Antimicrobial resistance (AMR) has evolved in environmental bacteria over billions of years, producing a vast reservoir of AMR genes that can potentially be transferred to clinical pathogens. Agricultural soils are exposed to antibiotics through the use of manures or sewage sludge as fertiliser, or irrigation with reclaimed water. There is a concern that such exposure may promote AMR in food producing environments, increasing the likelihood of AMR transmission to the human microbiome via contaminated crops or environmental matrices. There is a growing body of research using in vitro models to establish the minimal selective concentrations (MSCs) of antibiotics in the environment, but there is very little evidence relating to selection by antibiotic residues jn situ in soils. The field scale trials undertaken at Agriculture and Agri-Food Canada (AAFC) over the last 10-20 years offers a unique opportunity to investigate the effects of antibiotic application on soil communities and AMR, and how soils recover from long-term application of antibiotics. In this project, state of the art metagenomic and bioinformatic approaches will be applied to determine the evolutionary effects of antibiotic residues on the soil resistome. This will be investigated at three timepoints: short-term exposure (7 & 30 days after application); long-term exposure (after 10 years of annual exposure); and after cessation of antibiotic application (1, 2, and 3 years post-exposure). Macrolide and fluoroquinolone antibiotics will be studied, which have very different environmental fates and which have both been flagged as priority substances of concern by the EU Water Framework Directive's Hazardous Compound Watch List. Furthermore, we will assess whether or not in vitro experiments are predictive of selection in soils in situ. This work will provide the most comprehensive assessment of AMR evolution in antibiotic amended soils to date.

To secure a continued supply of safe, tasty, affordable and functional/healthy proteins while supporting Net Zero goals and future-proofing UK food security, a phased-transition towards low-emission alternative proteins (APs) with a reduced reliance on animal agriculture is imperative. However, population-level access to and acceptance of APs is hindered by a highly complex marketplace challenged by taste, cost, health and safety concerns for consumers, and the fear of diminished livelihoods by farmers. Furthermore, complex regulatory pathways and limited access to affordable and accessible scale-up infrastructure impose challenges for industry and SMEs in particular. Synergistic bridging of the UK's trailblazing science and innovation strengths in AP with manufacturing power is key to realising the UK's ambitious growth potential in AP of £6.8B annually and could create 25,000 jobs across multiple sectors. The National Alternative Protein Innovation Centre (NAPIC), a cohesive pan-UK centre, will revolutionise the UK's agri-food sector by harnessing our world-leading science base through a co-created AP strategy across the Discovery?Innovation?Commercialisation pipeline to support the transition to a sustainable, high growth, blended protein bioeconomy using a consumer-driven approach, thereby changing the economics for farmers and other stakeholders throughout the supply chain. Built on four interdisciplinary knowledge pillars, PRODUCE, PROCESS, PERFORM and PEOPLE covering the entire value chain of AP, we will enable an efficacious and safe translation of new transformative technologies unlocking the benefits of APs. Partnering with global industry, regulators, investors, academic partners and policymakers, and engaging in an open dialogue with UK citizens, NAPIC will produce a clear roadmap for the development of a National Protein Strategy for the UK. NAPIC will enable us to PRODUCE tasty, nutritious, safe, and affordable AP foods and feedstocks necessary to safeguard present and future generations, while reducing concerns about ultra-processed foods and assisting a just-transition for producers. Our PROCESS Pillar will catalyse bioprocessing at scale, mainstreaming cultivated meat and precision fermentation, and diversify AP sources across the terrestrial and aquatic kingdoms of life, delivering economies of scale. Delivering a just-transition to an AP-rich future, we will ensure AP PERFORM, both pre-consumption, and post-consumption, safeguarding public health. Finally, NAPIC is all about PEOPLE, guiding a consumers' dietary transition, and identifying new business opportunities for farmers, future-proofing the UK's protein supply against reliance on imports. Working with UK industry, the third sector and academia, NAPIC will create a National Knowledge base for AP addressing the unmet scientific, commercial, technical and regulatory needs of the sector, develop new tools and standards for product quality and safety and simplify knowledge transfer by catalysing collaboration. NAPIC will ease access to existing innovation facilities and hubs, accelerating industrial adoption underpinned by informed regulatory pathways. We will develop the future leaders of this rapidly evolving sector with bespoke technical, entrepreneurial, regulatory and policy training, and promote knowledge exchange through our unrivalled international network of partners across multiple continents including Protein Industries Canada and the UK-Irish Co-Centre, SUREFOOD. NAPIC will provide a robust and sustainable platform of open innovation and responsible data exchange that mitigates risks associated with this emerging sector and addresses concerns of consumers and producers. Our vision is to make "alternative proteins mainstream for a sustainable planet" and our ambition is to deliver a world-leading innovation and knowledge centre to put the UK at the forefront of the fights for population health equity and against climate change.

Milk is increasingly in global demand because it is a nutritious natural food that can be processed into many different products accessible to a wide population, It accounted for 16.4% of total agricultural output in the UK in 2020 and was worth £4.4bn in market prices making the UK the thirteenth-largest milk producer in the world. However, this supply of this important safe food source is under threat due to antimicrobial resistant bacteria that infect the udder of dairy cows, causing mastitis. Mastitis is an inflammation of the udder caused by microbial infections that compromise milk production, quality and safety. It is the foremost endemic infectious disease which remains a major challenge to the UK, Canada and global dairy industries. Mastitis has a high prevalence and incidence (~35 (UK) and 19 (Canada) cases /per 100/year). Furthermore, clinical management of mastitis is challenging because not just one but the multiple microorganisms are involved in the infection, making it difficult to diagnose. This is further compounded by the fact that many of these microorganisms that cause mastitis no longer respond to current available antibiotic treatments as they have become resistant to these antibiotics. Antimicrobial resistance (AMR) is closely linked to antimicrobial use and is a major global threat to human health, with projections that it could lead to 5 million human deaths per year. From a public health perspective, AMR in dairy cattle can jeopardize human health, due to the potential spread of mastitic AMR pathogens to humans via consumption of infected dairy products, indirectly when dairy products are disposed of in the environment, or through direct contact with the animals. AMR bacteria in mastitis infections not only poses a challenge for clinical management of mastitis but poses a threat to UK, Canada and global food security. Antimicrobial residues in milk after treatment also contribute to losses from milk discarded during treatment and from withdrawal period post-treatment. Therefore, alternate, new antibiotic-free treatments are urgently needed to fight AMR in dairy cattle. Consequently, it is paramount that we intensify research to enhance our knowledge about the prevalence of AMR determinants involved in the survival and persistence of mastitis isolates. This is vital for clinical management of the disease and for the development of alternative antibiotic-free treatments. Over the past 8 years, we have developed and characterised many novel and efficacious antimicrobial peptides (AMPs). Consequently, in this project, we will evaluate the activity of these new, non-toxic AMPs, which have proven antimicrobial and antibiofilm activity against species of multi-drug resistant (MDR) mastitis bacteria. Additionally, we will assess how treatment of clinical mastitis with these AMP formulations influence the presence and spread of AMR bacteria in dairy cattle. We will also investigate what the microbial and AMR composition of 'normal'/healthy milk versus mastitis milk and evaluate how this changes post treatment with AMPs. This project is timely as mastitis has been highlighted as a key focus by UK Government. The economic, environmental, and social needs to reduce mastitis in dairy herds require effective, targeted treatments for improved management, and the output from this proposed project will facilitate UK Government goal to combat the AMR challenge.

Soil is the largest continental carbon (C) sink and contributes to the global C cycle. Two thirds of soil C is organic (Soil organic carbon, SOC). SOC results from the balance between captured atmospheric CO2 (via photosynthesis) and the incorporation of litter decomposition products, and the CO2 emissions, via the respiration of roots and heterotrophic microorganisms. SOC plays a key role in the physical, chemical, and biological properties of soils. Understanding its dynamics is a major challenge for maintaining soil fertility while participating in the storage of C. However, one third of soil C is inorganic (Soil Inorganic Carbon SIC). SIC consists of lithogenic, or petrogenic, (primary) carbonate inherited from the bedrock and pedogenic (secondary) carbonate precipitated in the soil. Because SIC pools are generally considered more stable and less impacted by human activities than SOC pools, the SIC dynamics are of less interest in the short-term. Moreover, analytical di?culties in studying SOC and SIC separately have impeded knowledge on the dynamics of SOC in carbonate soils. The C stocks of these soils, even though they cover one third of the Earth's surface, are given little consideration in the global C balance. Although interactions between SIC and SOC pools have been described in the short-term, they are poorly understood. Isotopic analyses have shown that carbonate soils emit CO2 from both C pools. There is also an inherited or neoformed origin of SIC, as organisms (bacteria, roots, fungi) have the ability to precipitate biominerals from metabolic pathways of organic matter transformation. Our project proposes the study of both SOC and SIC contents, quality and dynamics in various contexts. The main objectives are to propose innovative analytical tools and to acquire knowledge on the C balance in carbonate soils according to their use and management. Knowledge of these processes and the development of analytical methodologies speci?c to these soils will facilitate the acquisition of data distinctive of these soils. Knowledge sharing will focus on training of young scientists (MS, PhD, post-doc), exchanges between scienti?c communities (geochemists, soil scientists, agronomists) and raise awareness in soil analysis. The project is based on 3 scienti?c work packages and a work package for coordination: 1- Integrated methodology to study SOC and SIC forms We propose to develop soil analysis on C pools in carbonate soils. A diversity of carbonate soils in terms of SIC features will be characterized. Protocols to analyse SOC and SIC pools will be compared and develop. We propose to couple thermal and isotopic analyses to characterise the forms of SIC and SOC in carbonate soils in a rapid and partially automated way. 2- Processes of SOC stabilisation in carbonate soils Thermal, physical (size), chemical and morphological analysis of SOC in di?erent calcareous contexts will help to explore the relationships between soil properties and SOC. The quanti?cation of SOC in its di?erent forms would allow understanding the processes of SOC stabilisation in these speci?c soils. 3- Contributions of SIC and SOC to C ?uxes between soil and atmosphere Relationships between soil properties, SIC and SOC forms and dynamics will be studied through soil incubations and modelled. Research will mainly focus on the solid phases of SOC and SIC in a collection of soils with varying SOC and SIC contents. Speci?cally, our objectives are (i) to establish protocols to measure SIC and SOC contents and their 13C natural abundance (ii) to identify stabilized SOC pools in soils with di?erent SIC features and (iii) to approach C balance in various carbonate environments. Finally, our ambition is to develop a scienti?c community studying C cycle in carbonate soils.