main aim of the project is to use crop rhizosphere microbiome datasets to address the impact of soil management processes on nutrient cycling. A trait-based framework will be used to assign life history strategies to microbiomes which can be used as indicators of soil health.

The work will be based on existing rhizosphere microbiomes derived from several major UK crops which have been grown in rotation on soils exposed to contrasting management over several decades at SRUC’s Craibstone campus. Both archive and contemporary soil samples can be used for laboratory and/or glasshouse-based testing to determine actual functional output alongside genetic functional capacity. The specific questions to be addressed are:

1. Have decades of contrasting agricultural management established microbiomes with differing nutrient cycling traits based on rhizosphere microbiome datasets?
2. Do soils have different functional abilities in terms of nutrient mineralisation having been under long-term contrasting management and are these correlated to traits found in the microbiome datasets?
3. Are there identifiable microbiome markers which can identify soils which will be successful in producing crops in low nutrient input scenarios?

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Prof Christine Watson, Dr A Malik, Dr Fiona Fraser and Dr N Holden.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Developing a mobility scale for canine veterinary patients

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Osteoarthritis is estimated to affect 20% of dogs. Additionally, other joint and neurological conditions, acute challenges and temporary restrictions impact our canine patients.

Management practices are broader than medical or surgical treatment, including nutritional management, activity modification and adapting the environment/daily routines. Understanding the changes in mobility enables decisions about patient management to be taken timeously, supporting slower deterioration and quality of life, or recovery where appropriate.

Mobility assessment in dogs is currently limited to gait analysis, pain scoring or instruments which evaluate negative impact on normal activities due to disease. The purpose of gait analysis is primarily diagnostic, commonly for osteoarthritis (OA). Existing systems are largely limited to assessing gait, meaning that the impact of restricted movement on other daily activities, such as eating, toileting and sleeping, is less well understood.

The aim of the project is to develop a canine mobility scoring system/scale which can be used by veterinary professionals (principally veterinary nurses - VNs) to assess mobility/movements in a range of conditions/contexts (acute and chronic or temporary).

The purpose of the scale would be to provide information on the patient’s ability to perform normal movements, understand the impact therefore on their daily activities, and assess changes in mobility/movement in response to interventions/treatments or disease/condition progression. The application of this scale would be by VNs in the hospital environment to assess their patient’s condition and needs, and potentially as a tool for owners to provide information for chronic conditions management (OA, chronic heart disease, diabetes), pain and weight management clinics and so on.

The aim of this project is to involve stakeholders in the development of a mobility scoring system, and then to test the validity of the system in acute and chronic disease situations. The project will have the following objectives:

1. Survey/focus groups with dog owners, VNs and veterinary surgeons to establish the range of normal activities which require a degree of mobility. Results will be analysed to establish commonality and agreement on the range of mobilities expected in dogs, and identify terms that describe the range of ability from normal, impaired and absent/unable to carry out
   
   
2. Based on Objective 1, create scales for the identified behavioural changes, that characterise the range of mobility variables. This will be used to develop a clinical metrology instrument
   
   
3. Validate the scale. The validation exercise will use three groups of subjects: those with no identifiable mobility challenges, those with a known chronic condition (such as OA), and those with an acute, temporary condition (such as limb fracture). Clinical assessments will be done to characterise the presence and severity of disease. Additionally, accelerometers will be attached to three or four points on each subject (head/neck, fore and/or hind limb, tailhead).
   Data gathered will establish the range of movements during daily activities, and the degree to which these activities are limited in affected subjects. The clinical and accelerometer data will be used to validate the mobility scoring system.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Prof Marie Haskell, Dr Kirsty Young and Dr D Clements.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Molecular epidemiology of Neoparamoeba perurans, causative agent of amoebic gill disease (AGD) in farmed salmonids

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

The amoeba Neoparamoeba perurans is the causative agent of Amoebic Gill Disease (AGD), one of the most significant health challenges faced by the global marine salmonid aquaculture industry. Treatments for AGD enable salmon producers to improve salmon welfare and reduce mortality, but the disease often returns in the same production cycle to the same fish.

Although we are starting to understand more about N. perurans and its interaction with the host, there remains little known about the phylogeographic history and population genetics in relation to its distribution, abundance and evolutionary process that influence its epidemiology.

As an important global pathogen, it is important to start understanding its transmission routes and molecular variation. Different variants of the parasite have been suggested to have emerged globally but there have been few studies that have attempted to identify the total number of variants, found within a particular locality, nor have there been any attempts to assess the potential movement of such variants within and between farms.

This PhD will use elements of both classic epidemiology and molecular epidemiology to assess movement and connectivity between fish farms and provide essential insights into transmission. The project will utilise both archived and contemporary samples to provide insights into the molecular population genetic structure of N. perurans in Scotland.

Similarly, phylodynamic analyses will be employed to assess movement between infected sites. To achieve this, we will employ already established nuclear and mitochondrial molecular markers and will also attempt to develop new markers to assess fine scale evolutionary processes which could affect the transmission and epidemiology of the parasite.

Within Scotland’s salmon aquaculture, field samples will form a basis for answering epidemiological questions, such as what the prevalence of AGD is, and can we quantify and explain infection pressure. Open-source data such as environmental variables obtained from satellite data will be used to complement existing data for meta-analysis. An overall understanding of the molecular epidemiology of N. perurans will enable us to provide better recommendations for health management of AGD.

Successful candidates will have the opportunity to work within internationally recognised teams at Epidemiological Research Unit of SRUC and Institute of Aquaculture, University of Stirling. They will also receive training in cutting-edge epidemiological analysis, molecular biology, and parasitological techniques.

Potential students should hold a good UK bachelor’s degree (first or upper second-class honours degree) and an MSc degree or equivalent international qualifications in an epidemiology / molecular biology / parasitology-related subject area.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Scott Lawton, Dr Annette Boerlage, Dr A Reeves, Dr S Monaghan and Prof James Bron.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: Coupling crop physiological change with multi-spectral imaging in winter wheat

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

The aim of this studentship is to couple changes in winter wheat physiological development with multi-spectral imaging in order to support development of advanced agronomy – through the next generation of crop and field management tools and technologies. This will be achieved by integrating ground-based physiological measurements on wheat with multi-spectral imaging data and analysis.

SRUC is at the leading edge in applying spectral sensing in agriculture, such as prediction of livestock traits. The combined advanced technologies in multi-spectral imaging supported by process modelling (deep learning) have already been used by SRUC to create phenotype signatures that indicate animal health and predict performance.

This wheat science studentship will gather high quality and high-volume growth and developmental and physiological signatures for crops using ground-based and unmanned aerial systems (UASs) to inform on crop health at key growth phases towards prediction of crop yield and quality.

The student’s work programme will consider how spectral imaging can be used to monitor crop growth phases, especially during yield creation and grain filling and ripening, as influenced by cultivar and crop growing conditions. The project will also precisely monitor crop moisture content during grain filling and ripening in order to improve guidance on crop maturity as harvest approaches.  

The student will have opportunity to link with crop genetic improvement by utilising wheat resources such as a diverse MAGIC wheat population and a breadth of different cultivars to link phenotypic expression in physiological change with other existing trait and marker data. This adds value towards quantitative analysis of physiological and maturity traits, as well as yield.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Steve Hoad, Dr Alistair Hamilton, Dr Simon Gibson-Poole, Dr Scott Denholm and Dr Gail Jackson.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/SH.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Unfolding the potential of alpine pennycress for nickel agromining

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Noccaea caerulescens (alpine pennycress) is a hyperaccumulator of zinc, also known to hyperaccumulate nickel in ultramafic soils. Alpine pennycress is a perennial plant from the family Brassicaceae, native to Europe, with patchy distribution from the United Kingdom and France to Slovakia and from Germany and Poland southward to northern Spain and Italy. In Scotland, it can be found in different locations, including ultramafic outcrops in the Cairngorms, Ayrshire, and the Isle of Rùm.

Ultramafic (or serpentine) soils are naturally occurring metalliferous soils that are typically enriched in nickel, chromium, and cobalt, and are deficient in essential nutrients and organic matter, making them unappealing for conventional agriculture. Ultramafic soils are widespread around the world and harbour an elevated number of nickel hyperaccumulators (>500 identified to date).

Hence, ultramafic soils are particularly interesting for agromining (or phytomining), a plant-based technique for the recovery of valuable elements, such as nickel, from metal-rich soils. Agromining relies on the ability of hyperaccumulators to uptake extraordinary amounts of the target metal into their shoots, which are then harvested and incinerated to produce a bio-ore.

Although significant progress has been made over the past two decades, nickel agromining remains an infant technology with plenty of room for improvement. In this light, assessing the potential of symbiotic microorganisms (such as mycorrhizal fungi, plant growth-promoting rhizobacteria), climate-friendly soil amendments (such as biochar), phytohormones, and sustainable chelating agents will be crucial to achieve further breakthroughs, enabling commercial-scale nickel agromining operations.

This project offers an exciting opportunity to work at the nexus of plant physiology, soil science, microbiology, and biogeochemistry to advance a promising resource recovery green technology. The doctoral candidate will investigate the nickel uptake ability of different alpine pennycress ecotypes and determine the effect of microbial inoculation, biochar, phytohormones, and low molecular weight organic acids in the overall agromining process.

The student will engage in significant field and laboratory work, and will receive cross-disciplinary training. The training might include the study of plant physiological and biochemical traits, soil physicochemical characterisation, elemental analysis via inductively coupled plasma mass spectrometry and X-ray fluorescence spectrometry, and isolation, identification and culture of symbiotic microorganisms.

The research will also provide valuable knowledge on the underlying mechanisms of phytoremediation. Publication of the results in peer-reviewed journals and presentation of the main findings in local and international scientific events are envisaged. The work will be carried out at SRUC and the School of Geosciences of the University of Edinburgh.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Luis Novo, Dr B T Ngwenya, Prof M Graham and Dr J Carfrae.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: Improving control of Rhynchosporium commune in barley through managing the pathogens’ population 

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Barley scald, caused by the fungal pathogen Rhynchosporium commune, is the most economically destructive disease of both winter and spring barley in Ireland and Scotland. The disease is capable of causing devastating yield losses of up to 40% in some crops.

In order to manage the disease effectively, growers need up to date information on the effect of agronomic practices, varietal resistance and fungicide applications on disease epidemics. R. commune has continually demonstrated an ability to adapt to changes in control measures and sustainable control remains a massive challenge. The adaptability of the disease is in part due to an overreliance of growers on the individual components of control, coupled with high levels of genetic diversity within local/regional R. commune populations.

A decline in sensitivity to the widely used group of fungicides strobilurins (QoI’s) has recently been reported in Ireland and the UK. If sustainable and durable control is to be achieved it is essential to both enhance the integration of control measures and to reduce, where possible, the potential diversity within populations. To achieve these goals, it is vital to first determine the levels of diversity that currently exist in the Irish and Scottish populations and subsequently determine how individual components of control impact upon it.

The proposed project will establish a representative R. commune populations from different regions in Ireland and Scotland to determine local/region diversity that may exist. Subsequently, the impact of major agronomic practices such as variety choice, seed source, chemical seed treatment, tillage regime, crop sequence or the use of cover crops, currently implemented at farm level will be investigated to determine how they impact upon local and national R. commune populations. Understanding how these factors influence Rhynchosporium epidemics is crucial to establish new robust control measures.

The experimental approach will be focussed on establishing populations of R. commune from leaf isolations from winter and spring barley, and in addition using molecular methods to study population diversity in seed (an important source of pathogen spread).

Field trials will be carried out in Scotland and Ireland using seed from diverse sources and single spore isolates of R. commune will be produced from infected leaf samples. R. commune population diversity will be assessed using SSR markers.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The student will benefit from the combined supervision of Dr Francois Dussart (expert in molecular plant pathology), Dr Henry Creissen (expert in integrated pest management), Dr Neil Havis (expert in plant pathology), Dr Beatriz Orosa and Prof Gary Loake (experts in molecular plant science).

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/FD.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Snail Trail: Using modelling, mapping, and molecular data from lymnaeid snails to identify the risk of liver fluke and rumen fluke transmission

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Snail-borne trematode infections such as fascioliasis, liver fluke of sheep and cattle, are major health issue on farms across the UK, causing significant losses in production and can cause mortalities. Fascioliasis is also now recognised as Neglected Tropical Disease (NTD, ref) and a re-emerging zoonotic disease with the first endemic infections in humans in the United Kingdom (UK) recently reported since the 1940’s.

Being able to assess and predict the risk of infection is paramount to provide sustainable cost-effective flock and herd management and implement practical control measures for fluke. It is widely accepted that to break transmission and limit the risk of fluke infection, control should focus on the mud snails that transmit them. However, to date few studies have attempted to assess the distribution and occurrence of mud snails, measure risk infection or try to identify the environments most likely to harbour a transmission risk to grazing animals and/or people.

This project will combine statistical modelling, mapping, and molecular approaches to accurately build a risk map of fluke infection across Scotland, based on the distribution and abundance of snail species.

Using satellite imaging data and machine learning techniques, environmental proxies that are strongly associated with habitats suitable for snail hosts of fluke will be selected to best predict snail presence. This information will then be used in species distribution models to predict the presence of fluke-infected snails across Scotland.

However, mud snails are notoriously challenging to find and identify, as are the parasites they transmit. Genetic approaches will be employed to accurately identify snails and associated parasites to species level, as well as to assess population structure and connectivity between populations. This crucial information will be used to improve the accuracy of the models and precision of the disease risk mapping.

The project will aim to address the following questions:

1. Which mud snail species in Scotland are responsible for the transmission of liver fluke?
2. What is the distribution and abundance of these snails and are there specific environments more susceptible to risk of infection?
3. Can risk of disease be predicted, based on distribution and abundance alone, is mapping snail distribution enough?

This is an interdisciplinary project run by SRUC, the Moredun Research Institute and the University of Aberdeen. The student will be provided with excellent training and develop skills in classical and molecular epidemiology, mathematical modelling and statistics, disease mapping, bioinformatics, parasitology and malacology.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Jude Eze, Dr Scott Lawton, Dr C S Jones, Dr P Skuce and Dr Sue Tongue.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Knowledge and information in sustainable food production: farmers’ mental representation of soil health and the environment

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

In this PhD you will investigate how information can influence decisions on sustainable food production in a case study on soil health in South Asia. Your results will help establish effective tools for sustainable soil management to improve livelihoods and the environment. You will gain academic and participatory practitioner skills while learning about soil health, food systems and sustainability.

How available information and advice is processed by individuals, including farmers, and how it influences their decisions depends greatly on the match between existing mental models and the information provided, and also on how and from whom they receive the advice.

While soil is the primary resource for agriculture, one-fifth of soils have been degraded, with long-lasting consequences on livelihoods and the environment. Farmers’ soil management decisions are constrained by agronomic and economic opportunities and conditions.

Within these constraints the decisions result from interactions between values, mental constructs, knowledge, and the information they receive. Farmers adjust their management to soil conditions using tools spanning from visual and manual examination to computer based decision support.

Industry, non-governmental organisations (NGOs) and governments aim to aid farmers with relevant information (such as the national programme of Soil Health Card in India). Deeper insights into how this information affects farmers’ actions can help to improve agricultural advisory services, leading to better livelihood and sustainability outcomes.

This PhD will address how farmers’ knowledge and the information they receive influences the sustainability of their management decisions, in particular regarding soil health and management. The outcomes of the PhD will inform the development of more effective tools and improved ways of information provision for sustainable soil management.

The PhD work will be linked to the South Asian Nitrogen Hub (SANH), a five-year partnership with over 30 research and 15 stakeholder institutions. You will benefit from the wide collaborative network in the Hub, including early career scientists and 15-20 PhD candidates.

This interdisciplinary research will use social science methods to explore agronomic decision-making. You will identify relevant research methods and design and conduct field data collection from farmers and other stakeholders. You will use a combination of observational methods and economic experiments.

The fieldwork will take place in a SANH partner country. However, the plan is adaptable to the Covid-19 situation. In case in-person fieldwork will not be possible in South Asia, alternative arrangements are available, including phone interviews, the use of secondary data, or refocusing the work to the UK.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Vera Eory, Joanna Cloy, Toritseju Begho (SRUC) and Alfy Gathorne-Hardy (University of Edinburgh).

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Spectral imaging and machine learning to evaluate physical integrity and processing quality in barley grains

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

The aim of this study is to couple spectral imaging and machine learning (ML) to determine grain quality signatures that differentiate desirable quality characteristics and undesirable quality defects in malting barley. Compared to existing methods of grain assessment used by the barley and seeds sectors, this research would underpin the development of new academic and industry tools in the longer term.

The quality of malting barley is of prime importance, for reasons of food safety, product quality and the competitiveness of the UK cereals industry. Evaluation of barley grain along the supply chain, during malting intake and merchant screening, includes crucial decisions on the value of grain bulks and their processing suitability.

Grain evaluation by maltsters, seed merchants and other end-users includes measurement of desirable features such as grain plumpness, specific mass, and tissue physical integrity, but also identification of defects such as grain skinning and pre-germination. Grain skinning, or husk loss, reduces processing output and efficiency during malting and brewing, whilst pre-germination in grains initiate premature enzyme development, which reduces malting potential and can encourage microbial growth.

At present, assessment of malting quality features is mainly based on manual and time-consuming sampling. For example, undesirable features such as grain skinning and pre-germination are assessed by counts, or mass, or by grain staining tests. Such methods have high levels of operator bias and often low precision, which gives rise to poor accuracy across the cereals sector.

In working towards the development of spectral and ML evaluation methods, this studentship will gather high quality and high-volume spectral signatures from well-defined training sets of malting barley. Data processing will embrace state-of-the-art machine learning techniques to examine spectral signatures for physical integrity and processing quality.

In developing a spectral imaging and ML based diagnostics system, this EASTBIO studentship will underpin practical applications for the grains research community and wider cereal industry, towards new precise and automated grain assessment protocols.

This fundamental study of grain textural, physical and chemical features will provide opportunity to engage widely with industry, including the malting sector, grain merchants and crop breeders who are seeking development of affordable and sustainable solutions for selection and screening of grains and quality traits. Building on expertise with existing grain assessment protocols and analytical equipment, such as hyperspectral systems, we expect the project to be a key step towards routine use of advanced technologies for grain quality evaluation and performance prediction.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Steve Hoad, Alistair Hamilton, Scott Denholm and Gail Jackson.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Nutritional strategies to stimulate endogenous antimicrobial peptides in poultry: A promising alternative to antibiotics with a smart solution for safe and sustainable poultry farming.

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Increasing antimicrobial resistance is a global concern for consumers, public health authorities, farmers and food standard agencies. Antimicrobial peptides (AMPs) are emerging as an effective non-antibiotic tool to combat infectious diseases in poultry.

However, the prophylactic application of synthetic AMPs is limited due to their higher production cost and product stability issues. Nutritional manipulation to induce and regulate the expression of endogenous AMPs can be a smart solution to tackle the strategic challenge of producing sustainable, resilient and safe poultry.

This PhD project aims to identify the ability of novel feed additives (β-glucan and oligosaccharides derived from yeast and cereal) to stimulate host AMPs in situ and to reveal how nutritional supplementation of feed additives can manipulate the expression of avian host AMPs in the gut under mild sub-clinical disease conditions. The main objectives of the study are:

1. Optimisation of β-glucan structure and function to maximise broiler immune and metabolic responses in antibiotic-free diets
2. Identification of the mode of action of these host AMP’s in the gut in order to establish a diagnostic marker to aid in promoting consistency in the commercial application of these novel feed additives
3. Develop a link between the concentration and inhibitory abilities of these host AMPs against bacterial, viral and parasitic pathogens in the avian gut.

The student will be registered at the University of Edinburgh and based at Monogastric Science Research Center (MSRC) of SRUC. In vivo studies will be conducted at the SRUC’s new state of art poultry research facility, which is the UK’s largest facility dedicated to fostering world-leading research to benefit agricultural food safety and security, animal health and welfare, public health, and environmental impact/climate change by trialling innovative ideas under near-commercial conditions.

The project will partner with AB Vista, an animal nutrition and technology company that is one of the largest feed additives suppliers globally. The student will work very closely with AB Vista, including an industrial placement of no less than 12 weeks. During placement, the student will be trained and supported by Dr Mike Bedford at AB Vista, Marlborough, UK. At this site, the student will obtain detailed practical knowledge of the sector by working with global team members with a range of expertise, including industrial production of feed additives, nutrigenomics, R&D development, manufacturing operations, financial management and communication skills (both academic and non-academic). 

Additionally, at SRUC and University of Edinburgh, skills training will be provided in personal effectiveness, communication skills, networking and team working, study design, molecular biology, metataxonomics (16S rRNA gene sequencing), metagenomics (whole shotgun metagenomic sequencing) and career management.

This project is multidisciplinary and combines nutritional, immunology, molecular, genomic and statistical science to provide insight into the effect of novel feed additives as an alternative to antibiotics. The supervisory team brings the necessary complementary expertise in each of these fields and will support the student in developing academic skills within each discipline. The combination of on-farm training, lab skills, and exposure to world-leading companies will ensure that the student is well prepared for a career in academia or industry.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Farina Khattak, Prof Jos Houdijk and Prof Lonneke Vervelde.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: EASTBIO Biotechnological approaches for sustainable monomers and polymers from waste biomass

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Due to increased population growth and growing people's demands, petro-chemicals have been widely utilised in our daily need products such as in digital devices, packaging, clothing, detergents, tyres and so on.

However, due to significant expenses, high density, non-biodegradable nature and growing environmental pollution because of these synthetic polymers or petroleum-based products, researchers are currently looking for modest, sustainable and biodegradable alternatives sources.

In this field biomass and biomass-based products could be an acceptable substitute, as these materials are readily available, possesses low density, are cheap, biodegradable, contains a significant amount of cellulose, hemicelluloses and lignin; and are biocompatible.

So far, a limited number of waste biomasses have been explored to develop sustainable materials using conventional chemical approaches. However, these approaches are also not economic and eco-friendly. It is a need of ours to explore new biotechnological processes to develop sustainable chemicals and materials for the effective utilisation of waste biomass in multiple fields.

In the proposed PhD programme the preliminary research will be carried out to explore waste agricultural by-products to prepare sustainable monomers and polymers for the circular bioeconomy and optimise the polymer material formulation. We will explore new strategies for the development of sustainable monomer/polymers using an enzymatically engineered biomass.

The developed sustainable monomer/polymers will be analysed for miscellaneous applications, including removing harmful heavy metal ions, detergents, water desalination and organic molecules from contaminated soil/water and nanocomposites for biodegradable packaging.

A pilot production system will also be designed and built to demonstrate the concept at a larger scale. From the pilot-scale data, economic evaluations and performance will be done to confirm the advantages of the proposed monomer/polymers over traditional chemical techniques.

The successful development of proposed monomer/polymers using agricultural by-products will increase waste resources for value-added products from agricultural materials, improve soil/water quality and conservation through effective soil/water treatment and reuse, and reduce environmental impacts of agricultural wastes.

The successful student will work with Prof Vijay Kumar Thakur at SRUC. The student will register at the University of Edinburgh where they will have access to the training environments of both SRUC and the University of Edinburgh. Both institutions are committed to the training of PhD students in both specific and transferable skills.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Prof Vijay Thakur, Dr V Gupta and Dr D Roy.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: E4 Understanding the ecological interplay between tree planting and natural colonisation processes to create future forests

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 6 January 2022

Woodland expansion is the focus of many restoration efforts because of its potential to aid biodiversity recovery, mitigate climate change, and contribute to people’s livelihoods and wellbeing. In the UK, woodland creation schemes have contributed to increasing woodland cover from a historic low of 5% in the early 1900s to the current figure of 13%, and the UK Government has pledged to plant an additional 30,000 ha of trees per year up to 2050.

Historically, tree planting has been the most common woodland expansion strategy in the UK, but this approach is increasingly questioned following failures, overestimates of benefits and poor targeting. Consequently, there is growing interest in incorporating ecological processes such as ‘natural colonisation’ (allowing trees to colonise new areas naturally) into large-scale woodland expansion strategies. This is partly because it is assumed that naturally created forests will be cheaper, more effective and more resilient, for example to tree disease and pests, than planted sites.

Naturally colonised sites are also perceived to lead to more heterogenous and complex woodlands of higher ecological value than planted woodlands. However, much of this evidence is drawn from regions with quicker habitat successional rates, such as the tropics, and where landscapes have not been as heavily degraded as in the UK, and it’s unclear how applicable this is to temperate regions.

Whilst both tree planting and natural colonisation have the potential to play important complementary roles in woodland cover expansion, a combination of these approaches may also be beneficial and assist natural processes by enhancing seed dispersal and ameliorating the local environment. However, there is a need to understand how tree planting and natural colonisation processes interact, and how they can most effectively be used in combination to speed up woodland creation and the accrual of biodiversity and other environmental benefits.

The overall aim of this studentship is to investigate how woodland development and habitat structure differ among woodlands created through planting, natural colonisation, and a combination of these two approaches (for example low density planting followed by natural colonisation). Specific questions to address include:

1. Do woodland development rates differ among woodlands created through different approaches along the natural-vs-planted continuum, and if so, what is the most effective strategy to speed up woodland creation?
2. What are the ecological mechanisms underlying woodland expansion/development in woodland creation sites along a natural-vs-planted gradient, for example does the relative importance of zoochory compared to allochory differ and is this reflected in the tree species composition?
3. How does woodland creation method (planted, natural and combined) influence woodland habitat structure and what are the consequences of this for woodland biodiversity?
4. How do woodland creation methods affect the ecosystem services provided by the woodland?

Fieldwork will be conducted in woodland creation sites established through a range of approaches encompassing planting and natural colonisation methods (and a combination of these). These will include sites already identified by Forest Research’s Woodland Creation & Expansion group, following a systematic site selection protocol to control the effects of woodland age and proximity to seed sources (distance to mature woodland).

Ecological surveys will be conducted along a transect from established mature (e.g. ancient) woodland to ‘new’ woodland areas to characterise the vegetation structure (such as tree size and density) and tree species composition with increasing distance to seed sources. Where available, open source LiDAR data will be used as an additional method to describe the three-dimensional structural complexity of the woodland sites.

The abundance and species richness of potential zoochoric vectors (such as ants, birds and small mammals) will be quantified using a combination of sampling methods, such as pitfall traps for invertebrates, point counts and acoustic recorders for birds, live traps and camera traps for mammals.

Societal perspectives and wider public benefits (for example recreational use and amenity value) will be assessed through empirical observation and (walking) interviews. There is also scope for the student to investigate how woodland biodiversity (taxonomic group(s) of their choice) utilise new woodland areas created through planting, natural colonisation and a combination of these methods.

The ideal student would hold an excellent first degree in ecological/environmental science (or related biological discipline) and have good quantitative skills. Previous knowledge of woodland ecology and experience in relevant field surveying methods would be advantageous, but it is not essential.

TThis PhD project is part a competition funded by E4 NERC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Elisa Fuentes-Montemayor (SRUC), Marc Metzger (University of Edinburgh), Kevin Watts (Forest Research) and Kirsty Park (University of Stirling).

Apply

Please visit the University of Edinburgh website for full application instructions and needed forms.

Title: EASTBIO Valorisation of dairy waste to recyclable packaging materials: Potential to contribute towards circular economy

Start date: 1 October 2022

Duration: 4 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Dairy is a burgeoning industry following the global population growth, resulting in the generation of waste such as wastewater, whey, and sludge. The dairy industry in Scotland produces 1.5 billion litres of milk annually of which around 40% is processed into cheese, 40% is supplied to the liquid milk market, and the rest is processed into other dairy products such as butter, cream, yogurt and so on.

These components are rich in nutrients, organic and inorganic materials. Additionally, the presence of alkaline and acidic detergents along with sterilizing agents in dairy waste makes it an environmental hazard. Thus, sustainable valorisation of dairy waste is currently the forefront area of research.

Whey is a major component in dairy effluent and is composed of important components such as lactose and protein. In different food packaging applications, packaging materials with good gas and water vapor blockade are critical for protecting the food product quality.

This basis is normally met by the utilisation of multi-facet films, which are by and large comprised of a blend of polymers. However, utilization of various polymers hampers reusing and reprocessing. The polymers utilised are also petrochemical-based and not biodegradable. Consequently, to supplant petrochemical plastics with low carbon impression materials, huge researches are centred around the improvement of biodegradable polymer-based materials.

This doctoral work will focus on the valorisation of dairy waste through microbial bioprocessing to produce lactic acid and converting it to biodegradable polymer-based materials poly lactic acid (PLA) films. This PLA will be used for the development of biodegradable films and foils.

Its utilisation in recycled packaging applications can be additionally upgraded by whey protein-based coatings to further develop its gas permeation and resistance, which regularly restrict packaging components. The blend of PLA film with a whey protein-based layer is promising and can be used for packaging applications. The core strategy of this work is to promote circular economy and reducing the impact of waste disposal on the environment.

This project builds on experience in bioprocessing at SRUC and expertise in Biochemical Engineering at University of Edinburgh (UoE). The student will benefit from training across these disciplines.

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. The studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr V Gupta, Prof Vijay Thakur and Dr D Oyarzun.

Apply

Please visit the EASTBIO website for full application instructions and needed forms.

All forms must be sent to pg.research@sruc.ac.uk. Please ask your referees to use the same email address to send your references. 

We anticipate that our first set of interviews will be held 7–11 February 2022 with awards made from 18 February.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: Horticultural production in Scotland: vertical or horizontal for Net Zero

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC King's Buildings, Edinburgh

Closing date for applications: 16 December 2021

Vertical farming or urban farming – which is better for the environment?

The Paris Agreement and the drive to Net zero has focused attention on reducing greenhouse gas (GHG) emissions from agricultural systems. Agricultural systems deliver a wide range of ecosystem services. Nevertheless, it is imperative that the negative impacts of agricultural systems on the wider environment are minimised.

Fuelled by the recent pandemic, consumers have become increasingly interested in locally grown fruits and vegetables that support healthy diets. Current UK vegetable production is predominately field based, including large-scale production across the Eastern UK and small-scale, local organic or conventional producers in rural and urban settings.

A recent rise of vertical farming offers new opportunities to expand the quantity of locally produced vegetables, including extending the season to year-round supply. Vertical farms can produce high yields of vegetables in controlled and protected systems.

While this reduces the exposure of the plants to pests and pathogens, with minimal pollution of the wider environment, they are energy intensive and offer no direct ecosystem service benefits beyond provisioning. At the other end of the technological scale, urban agriculture shortens the supply chain and has been shown to increase the intake of vegetables locally as well as other health benefits, but with lower yields.

As well as producing healthy foods, production methods must also be cognisant of direct and indirect impacts on the wider environment. Increasing fruit and vegetable production in urban environments will potentially reduce the need for imports and have knock-on consequences on the area currently devoted to field scale production. There are opportunities to devote land to other food crops or land management practices that will enhance carbon storage. This PhD will explore the relative environmental impacts of these different systems.

The student will receive appropriate training on agricultural systems and modelling approaches.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Kairsty Topp, Prof Christine Watson, Prof Mads Fischer-Moller, Prof Nicola Holden and Prof Alfred Gathorne-Hardy.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/KT.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: How can blurred boundaries between schistosome species affect the molecular epidemiology of antigen variability and drug resistance of zoonotic schistosomiasis

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: Inverness

Closing date for applications: 16 December 2021

Human intestinal schistosomiasis is a debilitating zoonotic disease and presents with several symptoms including abdominal pain and diarrhoea and, in chronic cases, with hepatosplenomegaly. It is estimated that 230 million people across Africa, Asia and South America are infected, affecting predominantly poor rural communities engaged with agricultural and fishing activities.

Currently it is only through wide scale distribution of praziquantel PZQ the parasite is being controlled and there is an increasing concern of the emergence of genetically heritable drug resistance within parasite populations, there is still no effective vaccine that prevents schistosome reinfection.

Schistosoma mansoni is one of the most prevalent and widespread species, which causes human intestinal schistosomiasis with infections being highly heterogenetic with different diseases presentations seen in different geographical localities.

Schistosoma mansoni is also known to infect other mammals particularly using rodents as reservoirs, considered to generate novel highly virulent genotypes that could be a considerable public health concern. Schistosome infections do not occur in isolation and S. mansoni infections have been shown to occur with a sympatric sister species Schistosoma rodhaini in rodent populations.

Our recent work has identified introgressed S. mansoni x S. rodhaini genotypes, detected in parasite populations collected from children that could not clear infection after treatment. To date there have been no studies that have attempted to assess the frequency of these 'hybrid' parasites infecting both human and rodent populations. Nor has there been any attempt to investigate the impact that such processes could have on antigen coding gene variation, which may account for variation in disease presentation and lack of vaccine efficacy.

Schistosome hybrids are now considered to be an emerging climate sensitive disease. They are causing endemic infections in Europe, so an understanding of these parasites in their natural foci is paramount for effective surveillance and potential control.

This project will focus on schistosome populations collected from human and rodent populations from Uganda and using gene/chromosome specific molecular markers will address the following questions:

• What is the frequency and distribution of introgressed genotypes infecting rodents and humans?
• Do levels of introgression between mansoni and S. rodhaini vary between locations and hosts?
• What is the impact of introgression on the genes that code for surface antigens and drug receptors within and between hosts?

The successful candidate will receive training in classical and molecular epidemiology, bioinformatics, in silico antigen identification parasitology, and there may be the opportunity for field work.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Scott Lawton, Prof Neil Foster, Prof George Gunn and Dr Poppy Lamberton.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/SL.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: Establishment and control of microbiomes at various body sites of dairy cattle

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: Dumfries, Belfast

Closing date for applications: 16 December 2021

A fully funded PhD studentship is available as part of a €10 million, collaborative European project, 'HoloRuminant', starting in October 2021.

HoloRuminant will explore the role of ruminant-associated microbiomes and their interactions with the host animal in early life, and throughout fundamental life events, such as weaning, which are known to affect health, welfare, and environmental efficiency in ruminant production systems.

The project involves sampling from several sites of dairy cows from birth through to established first lactation and uses metataxonomics approaches to explore patterns of microbiome establishment and possible common control.

The students will gain skills ranging from working with animals to advanced molecular biology and bioinformatics techniques. Whilst being registered at Queens University Belfast and having the opportunity to work in their state-of-the-art molecular and microbial labs and high-performance computational infrastructure the student will work mostly with the world-leading Langhill Genotype x Environment study at SRUC’s Dairy Research and Innovation Centre in Dumfries. Annual progress evaluations and viva voce examinations will be held in Belfast.

Further details of the facilities and groups can be obtained in the Dairy Research Centre section, the Huws Lab website and the Creevey Lab website.

Students should have at least an upper second class degree (or equivalent) in a life science subject and some awareness of livestock production challenges. A postgraduate qualification would be desirable, but is not essential.

To have an informal discussion about this studentship, contact Professor Richard Dewhurst via email richard.dewhurst@sruc.ac.uk or telephone 0131 535 4050.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend, UK level tuition fees, with experimental and travel costs covered by the project.

The project will be supervised by: Prof Richard Dewhurst, Prof Chris Creevey, Dr Holly Ferguson and Prof Sharon Huws.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/QUB/Control.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: Interactive effects of moorland management and wilding on predator/prey relations

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC Craibstone, Aberdeen

Closing date for applications: 16 December 2021

Upland areas of the United Kingdom are at a crossroads for future management. Land used for traditional sporting activities (especially Red grouse shooting), and its associated input to rural economies, is increasingly under the spotlight.

The role of such activities in legal predator control, protected species persecution, habitat modification and contribution to climate change are under scrutiny, and the activity faces increased regulation in Scotland. There is, at the same time, a rise in areas under management that can be described as 'wildling' (or 'rewilding'). Typically, whole estates are managed in a way in which ecological processes take priority over individual species or habitat targets.

These two approaches may affect predator assemblages in different ways. Sporting management may lead to non-tolerance of avian and mammalian meso-predators such as foxes, stoats and crows, with such management associated with higher numbers of some species such as ground-nesting waders [1]. On wilding estates, predator control will be at a lower level or absent.

This project will investigate the relationships and interactions of these contrasting management directions in terms of how they are mediated through predator activity.

There will be a focus on assessing relative activity levels of prey species, especially small mammals. This will involve developing techniques for effective monitoring in remote environments. Specifically, the student will combine a novel camera trapping technique [2] with recently developed acoustic identification approaches for small mammals [3] to devise optimal sampling strategies. There will be opportunities to tie in with crowd-sourced citizen science classification of camera trap images through MammalWeb [4].

Data on year-round prey availability (small mammals) and seasonal prey availability (birds) will be used to investigate predator activity.

The following questions will be assessed: Do (re)wilding areas support elevated prey resources that sustain predator populations and act as a predator source for adjacent intensively managed (grouse) moors? Or do wilding areas draw predators away from grouse moors, especially when small mammal prey abundance is low [5].

Prospective students should have strong ecological field skills, a passion for working in beautiful and remote landscapes, and be able to liaise confidently and sensitively with rural stakeholders.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Nick Littlewood, Dr Sarah Marley and Prof Mark Whittingham.

[1] (2019) Ecology and Evolution, 9, 11089–11101.
[1] (2021) European Journal of Wildlife Research 67, Article number 12.
[1] (2020) British Wildlife, 32, 186-194.
[1] (2018) Remote Sensing in Ecology and Conservation, 4, 361-374
[1] (2017) Ibis, 159, 541–553.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/NL.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: Exploring the milk microbiome and its impact on mastitis susceptibility and inflammatory responses in dairy cattle

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: Dumfries, Belfast

Closing date for applications: 16 December 2021

A fully funded PhD studentships is available as part of a €10 million, collaborative European project, 'HoloRuminant', which started in October 2021.

HoloRuminant will explore the role of ruminant-associated microbiomes and their interactions with the host animal in early life, and throughout fundamental life events, such as weaning, which are known to affect health, welfare, and environmental efficiency in ruminant production systems.

The project will develop a novel understanding of the milk microbiome of cattle and explore how host genetic merit relates to milk microbiome, mastitis susceptibility and the immune and inflammatory response in the udder.

The students will gain skills ranging from working with animals to advanced molecular biology and bioinformatics techniques. Whilst being registered at Queens University Belfast and having the opportunity to work in their state-of-the-art molecular and microbial labs and high-performance computational infrastructure the student will work mostly with the world-leading Langhill Genotype x Environment study at SRUC’s Dairy Research and Innovation Centre in Dumfries. Annual progress evaluations and viva voce examinations will be held in Belfast.

Further details of the facilities and groups can be obtained in the Dairy Research Centre section, the Huws Lab website and the Creevey Lab website.

Students should have at least an upper second class degree (or equivalent) in a life science subject and some awareness of livestock production challenges. A postgraduate qualification would be desirable, but is not essential.

To have an informal discussion about this studentship, contact Professor Richard Dewhurst via email richard.dewhurst@sruc.ac.uk or telephone 0131 535 4050.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend, UK level tuition fees, with experimental and travel costs covered by the project.

The project will be supervised by: Prof Richard Dewhurst, Prof Chris Creevey, Dr Holly Ferguson and Prof Sharon Huws.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/QUB/Milk.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: Microbial cell factories for industrial biopharmaceutical enzymes production

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC Barony, Dumfries

Closing date for applications: 16 December 2021

Microbes are one of the most important and diverse groups of organisms on the sphere. They offer essential products for agri-food and biotechnological inventions. This projected PhD work is planned to exploit native microbial cell factories for industrially important enzymes (such as Tyrosinases, Carbonyl reductase and Amine transaminase) for biomedical applications.

This work aims to selectively mine the potential of microbes for enzyme development/engineering and subsequently depicting these enzymes for fundamental research and biopharmaceutical applications.

The proposed work will apply novel low-cost production technologies to achieve the efficient production of biomedical enzymes. This work will have both UK and International impacts. The potential of candidate microbes as cell factories for the production of these unique enzyme molecules will be revealed through metabolic flux analysis to optimise conditions. Thus, inventive, advance and naturally well-suited and very specific biopharma enzymes will be identified from respective microbial systems. 

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Dr Vijai K. Gupta, Prof Vijay Thakur, Dr Jolanda van Munster and Prof Dr Diego A. Oyarzún.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/VG.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: Rational design and synthesis techniques for the transformation of agricultural waste to sustainable biocompatible nanomaterials for a circular bieconomy

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC Barony, Dumfries

Closing date for applications: 16 December 2021

The technology-based on synthetic plastics has played a vital role in various applications in numerous industries, including packaging to automotive.

The use of plastics in the modern world has been increasing rapidly due to the relative ease of production and specific set of properties of polymers employed in producing these materials compared to traditional metallic and ceramics based materials. However, some critical disadvantages of these materials regarding human and environmental ecology, including being unsafe to handle and posing health risks when inhaled, non-biodegradability, corrosiveness, and non-recyclability, have raised several apprehensions in the community.

In recent years, the use of renewable biomass as raw material to produce fuels and chemicals to displace fossil resources has been the focus of many research activities. These activities have been motivated by the possibility of positive contributions to a sustainable resource supply, enhanced national security, and macroeconomic benefits for rural communities and society all around the globe.

Undoubtedly, there is an urgent need to develop new sustainable materials from biorenewable resources. Essentially all materials used in the production of synthetic plastics are derived from the petroleum-based feedstock. Additionally, a few synthetic materials contain some biobased components in actual industrial applications.

We are faced today with unique opportunities to further the effective and efficient use of biorenewable resources like agricultural biomass waste (such as hemp fibres). The increased usage of synthetic polymers and related appliances at home and in industries has raised significant concern for a sustainable environment.

Little attention has been directed towards utilising bio-renewable resources like agricultural biomass waste (for example hemp/flax and sugar cane/beet) combined with bio-derived carbon nanomaterial for value-added materials and their industrial applications.

Adding value to waste biomass production from biorenewable resources and finding sustainable alternative sources for existing petroleum-based products will have a substantial and long-term impact on the economy, the environment and energy independence and security of Scotland and the UK. 

This research explores the transformation of agricultural biomass sourced waste materials into value-added nanoproducts, taking full advantage of the incredible structural richness and diversity of the agricultural materials for packaging and automotive, to name a few.

The project aims to result in breakthrough step-changes in the effective utilisation of biorenewable resources leading to sustainable materials with new and improved properties, lower cost, more environmentally friendly, and thus more acceptable to consumer markets. It will also generate advanced technologies enabling new market opportunities for biorenewable resources while reducing the environmental footprint relative to synthetic materials from petroleum feedstock.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Prof Vijay Thakur, Dr Vijai K. Gupta and Dr Dipa Roy.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/VT.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.

Title: Does the cyto-lethal distending toxin aid environmental transmission of pathogenic bacteria?

Start date: 1 October 2022

Duration: 3.5 years, full time

Salary: £15,609 per annum

Location: SRUC Craibstone, Aberdeen

Closing date for applications: 16 December 2021

Cytolethal distending toxin (CDT) is a genotoxin produced by a number of different bacterial pathogens. Although it is carried by a range of Gram negative bacteria, it is not universal and seems to be limited to specific genetic lineages within a species. Many of the pathogens that encode CDT have multiple transmission pathways that result in human disease, including interactions with environmental hosts and habitats, such as soil, water and plants.

Surveillance studies of animals have shown that CDT is also present in non-pathogenic isolates. Furthermore, we identified CDT in the genomes of some environmental Escherichia coli isolates. Functional characterisation shows it acts as a virulence factor in higher animals, but there is little information beyond that.

Together, these facts point to a potential for a functional role of CDT in a wider context, where it may confer a type of ecological fitness advantage, for example by protecting against predation from nematodes or other invertebrates.

This project will examine the potential role of CDT in environmental transmission or persistence of the microbes. We will focus on the environmental E. coli isolates in three interlinked aims:

1. to understand whether CDT is produced under conditions relevant to environment hosts and habitats
2. to look at functional roles including its impact on grazing nematodes, or its ability to cause disease in invertebrates
3. to relate the findings to well-known pathogens for which CDT has a characterised role in pathogenesis

The overall aim is to understand the ecological role of CDT, so that we can determine the risk to public health for pathogens that are transmitted via environmental routes. The outcomes will also inform on emergence of pathogens from environmental sources.

The project is a collaboration between different disciplines that brings together a range of expertise to draw on, from molecular microbiology to cellular biology and entomology. It offers an excellent opportunity to understand how pathogens cause disease and how they survive or even thrive in non-animal habitats.

This PhD studentship is open to UK and international students, providing funding to cover UKRI level stipend and UK level tuition fees.

The project will be supervised by: Prof Nicola Holden, Dr Rob Graham and Dr Massimiliano Baldassarre.

Apply

Please fill out the application form and equal opportunities form and send it along with your academic qualifications to pg.research@sruc.ac.uk, quoting reference SRUC/NH.

Please send the academic reference form to two academic/professional referees, and ask them to submit it by the deadline mentioned above to pg.research@sruc.ac.uk.

If you have any queries please contact pg.research@sruc.ac.uk.