Xianghu Laboratory Partnership

The School of Biological Sciences is very pleased to have partnered with the James Hutton Institute and the Xianghu Laboratory in Hangzhou, China to form a PhD Training Centre. This international and interdisciplinary centre will train the next generation of environmental and agricultural scientists through a range of PhD projects.

Information on the currently advertised projects and how to apply for them can be found, below.

Plant signalling crosstalk in response to light and temperature stresses

Supervisors: Dr Gareth Norton, Prof. Rongcheng Lin, Dr Craig Simpson

Application Deadline: 3 June 2024

The circadian clock co-ordinates internal gene expression rhythms with external light and temperature cycles and is constantly entrained by changes in light and temperature. The signalling crosstalk in response to light and temperature stresses is largely unknown and will alter gene expression and transcriptome profiles. Changing transcriptome expression profiles will provide clues to the genes that are part of the crosstalk between light and temperature. In barley, we have established reliable global quantification methods from RNA-seq data that allow us to measure differential gene expression and differential alternative splicing in response to changing conditions. We also utilise RT-PCR methods to study the expression of selected genes across a broader range of samples. The same procedures can be utilised in rice allowing us to study variation in signalling  between tropical/sub tropical and  temperate grown crop species. The studentship will use a range of temperatures and light wavelengths to study changes in the transcriptome of barley and rice to identify key genes that respond to light and temperature stresses.

Genetics and Genomics of Disease Resistance in Wheat

Supervisors: Prof. Paul Hallett and Dr Zhiyong Liu

Application Deadline: 3 June 2024

Wheat (Triticum aestivum) is a staple food for about 40% of the world's population. As the global population has grown and living standards improved, high yield and improved nutritional quality have become the main targets for wheat breeding. However, wheat production has been compromised by global warming through the more frequent occurrence of extreme temperature events, which have increased water scarcity, aggravated soil salinization, caused plants to be more vulnerable to diseases, and directly reduced plant fertility and suppressed yield. One promising approach is to identify and incorporate genes that confer resistance to environmental stresses such as heat, drought, salinity, and disease into wheat cultivars. This can be achieved through traditional breeding methods as well as more advanced genetic engineering techniques like CRISPR-Cas9.

Plant-Microbe Interaction in Sustainable Agriculture

Supervisors: Prof. Graeme Paton, Prof. Peiwu Li, Dr Jens Tilsner and Dr Pete Iannetta

Application Deadline: 3 June 2024

Intercropping is recognised as a viable alternative to conventional (high input) agriculture, optimising yields above that which can be achieved by monocropping. High intercrop yields are characterised by ‘land equivalent ratios’ (LERs) >1 and are achieved under minimum inputs of synthetic nitrogen (N) fertiliser; and pesticide, since intercropping also presents an IPM (integrated pest management) strategy. Such benefits are a function of facilitative- and competitive-interactions among the mixed crop types, including soil-processes mediated by legume’s (symbiotic) microbiome. Furthermore, traditional intercropping usually involves combining a legume species with a cereal (non-legume) species. However, recent research has established that legume-legume combinations can demonstrate very high LERs. Additionally, study of [legume x legume] intercrops have focused on (protein) yield, and so the above- and below-ground symbiotic and/or IPM potential of such combinations has still to be explored.Therefore, this study will seek to understand and characterise the basis of the potential demonstrated by [legume x legume] intercrops (including in response to inoculation with different rhizobia strains) and optimise combinations offering enhanced yield and yield-quality potential. Specific genotype (and rhizobia strain) combinations could be tested for their potential in-field.

Analysis of the potential of Dark Septate Endophytic (DSE) fungi to help mitigate climate change induced plant stress

Supervisors: Prof. Pieter Van West and Prof. Fucheng Lin

Application Deadline: 3 June 2024

Healthy soil with enough nutrients and a good microbial population helps plant growth and maintains plant health. The challenge remains to really understand the soil microbiome, but our knowledge of the rhizosphere, its constituent species and how they interact together to form healthy soils remains to be dissected. A largely untapped resource is Dark Septate Endophytic (DSE) fungi, that are also present in soils.  Endophytes can colonise internal tissues of plants without causing disease. Many of these DSE fungi form endophytic interactions with a range of plant species and in doing so can suppress diseases, promote healthy plant growth and increase tolerance to stress. The focus of this work is to tap into the potential of DSE fungi to mitigate stresses induced by climate change and help plants increase shoot/root biomass and nitrogen and phosphorus content, increase resistance to pathogens as well as increase tolerance of drought stress. Our objectives are to systematically determine the diversity and abundance of DSE fungi in soil samples of the root microbiomes of crops in the context of agricultural systems. Investigate the dynamic aspects of specific DSE-plant interactions through in vivo and in vitro studies, aiming to comprehend the temporal and spatial patterns of their associations and conduct in-depth molecular analyses to characterize the DSE-plant interactome within agricultural systems. The outcomes of this investigation are anticipated to pave the way for the development of new and complementary agricultural practices which consider the underground fungal communities alongside usual and other novel agricultural practices.

Sustainable removal of emerging contaminants by persulfate-based advanced oxidation process

Supervisors: Prof. Graeme Paton, Dr Yongfei Ma, Dr Zulin Zhang and Dr Sandhya Devalla

Application Deadline: 3 June 2024

Undesirable removal efficiency of emerging contaminants (ECs, e.g., PFAS and antibiotics) by traditional wastewater treatment technologies resulted in large amounts of their residuals being discharged into environment, which might pose potential risks to animal and human health. Advanced oxidation processes (AOPs) were proved to be a promising approach as it was able to completely remove the target contaminants by oxidizing them into non-toxic (e.g., CO2 and H2O) or less toxic transformed products (TPs). Specially, activated persulfate (PS) technology has aroused broad attention due to its higher redox potential (E0=2.6-3.1 V) and longer half-life (28-40 μs) of SO4•- derived from PS activation. The main objective of this project is to develop and optimize an in-situ generation (e.g., electro-generation from the solution containing sulphate in water and offering the possibility without adding exogenous PS for this technology) technology of persulfate-based AOPs for ECs (e.g., PFAS and antibiotics) removal. A second key objective is to synthesize functionalized biochar from waste materials (e.g., municipal sludge) to efficiently activate PS for the contaminant degradation. A final objective is to couple in-situ electrogenerated PS with carbon-based material for contaminants degradation, including the extension to other  or combined ECs elimination and testing for real water treatment.

Accurate genomic annotation of farmed fish and shrimp using Oxford Nanopore Sequencing 

Supervisors: Dr Jason Holland, Prof. Sam Martin. Prof. Zhimin Gu and Dr Runxuan Zhang

Application Deadline: 3 June 2024

Accurately determining genome organization and sequence enables efficient genetic improvement of fish and shrimp species. Long-read sequencing technologies such as Oxford Nanopore Technologies (Nanopore) are essential for capturing structural and sequence variation as well as the complete transcriptome, however, challenges remain, including false mapping, mis-assembly and failure to identify full-length isoforms. We are working to improve long read sequencing in farmed fish and shrimp species, with key targets being yield, flavouring or other desirable traits.                                                                                       
The aim of this interdisciplinary project is to develop computational methods to enhance the accuracy of Nanopore sequencing analysis and use these methods to annotate and increase our understanding of the fish and shrimp genome, variation across farmed fish and shrimp lines, and transcript-specific expression. This will provide key information to underlie a mechanistic understanding of farmed fish and shrimp traits. 

Biosensors for rapid and sensitive detection of pathogenic bacteria 

Supervisors: Prof. Graeme Paton and Prof. Jianhan Lin

Application Deadline: 3 June 2024

Conventional and standard bacterial detection methods such as culture and colony counting methods, immunology-based methods and polymerase chain reaction based methods, may take up to several hours or even a few days to yield an answer. Obviously this is inadequate, and researchers are focusing towards the progress of rapid methods. Although technologies including biosensors show potential approaches, further research and development is essential before they become a reliable choice. This project will develop and deploy novel bio-molecular techniques for pathogen detection through the improvement of  biosensor characteristics such as sensitivity and selectivity to create rapid, reliable, and effective solutions for in situ analysis.

Enhancing agricultural waste utilisation through assessing soil husbandry and crop yield 

Supervisors: Prof. Astley Hastings, Prof. Graeme Paton and Prof. Yanlai Yao

Application Deadline: 3 June 2024

With the challenges associated with climate change and rising global population; agricultural waste presents a growing challenge due to its potential to cause environmental degradation. This makes agricultural waste utilisation essential for creating more environmentally sustainable farming. Despite this, it can be challenging for farmers (at the granular scale) to efficiently utilise agricultural waste due to financial and resource constraints. Such failure can result in negative environmental effects and potential lost revenue for farmers. This project will investigate how agricultural waste/byproducts from selected crops can be more efficiently utilised to reduce environmental impact and improve farmer revenue. This project will involve both empirical (laboratory and field) and model-based approaches to assess how the challenges of soil husbandry and crop yield can be balanced against material re-uses. It is anticipated that this Sino-centric project will develop visions of an agricultural circular economy by integrating global models and best practice. 

Turn it up! Developing innovative acoustic techniques to control agricultural pests 

Supervisors: Dr Juliano Morimoto, Dr Xinyang Zhang

Application Deadline: 3 June 2024

Agricultural pests are major threats to food security worldwide. In storage grains, there are multiple ways in which pests can reach and destroy commodities, causing huge economic losses to agri-industries as well as small scale farmers across the globe. New techniques to prevent and protect grains from agricultural pests, during harvest and storage, are urgently needed. This project will develop novel acoustic-based techniques to protect, prevent, and control insect pests present in storage grains. The student will have the opportunity to learn a wide range of sampling techniques, acoustic, behavioural, and physiological assays, as well as key data analyses skills to succeed as a pioneer in digital agriculture. With an interdisciplinary and vibrant team of supervisors, the candidate will have the freedom to explore avenues of research to innovate on pest control of storage grains, which can lead to real-world impact to our food systems. We welcome applications of all backgrounds, and we value diversity and inclusion as part of our core team values.

Evaluation of candidate genes involved in abiotic stress (including waterlogging/heat/drought) tolerance in wheat 

Supervisors: Prof. Paul Hallett and Prof. Shengchun Xu

Application Deadline: 3 June 2024

In field conditions, crops are adversely affected by a wide range of abiotic stresses including drought, cold, salt, and heat, as well as biotic stresses including pests and pathogens. These stresses impact crop yield. The impact of climate change necessitates crop stress tolerance to be further developed and future-proofed. Plants have evolved sophisticated stress response strategies, and genes that encode transcription factors (TFs) are master regulators of stress-responsive genes. These are excellent candidates for crop improvement. However, much remains to be discovered about the diverse plant TFs. Of the >80 TF families only a few, such as NAC, MYB, WRKY, bZIP, and ERF/DREB, with vital roles in abiotic and biotic stress responses have been intensively studied. As a model drought-tolerant crop, wheat is the focus of this project. This project will review recent progress on major TF families associated with abiotic and biotic stress tolerance and their potential for crop improvement. Other TF families and non-coding RNAs that regulate gene expression will be evaluated.  Using CRIPSR-based genome editing abiotic stress tolerance germplasm/materials will be found and isolated. The application of newly developed diverse genome-editing toolboxes will enable researchers to pyramid desired alleles in wheat varieties quickly and efficiently, without compromising other agronomic traits or introducing deleterious genes. Additionally, integrating genome editing with whole-genome sequencing, GWAS (genome-wide association studies), trait dissection, and speed breeding there will be a provision of extensive genetic information to accelerate wheat improvement through understanding the steps and the priorities needed. The project will also integrate genome editing with other cutting-edge breeding technologies to postulate the development of "green super wheat" varieties that are not only high-yielding and resilient but also environmentally sustainable.

The adaptation to heat stress and biofortification in soybean seeds

Supervisors: Dr Gareth Norton, Prof. Fengjie Yuan

Application Deadline: 3 June 2024

Globally, soybean is an important crop because of its high nutritional value (for both humans and livestock), its versatility in terms of final products, its suitability for a variety of crop rotations and because it has wide industrial applications beyond being a food source. The crop's widespread cultivation and consumption contribute significantly to agricultural economies worldwide. Isolation and characterization of stress-responsive genes is the first step in the generation of stress-tolerant cultivars. Once established these can be developed through genetic engineering approach. DREB genes from soybean can be isolated and analyzed to understand DRE-binding activities. Transcriptional activation activities will be examined in this project to understand genomic organizations, and expression patterns of these genes under pre-defined stress conditions. Developing techniques to analyse  DRE-binding activities will enable the project participants to understand how these genes interact with specific DNA sequences under defined stress conditions. By focusing studies on the transcriptional activation activities it is possible to understand the processes that initiate the expression of stress-related genes. By examining and understanding the genomic organization alongside their structural features and regulatory elements an assessment of the influences on expression and function can be made.The project will also investigate expression patterns under different stress conditions to provide insights into their roles in the plant's response to various pre-defined stressors.

Understanding the persistence of multi-drug resistant E. coli in farm soils 

Supervisors: Prof. Graeme Paton, Dr Hui Lin, Dr Zulin Zhang and Dr Eulyn Pagaling

Application Deadline: 3 June 2024

The threat of antimicrobial resistance (AMR) is one of the biggest challenges to society today. In the EU, about 25,000 patients die annually from an infection with a multi-drug resistant pathogen (‘superbug’), resulting in estimated losses of at least EUR 1.5 billion. It is recognised that the environment has in significant role in the spread AMR, and researchers agree that a holistic ‘One Health’ approach, incorporating environmental perspectives to a clinical problem, is required to tackle this issue. AMR in the farm environment is a particular issue due to the potential to enter the food chain. We have a collection of environmental E. coli isolates taken from different environmental matrices (soil, water, faeces) in an agricultural catchment in Aberdeenshire. Phenotypic analysis showed that many are multidrug resistant. This project aims to understand how AMR is maintained and potentially spread in the environment, using our environmental E. coli isolates as sentinel species. Our Objectives are to: 1) confirm the resistance profiles of the E. coli; 2) test how well they survive in the environment using soil microcosms; 3) determine the phenotypic and genotypic characteristics that allow resistant E. coli to survive and potentially spread resistance in the environment.

Deciphering new biosynthetic pathways of insects that are of economic significance in Chinese agriculture 

Supervisors: Dr Juliano Morimoto and Prof. Christer Löfstedt

Application Deadline: 3 June 2024

Pest pheromones are information compounds released by pests and can effectively regulate the behaviour of pests. Pest behaviour regulation technology created based on pheromones is an important means of effective monitoring and green prevention and control of pests, and it is the core technology of green prevention and control of pests and the key technology for guaranteeing the quality and safety of agricultural products. The premise of using pest pheromone is to synthesis the pheromone artificially in large quantities. At present, pheromones and related products on the market are obtained by chemical synthesis, but chemical synthesis is not only costly, but also seriously pollutes the environment and damages human health. Therefore, how to develop green and low-cost synthesis technology is the key to the development of the pest pheromone industry.