Microbial cycling at the farm - A systems approach to assess risks and opportunities.

Abstract This thesis offers comprehensive characterisation of the farm microbe cycle. It tests the overall hypothesis that targeted stakeholder interventions may mitigate the generation and proliferation of microbial hazards on-farm and subsequently to the wider environment. Grazed livestock production is the leading UK land use, a source of high quality human nutrition, a key component of the landscape and crucial environmental custodian. At its simplest it involves livestock rearing/producing upon their pasture food source, in landscapes not primarily suited to arable farming. This interaction between production animals, soil, forage and the wider environment (via water transport) poses unique challenges in managing disease and antimicrobial resistance (AMR) risk. Current controls focus upon veterinary interventions at animal scale and the resulting microbial hazard in water outflows external to farms. This research identifies and defines specific increased disease potential and AMR hotspots within soil and grass at pasture on the North Wyke Farm Platform, a unique hydrologically isolated farm-system research facility. Microbiological risk was investigated alongside complementary soil chemistry and forage quality parameters. Field microbial hazard hotspots resulted through increased livestock interaction at locations due to traditional grazing management practices which do not take account of these risks. This increased animal activity resulted in higher faecal deposition rates, intensity of pathogen accumulation and transfer of AMR. The influence on bacterial population of these hotspots was greatest at 10 m proximal to location and did not extend beyond 20 m. Field hotspots role in subsequent hydrologic transfer was studied, with increased disease and AMR risk predicted by water outflow rate and hydrograph slope. Outflow was driven by precipitation events and field hotspots were disproportionate microbial hazard sources at a field catchment scale. The negative impact of aerobic exposure upon silage nutritional and hygienic quality was found independently of soil contamination. The external depth of 0-30 cm in silage bales was found to present an increased Escherichia coli concentration and AMR prevalence. This increased microbial risk resulted through vulnerability to air ingress during silage storage due to sub-optimal production techniques. The impact on silage nutrition and health risks of prolonged feeding periods, extended aerobic exposure, was studied over 32 days. Correlation between increased Listeria monocytogenes pathogen concentration, decreased silage nutritional quality and increased temperature indicative of silage aerobic spoilage was found. The conclusion of this multidisciplinary research found key temporal-spatial points exist within the farm microbial cycle where relatively simple stakeholder interventions, such as optimising pasture utilisation during grazing or ensuring aerobic exposure of silage is minimised, can generate mutual benefits to system productivity as well as reducing potential disease and AMR risk.