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

Getting the most out of a post-column EELS spectrometer on a TEM/STEM by optimising the optical coupling

Ray tracing is used to find improved set-ups of the projector system of a JEOL ARM 200CF TEM/STEM for use in coupling it to a Gatan 965 Quantum ER EELS system and to explain their performance. The system has a probe aberration corrector but no image corrector. With the latter, the problem would be more challenging. The agreement between the calculated performance and that found experimentally is excellent. At 200kV and using the 2.5mm Quantum entrance aperture, the energy range over which the collection angle changes by a maximum of 5% from that at zero loss has been increased from 1.2keV to 4.7keV. At lower accelerating voltages, these energy ranges are lower e.g. at 80kV they are 0.5keV and 2.0keV respectively. The key factors giving the improvement are an increase in the energy-loss at which the projector cross-over goes to infinity and a reduction of the combination aberrations that occur in a lens stack. As well as improving the energy-loss range, the new set-ups reduce spectrum artefacts and minimise the motion of the diffraction pattern at low STEM magnification for electrons that have lost energy. Even if making the pivot points conjugate with the film plane gives no motion for zero-loss electrons, there will be motion for those electrons that have lost energy, leading to a false sense of security when performing spectrum imaging at low magnifications. De-scanning of the probe after the objective lens is a better way of dealing with this problem

Porosity Variations Between Fine Grained Rims and Matrix in a CM Chondrite by 3D Serial Sectioning

No abstract available

Engineering magnetic domain-wall structure in permalloy nanowires

Using Lorentz transmission electron microscopy we investigate the behavior of domain walls pinned at non-topographic defects in Cr(3 nm)/Permalloy(10 nm)/Cr(5 nm) nanowires of width 500 nm. The pinning sites consist of linear defects where magnetic properties are modified by a Ga ion probe with diameter ~ 10 nm using a focused ion beam microscope. We study the detailed change of the modified region (which is on the scale of the focused ion spot) using electron energy loss spectroscopy and differential phase contrast imaging on an aberration (Cs) corrected scanning transmission electron microscope. The signal variation observed indicates that the region modified by the irradiation corresponds to ~ 40-50 nm despite the ion probe size of only 10 nm. Employing the Fresnel mode of Lorentz transmission electron microscopy, we show that it is possible to control the domain wall structure and its depinning strength not only via the irradiation dose but also the line orientation.Comment: Accepted for publication in Physical Review Applie

On the production of plasma fibronolytic activity within veins

Abstract Not Provided

Towards climate-smart dairy development

Bill & Melinda Gates Foundatio

Application of monoclonal antibodies in quantifying fungal growth dynamics during aerobic spoilage of silage

Proliferation of filamentous fungi following ingress of oxygen to silage is an important cause of dry matter losses, resulting in significant waste. In addition, the production of mycotoxins by some filamentous fungi pose a risk to animal health through mycotoxicosis. Quantitative assessment of fungal growth in silage, through measurement of ergosterol content, colony forming units or temperature increase are limiting in representing fungal growth dynamics during aerobic spoilage due to being deficient in either representing fungal biomass or being able to identify specific genera. Here, we conducted a controlled environment aerobic exposure experiment to test the efficacy of a monoclonal antibody-based enzyme linked immunosorbent assay (ELISA) to detect the proliferation of fungal biomass in six silage samples. We compared this to temperature which has been traditionally deployed in such experiments and on-farm to detect aerobic deterioration. In addition, we quantified ergosterol, a second marker of fungal biomass. At 8 d post aerobic exposure, the ergosterol and ELISA methods indicated an increase in fungal biomass in one of the samples with a temperature increase observed after 16 d. A comparison of the methods with Pearson’s correlation coefficient showed a positive association between temperature and ergosterol and both markers of fungal biomass. This work indicates that the technology has potential to be used as an indicator of microbial degradation in preserved forage. Consequently, if developed as an on farm technique this could inform forage management decisions made by farmers, with the goal of decreasing dry matter losses, improving resource and nutrient efficiency and reducing risks to animal health