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Epigenetics is concerned with information in the genome in addition to that contained in the DNA base sequence. It comprises several mechanisms that involve chemical modification to the genome with functional consequences. It is emerging as a key mechanism through which the environment can directly influence the genome in ways that may be short term or may persist over decades, or even more than one lifetime, with significant consequences for biological function and health. Epigenetic regulation is important in species that contribute to the human food chain. An increasing number of reports cover the epigenetic changes following exposure to stress, toxicants and infectious disease, procedures such as artificial reproduction and cloning, both in the animals directly exposed and the offspring produced. These phenomena have been studied in sheep, cattle, and pigs and aquatic species, such as salmon and sea fish.

Such studies point to the epigenome as a record of a wide range of environmental exposures, physiological states, and reproductive and dietary histories relevant to multiple species that can be used to track provenance and many other aspects of the food chain. The task is to identify the genomic locations where the signals of interest reside, the conditions under which they can be used, and to use this information to develop reliable, precise, accurate, rapid, and low-cost, tests.

Stable-isotope ratios and elemental composition have also been used extensively to establish provenance in a wide range of foods including, shellfish, salmon, meat, sea fish, and milk and in regulatory systems designed to identify foods with Protected Designation of Origin. We have developed stable isotope natural abundance analytical techniques to trace food origin, provenance, and the flows of nutrients through the whole food system - from primary production and processed food to individual consumption - to explore the potential value of a Food Systems approach. The next required step relates to the sub-fractionation of organics (primarily the various saturated, mono- and poly-unsaturated fatty acids), their analysis for both H2 and C13 isotopes, and the interpretation based on knowledge of metabolic transformations.

Farm animals are a major source of key zoonotic pathogens of humans, including those causing enteric disease like Campylobacter spp., Salmonella spp., enterotoxigenic Escherichia coli and Clostridioides difficile. There are around 2.4 million cases of foodborne pathogen infections annually in Scotland, with a financial burden of £9 billion. Reducing the carriage of zoonotic pathogens within the gastrointestinal tract of farm animals has clear potential to reduce the incidence of human foodborne disease. Importantly, many bacteria (both pathogenic and those commensal bacteria inhabiting the gastrointestinal tract) carry antimicrobial resistance genes, often located on mobile DNA. The transfer of AMR genes between unrelated bacteria contributes both to the environmental spread of AMR and to the evolution of multidrug resistance (MDR) pathogens.

Given the rise of MDR pathogens, and the need to reduce antimicrobial use, alternative approaches are required to reduce pathogen carriage in animals, and subsequent transmission to humans. One of the most potent defences animals have against invading pathogens is their indigenous microbiome. This dense community of beneficial microbes provides a robust defence against incoming pathogens by outcompeting or killing them, thereby reducing their colonisation, disease-causing activity, and onward transmission. This has led to increasing interest in developing gut bacteria as “Live Biotherapeutics” and their associated bioactive products, as alternatives to antibiotics.

In short, it is paramount to further understand the role of zoonotic pathogens in the dual crises of foodborne pathogens and antibiotic resistance and to identify novel avenues for interventions to reduce the incidence of foodborne disease derived from pathogens and AMR transmission from the environment.

Scotland’s future landscape will look very different having to accommodate increased urban spread, larger areas of afforestation and peatland restoration. Simultaneously, there is an immediate necessity to produce our food in the most efficient and environmentally friendly way possible, but mindful of restoring and enhancing important habitats for biodiversity. 

Mainstream agriculture will have to quickly adapt to incorporate novel crops with the potential to contribute to Scotland’s emission targets. We must also identify opportunities for nature-based solutions as they could be pivotal in mitigating and adapting to climate change whilst restoring nature. Within this, there is a role for underutilised semi-natural and urban land to contribute best practices for the provision of Scotland’s nutrition, while protecting our natural capital.

Delivering a sustainable food system requires ambition to think beyond domestic agriculture, more widely than from farm to fork. While contributing to the economy, people’s livelihoods, and the health of the nation, it must also contribute to the protection of Scotland’s natural habitats. Wild plants are naturally resilient to pests and climate fluctuation, their ability to grow on marginal lands necessitates a need to thrive in poorer soil, without additional water or energy requirements. Their productivity does not compare to domesticated crops developed to depend on high nutrient and pesticide demands. However, their role to support the food supply chain should be revisited. Furthermore, many species grow within much-needed wildlife habitats, an important example being forests, which will be an increasing feature of Scotland’s Landscape.

Cultivation of wild plants is achievable across much of Scotland’s lands, particularly semi-natural lands, but also underutilised urban and coastal areas. It is amendable to scale providing opportunities from small independent producers to commercial scale on land not currently suitable for mainstream domestic agriculture. The wide range of species presents opportunities for unique locations, supporting a wide range of both rural and urban communities. Incorporation of wild plants into the food supply would not only supplement nutritional requirements but would help relieve part of the demand placed on a limited variety of crops to supply nutrition, which is undesirable from both a food security and biodiversity perspective.

In Scotland, climate change is expected to increase both the average temperature and the variability in precipitation patterns. These changes will increase the frequency of both drought and waterlogging events, with disproportionate effects on susceptible crops. Changes in soil water availability will impact and interact with nutrient availabilities; reductions in nutrient inputs to minimise agricultural greenhouse gas emissions will require crops that can cope with the reduced availability of key nutrients. In addition, the changes in cloud cover bought about by changing weather patterns will impact light quality which will have a profound effect on crop quality, particularly berries. Many of these stresses have been studied in isolation, but rarely have they been considered in an integrated way.

Increasing temperatures in Scotland are likely to alleviate the limiting impact of minimum temperature for growth for many crops and when combined with elevated carbon dioxide in the atmosphere, may create an opportunity to enhance the sustainability of production. However, this will only be possible if genotypes and cropping systems can cope with the allied abiotic stresses and nutrient limitations. While agricultural intensification has successfully delivered food and fuel, it has simplified agricultural landscapes, reducing biodiversity, depleting natural resources, and threatening ecosystem services. This loss of diversity might also reduce resilience to abiotic stress, creating uncertainty about the effects of changing climate on agricultural production and environmental degradation.

There are still major gaps in our knowledge about how crops respond to environmental stress scenarios. Perennial fruit crops are grown in significant quantities in Scotland and beyond and have strategic importance because of their high value, health-related attributes, and their potential environmental benefits from being long-lived crops. It is becoming increasingly difficult for growers to schedule varieties for optimum harvest with predictable yield. We need to understand the genetic, epigenetic, and environmental drivers controlling key developmental traits that impact yield.

With a value of around £14 billion each year, the food and drink industry in Scotland is a significant contributor to the economy. This significant capacity has underpinned Scotland’s reputation as a land of high-quality, healthy food and drink. All of this has helped formulate Scotland’s Food and Drink Ambition 2030 aims to double the value of the food and drink sector by 2030 to £30 billion. However, the increasing problems of climate change, in terms of long-term basic environmental change and increased weather extremes, are making production increasingly challenging.

The drive to net zero recently has been accelerated by the update to the Scottish climate change plan with the associated potential to transform the agricultural and food production system. At the same time, it is well recognised that greenhouse gas emissions from agriculture and related land use accounted for 24% of the total emissions in 2017, down 29% from the baseline levels of 1990.

Major changes to farmer behaviour are needed to achieve the Scottish Government’s climate change targets whilst developing a resilient, productive agricultural sector following the UK’s departure from the European Union. Improving agricultural practices will be critical for ensuring sustainable and resource-efficient food production, supporting rural community resilience and economic development, addressing the biodiversity and nature crises, facilitating green recovery, and tackling the global climate emergency.

Scotland faces a significant societal challenge in increasing the production and use of fruit and vegetables as part of a healthy and affordable diet accessible to all. It is accompanied by the technical challenge of producing enough fruit and vegetables sustainably, and the economic challenges in creating innovative and profitable value supply chains.

There is growing recognition for increased domestic fruit and vegetable production, including the development of national food strategies for each of the devolved nations. While the need for a national food strategy was recognised before the Covid-19 pandemic there has been a greater focus on re-shaping policy decisions on local food production systems, especially around resilience, and nutrition.

Other key drivers for increasing fruit and vegetable production include:

• Addressing food production’s contribution to climate change through the reduction of greenhouse gas emissions
• Enhancing food security at different scales and improve diets
• Creating secure and meaningful jobs and incomes for those working in the food supply chain.

The latter driver includes production (tackling value chain, local food systems and food justice); and the need to ensure access to markets for increased domestic production.

Achieving increased fruit and vegetable use and production for secure supply and healthy diets requires the uptake of social and technical innovations and stakeholder engagement across the supply chain, coupled with policy interventions to facilitate and support innovations and behaviour change from farm to fork. Addressing these holistic challenges and drivers requires a systems-led approach engaging all actors along the food supply chain, enabling contributions from scholars, food scientists, policymakers, civil society activists and environmentalists.

Farm animals are a major source of key zoonotic pathogens of humans, including enteric disease-causing Campylobacter spp., Salmonella spp., enterotoxigenic Escherichia coli and Clostridioides difficile. There are around 2.4 million cases of foodborne pathogen infections annually in Scotland, with a financial burden of £9 billion. Importantly, many gut bacteria carry antimicrobial resistance genes (ARG), some of which are located on mobile genetic elements with the potential to transfer to other bacteria (commensal or pathogenic). It is predicted that by 2050, deaths caused by antimicrobial resistance (AMR) will exceed those caused by cancer and diabetes. Reducing the carriage of zoonotic pathogens within the gastrointestinal tract of farm animals has clear potential to reduce the incidence of human foodborne disease and the spread of AMR - both of which are real health crises.  

Despite a significant body of research globally on AMR in the environment, there are still many unknowns about transmission from the environment to humans. We need to improve our understanding of the routes of transmission of resistance including the impact of the environment and food. There is a lack of understanding of how differences in farming practices can drive AMR and pathogen transmission combined with a paucity of data quantifying antimicrobial gene load onto food crops. There are also challenges around identifying increased risk to farmers due to their proximity to antimicrobials and animals. There is also a limited understanding of how farmers perceive the link between antimicrobial use and AMR, and how this may influence behaviours. Lastly, there is a lack of a unifying model to predict future scenarios of hazards to food.

The interactions between livestock productivity, climate change and biodiversity are multi-factorial. Livestock certainly contributes to greenhouse gas (GHG) emissions and uses a significant proportion of available land, but they are also an integral part of the solution to both the climate change and biodiversity crises. Improving livestock health is a key priority for important stakeholder groups. The control of endemic disease has frequently been shown to correlate with improved livestock productivity, in terms of improving reproductive success, optimising growth rates, and reducing waste and losses.

Helminth parasites (worms and fluke) are a major constraint on efficient livestock production worldwide. They are directly affected by changing climatic conditions and farm management practices and contribute to livestock’s carbon footprint through reduced biological efficiency and increased emissions. Helminth parasites influence many factors that directly affect methane emissions, including feed conversion efficiency and nutrient utilisation. Effective worm control in sheep has been shown to lead to a 10-33% reduction in GHG emissions intensity, whereas, in abattoir studies, liver fluke has been shown to increase emissions from beef cattle by a small but statistically significant 2%, which is likely an underestimate.

The benefits of ‘farming with nature’ have been advocated to help achieve climate change targets and redress biodiversity loss on farmland. While initiatives such as wetland creation, woodland expansion and peatland restoration help in this regard, they require livestock grazing to function optimally, bringing with them potential risks to animal health. In addition, improved pasture management strategies may help to increase grass production, improve livestock productivity, reduce disease incidence, and promote sustainability on pasture. When considering all these options, we need further evidence on how to achieve a balance between improving biodiversity, reducing climate impact, sustainable intensification and food security whilst maintaining a healthy and vibrant rural economy.

Helminth parasites (worms and fluke) are a major constraint on efficient and sustainable livestock production in Scotland, and beyond. Parasitic gastroenteritis as well as fluke and anthelmintic resistance featured prominently in a list of priority diseases and syndromes identified through a Ruminant Health and Welfare Group consultation with 600 UK stakeholders.

Most farmers attempt to control helminth infections in their stock by the routine administration of chemical (anthelmintic) treatments. However, this is not sustainable for several reasons, including the development and spread of anthelmintic resistance, rendering treatments ineffective. There is also increasing concern about the fate of such chemicals (wormers and flukicides) in the environment, when released in the dung and or urine of treated animals. Most, if not all, compounds used to treat or control pests and parasites have the potential to negatively impact important invertebrates, such as dung beetles, flies, and aquatic fauna. This can occur when the actives or their metabolites are excreted in the faeces and or urine of treated animals, or leach into the environment because of poor storage, application, or disposal. These factors have highlighted the need to integrate veterinary medicines with alternative control approaches, such as rotational or heather grazing, to reduce dependence on anthelmintic products and minimising environmental impacts.

The essential role that dungs beetles play in the breakdown and integration of faecal matter into the soil is well established. Recently, there has been some interest in the role of the phoretic mites carried by dung beetles; as these have been shown to be extremely effective in reducing the incidence of nuisance horn flies in Australia and the USA, by directly ingesting fly larvae in faecal pats. There is, however, little information on their potential role in reducing the number of helminth eggs and larvae and subsequent pasture contamination under Scottish and UK farming conditions.

Feeding on plants rich in plant secondary metabolites is an active area of research and can be included in sustainable parasite control strategies, to minimise the environmental impact of parasitic disease control. There are potential production and sustainability benefits from using these novel alternative approaches, as a healthy pasture invertebrate community is important for the structure and function of soils and grasslands. For example, soil invertebrates contribute to improving soil microbial composition and health, nutrient recycling, aerating soils and improving soil and plant environments as well as providing food sources for birds and mammals.  Very little is however known about the impacts of these alternative approaches on areas like parasite epidemiology, parasite longevity and life history traits or the interactions between host and environment.

There are significant gaps in our knowledge regarding the epidemiology and transmission of two foodborne pathogens: Campylobacter spp. and Toxoplasma gondii. These pathogens are some of the most important foodborne pathogens in Europe in terms of disease burden. Despite this, there remain gaps in our understanding, and have been identified as priorities for future research by food safety authorities:

• How certain animal reservoirs contribute to the overall burden of disease
• Information relating to the genetic diversity of strains circulating in livestock populations
• The role of the environment in their transmission

Campylobacter is a versatile foodborne pathogen with the ability to evolve rapidly. Foodborne Campylobacter spp., which includes Campylobacter jejuni and Campylobacter coli, colonise the gut of a wide range of animal species and while some genotypes are associated with specific hosts, others have evolved to become more generalistic. While the major source of campylobacteriosis in Scotland is raw or undercooked poultry, studies have also highlighted livestock as an important reservoir. Furthermore, Campylobacter spp. may also play a role as a vehicle for antimicrobial resistance genes (ARGs) through the food supply chain. However, the role of antimicrobial selective pressure in the emergence of Campylobacter resistance in livestock is not well understood.

Toxoplasma gondii is a zoonotic parasite of global importance and can infect all warm-blooded animals, including humans. One of the most important transmission routes for people is through the consumption of undercooked meat from infected animals. Indeed, foodborne transmission is thought to be attributable to up to 50% of cases of toxoplasmosis. Despite this, there are still significant knowledge gaps surrounding the sources and epidemiology of foodborne toxoplasmosis. In particular, the role of livestock in transmission as well as the genetic diversity of strains circulating in food animals and the environment. Both the European Food Safety Authority and the UK Food Standards Agency have highlighted the urgent requirement for further studies to address these knowledge gaps.