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Internal farm roadways are connectors within agricultural landscapes, which act as sub-components of the nutrient transfer continuum (NTC). On dairy farms, roadway surface runoff dissolved and particulate phosphorus (P) sources stem from a combination of cow excreta deposited at locations that impede animal flow, soil deposited from cow hooves or machinery tyres, run-on from up-gradient fields, public roadways or farmyards and incidental spill of organic/inorganic fertilizers. The present study investigates the storage and potential release of P from the underlying roadway material (i.e. composite of soil and stone aggregates) as this source component is not considered in the NTC framework or documented in the literature. Herein, farm roadway materials were sampled (to 1 cm depth) at 17 locations avoiding fresh cow excreta. Multiple location types were selected e.g. straight roadway sections, roadway junctions, before and adjacent standoff areas associated with cattle underpasses, with all locations varying in distance from the farmyard. Roadway samples were analysed for phosphorus (P) and metals (Al, B, Ca, Co, Cu, Fe, K, Mg, and Mn) content. Results showed that the soil component of roadway materials are significant P legacy sources and are in themselves a P-storage component that merits inclusion in the NTC framework. All sampled locations, when compared with fresh roadway stone aggregates or surrounding fields, had highly elevated P with plant available Morgans P > 8 mg L-1 (Index 4, ranging from 10 – 110 mg L-1). Sampling points within 100 m of the farmyard together with roadway junctions and underpasses beyond this distance had highest P concentrations. Critical source areas, where source, mobilisation and transport of P to waters coincided, formed at three locations. Possible mitigation measures are a) divert roadway runoff into fields using low-cost surface water breaks, b) disconnect cattle underpass tanks from receiving waters and c) change roadway infrastructure to improve cow flow and minimise source build-up. Future research should examine P loads in runoff from roadway sections across farm typologies and roadway material types.

Sustainable intensification of agriculture (SIA) has become an important concept to ensuring food security in the context of increasing agricultural production while minimising negative externalities in contemporary agronomic systems. In supporting this, there is a need to establish a decision-making and management system that involves the views and opinions of different stakeholders and unifies the goals of SIA amongst them. The objective of this work is to identify and describe pathways toward farm-level SIA. An explanatory network approach and fuzzy cognitive maps (FCMs) support the analysis of stakeholder views across the three pillars of sustainability: social, economic and environmental. Different stakeholder groups were asked to collectively map the pathways towards farm level SIA in a workshop exercise. The respective groups considered a common set of pre-selected factors as potential descriptors of sustainability and created unique maps by adding their own components and descriptors and identifying causal links between them. While the relative weighting of factors by each group differed, according to their perspectives and interpretation, yield, knowledge transfer, water quality, weather extremes and technology/infrastructure were scored as priority descriptors of farm-level sustainability by all groups in an aggregate analysis. Exploratory analysis of FCMs was found to provide an efficient mechanism to investigate stakeholder views on pathways towards farm-level SIA, by identifying causal relationships and interactions between factors and actors that affect its achievement. The study shows that sustainable intensification is a complex dynamic system that includes institutional structures, personal goals, stakeholder interests and socio-economic factors, and is affected by cognitive beliefs and particular knowledge within stakeholder groups. Our results show how experience, knowledge and beliefs affect the perception of farm-level SIA by various stakeholder groups, and how this knowledge is often fragmented and miscommunicated. The exercise confirmed the hypothesis that farm-level SIA has to be seen as a dynamic process in which farm performance is affected by various factors, with the complexity of the process increasing when different stakeholder interests and beliefs combine for farm management.

Dairy farms produce dairy soiled water (DSW) during the milking process, which consists of a mixture of water, cow faeces, urine, milk, detergents, and sediment. Land spreading is the most common disposal method for DSW. However, when applied at rates that exceed the nutrient demand of the herbage, or when applied under unfavourable soil and weather conditions, land application of DSW can result in pollutant loss to associate receiving water bodies (ground and surface waters). Constructed wetlands (CWs) and intermittently loaded sand filters (ISFs) have been investigated for the treatment of agricultural wastewaters, and have been shown to provide efficient and sustainable treatment of DSW. Nevertheless, the large surface area requirements for treatment, poor long term phosphorus (P) removal, and media clogging, are the main limitations of these systems. The addition of chemical coagulants to DSW, such as aluminium and ferric salts, have been found to be effective in clarifying DSW and removing organic matter (OM), suspended solids (SS), P, and pathogens. Such chemicals are already being used on Irish farms. For example they have been shown to be effective at reducing gaseous emissions during storage of slurry and DSW and indeed preventing P losses in runoff from subsequent land application of these wastes to fields. To date, a combination of a coagulation process and CWs or ISFs have not been used to treat DSW. The present research introduces a novel coagulation step before wastewater is treated by CWs or ISFs. The hypothesis of this thesis is that the addition of a coagulation process as a pre-treatment step could improve the performance of CWs and ISFs, and overcome the shortcomings of the individual capacities of these systems. In addition, this step would negate the need for CWs to expand in size as their P remediation capacity would be maintained at a high level. This is likely to increase the uptake of such systems on farms in the future. Therefore, the objective of this thesis was to investigate the combined capacities of coagulation-CWs and coagulation-ISFs and compare the results to the individual capacities of conventional CWs and ISFs. To achieve this objective, an optimum chemical coagulant, mixing time and dosage was identified in improving effluent quality of DSW. Following this, replicated pilot-scale hybrid CWs and ISFs, each employing a preliminary coagulation process using ferric chloride (FeCl3), were operated for a 43-wk period on a dairy farm (representing an entire milking season in Ireland). Conventionally designed CWs and ISFs were used as study controls. The hybrid systems performed better and were able to operate effectively at higher hydraulic loading rates than conventional CWs and ISFs. The performance of the hybrid systems exceeded that of the conventional systems, obtained removal efficiencies ≥ 99% for all measured water quality parameters (chemical oxygen demand, SS, P, nitrogen and turbidity), and complied with EU directives concerning urban wastewater treatment. The effluent quality from the conventional ISFs deteriorated over the timeframe of the study until clogging occurred, while the hybrid ISFs continued to perform effectively without any evidence of clogging or P breakthrough. Examination of the filter media in both filter types showed that conventional ISFs retained more biomass than hybrid coagulation-ISFs. Conventional ISFs lost approximately 85% of their initial infiltration capacity in the uppermost layer due to biomass build-up versus 40% loss for hybrid ISFs. Overall, hybrid coagulation-CW/ISFs are a promising technology that require a small area (75% reduction in footprint in comparison to conventional systems) and minimal maintenance, and produce excellent effluent quality. The final effluent from the hybrid system may be legally discharged to receiving waters, or recycled to wash farm yards, protecting water quality and saving water, respectively. In parallel, the sludge portion generated from the coagulation process, can be applied to land as a bio-based fertilizer without adverse impacts on the grass growth, and with the added benefit that there would be a substantially lower risk of nutrient losses from such a fertilizer to waters. This management approach could eliminate or reduce the pollution risk along surface pathways to waters, and minimise the overall net cost compared to land application of raw DSW (without treatment). Future research should focus on the life cycle and circularity assessment of these hybrid systems.

The current work has taken a holistic approach to understanding the potential for mitigation of pollution from agriculture using anaerobic digestion (AD), with a particular focus on reduction of pathogen load to the environment. AD is a natural process whereby multi-species microbial communities operate synergistically to break down complex organic matter. This process produces biogas which can be used to generate electricity and/or heat, or upgraded to biomethane and injected into the gas grid or used as transport fuel. The residue from AD is called ‘digestate’ and can be used as an organic fertiliser/soil improver. Materials that fall under the scope of the EU Animal By-product (ABP) Regulations (EU Regulation 1069/2009 and EU Regulation 142/2011) are subject to rules aimed at protecting public and animal health. These Regulations require pasteurisation of AD raw materials or digestate at 70 °C for a minimum of 60 min with a maximum particle size of 12mm. The EU legislation allows for derogation from the requirement for a pasteurisation treatment in AD plants transforming manure and non-ABP materials such as fats, oils and grease, “provided the competent authority does not consider it to present a risk for the spread of any serious transmissible diseases.” The Irish Department of Agriculture, Food and the Marine, the competent authority responsible for adherence to EU ABP legislation, established an alternative pasteurisation standard for digestate, known as the “National Transformation Parameter”, 60 °C for 96 hours. The overall aim of this work was to determine the microbial sanitisation efficacy of the National Transformation Parameter when compared with the EU standard. Within this aim, the possibility for optimising the efficacy of AD as a tool for mitigation of the environmental impacts of agriculture was examined. Finally, a holistic analysis was undertaken of the potential for microbial, nutrient and metal transmission to watercourses, soil and grass, as well as gaseous emissions from landspreading of unprocessed slurry compared with slurry co-digested in AD. Initial storage experiments demonstrated the efficacy of slurry co-digestion with fats, oils and grease as a means of reducing faecal indicator bacteria. Miniature-scale trials were validated as proxies for investigation of faecal indicator bacteria (FIB) survival and biogas production where necessary for simultaneous examination of multiple variables. On that basis, 50 mL CSTR trials were established at different ratios of co-digestion feedstock, temperatures, retention times and loading rates. Response surface analysis was applied to model and optimise process parameters for different operational conditions. The model developed identified that with a combination of low organic loading and longer retention time, digestate sanitisation sufficient to satisfy EU standards is possible in AD at temperatures of 20 or 25°C, whilst also maintaining satisfactory methane production. The Irish AD industry predominantly utilises mesophilic CSTR of slurry co-digested with food production waste. Hence, the aim of optimisation of sanitisation and biogas production under those conditions was addressed. By changing the feeding regime from daily to a three-day system, biogas yield per gram VS fed was increased by greater than 50% and coliform and E.coli numbers were reduced below the EU pasteurisation standard. An initial examination of the metagenomic datasets demonstrated the changing community dynamics, with increased abundance and diversity of key hydrolysers and methanogens, as well as some interesting shifts in bacteriophage concentrations. Landspreading of unprocessed slurry presents risks of mobilisation during rainfall events thereby contributing to pathogen, nutrient and metal incidental losses. Field trials carried out as part of this work demonstrated the reduced microbial load from application of digestate from slurry co-digestion to grassland and consequent reduced runoff compared with unprocessed slurry. Pasteurisation at two conditions further reduced microbial contamination. These results have been used by project partners in a risk analysis to demonstrate reduced risk to human and animal health from landspreading of pasteurised and unpasteurised digestate, compared with slurry. Metal and nutrient analysis of soil, grass and runoff also demonstrated reduced pollution potential from digestate compared with slurry. Finally, a comparative examination of greenhouse gas and ammonia emissions following landspreading found 72% and 50% lower methane and N2O emissions respectively from plots treated with digestate compared with slurry. NH3 emissions were not significantly different between treatments but were higher than untreated controls, while CO2 emissions were not significantly different between treatments and controls. Taken holistically, this work highlights the efficacy of AD with or without pasteurisation as a means of reducing agricultural pollution. Where the requirement for pasteurisation is a prohibiting factor for development of agriculture-based AD, this work demonstrates the potential for optimisation of sanitisation through adjustment of operational parameters. In that scenario, processing of slurry with food production waste is a multi-beneficial solution to reducing the environmental impacts of unmitigated landspreading of animal manure slurries. 2023-04-12

Intensification of agriculture in the European Union has resulted in nutrient losses from farms, which have contributed to a deterioration in water quality. As soil in drainage water ditch networks has limited capacity to attenuate nutrients leaving farms, efforts to reduce nutrient loads have been unsuccessful. Therefore, innovative solutions and experimental approaches are needed to intercept nutrients in ditches before final discharge to receiving waters. The existing ditch networks on farms may offer an opportunity for implementation of nutrient attenuation measures, by combining the natural attenuation capacity of the ditch with in-ditch engineered structures containing media capable of adsorbing nutrients. Although these structures have gained in popularity as a mitigation option, their configuration or optimal placement in the landscape has not yet been fully considered. The selection of appropriate media depends on the type of nutrient losses, the nutrient loads, media adsorption capacity and lifetime. In addition, the identification of an optimal location for the placement of in-ditch engineered structures is crucial for successful implementation as such structures are capable of only removing a proportion of nutrient loads exiting the farm, so the natural attenuation capacity of the ditch is important to further reduce the load. This thesis proposes two innovative mitigation techniques to remove both nitrogen (N) and phosphorus (P) in an agricultural drainage system: an in-ditch engineered system filled with reactive media and a natural solution which utilises soil chemistry of the ditch network for nutrient removal. In order to develop the first technique, a novel, internationally applicable decision support tool (DST) was developed to select locally sourced media for single or dual mitigation of N and P. The developed DST was validated in several case studies and it was then used to select an optimal combination of media for the removal of ammonium (NH4+) and P in water draining from an intensive dairy farm in south-east Ireland. Normally, large-scale column tests need to be conducted to develop design criteria for engineered structures, but as these are time consuming and expensive, rapid small-scale column tests (RSSCTs) were used, for the first time, to assess the media performance and longevity in simultaneous N and P removal in comparison with large-scale columns. The adsorption capacity and lifetime of the selected media in large- and small-scale column studies were consistent and the generated data using RSSCTs were successfully used to model P and N removals in the large-scale filters. This indicated that RSSCTs may be used to accurately and quickly develop design criteria for in-ditch engineered structures. In the second technique, the natural P remediation capacity of the ditch network of the study site was investigated with a view to identifying the optimum location for the placement of an engineered structure and to examine the capacity of a ditch in retaining or mobilising P. Experimental analyses indicated that the ideal location for installation of an in-ditch structure was at the point where a sharp increase in nutrient concentration was observed, which was due to discharges from the farm yard. The results also showed that P inputs into the drainage network accumulated in the sediments and bankside over time. This not only contributed to degradation of water quality leaving this farm, but the stored nutrients in the ditch network, as a result of decades of application, had also changed the chemistry of sediments to act as a secondary source of P, adding to the already polluted water. Arising from the findings of this thesis, in order to limit nutrient losses from intensive farms into drainage waters, implementation of an enhanced remediation technique is essential where natural attenuation is insufficient to eliminate pollution. An efficient mitigation measure starts with characterisation of the type of nutrient losses and then the development of appropriate in-ditch engineered structures filled with media to remove the identified nutrients. However, cognisance must also be taken of potential pollution swapping as a result of using the media, appropriate structure dimension and optimal location, and the nutrient remediation or immobilisation capacity of the ditches. This thesis provides a design framework that will contribute to sustainable, environmentally friendly farm management. 2024-01-30

Thousands of human diseases could be treated by selectively controlling the expression of specific proteins in vivo. A new series of alkenyl amino alcohol (AAA) ionizable lipid nanoparticles (LNPs) capable of delivering human mRNA with unprecedented levels of in vivo efficacy is demonstrated. This study highlights the importance of utilizing synthesis tools in tandem with biological inspiration to understand and improve nucleic acid delivery in vivo., National Science Foundation (U.S.). Graduate Research Fellowship Program, Shire Pharmaceuticals, Wellcome Trust-MIT Postdoctoral Fellowship

A photocurable thiol-ene network polymer, poly(limonene thioether) (PLT32o), is synthesized, characterized, fabricated into tissue engineering scaffolds, and demonstrated in vitro and in vivo. Micromolded PLT32o grids exhibit compliant, elastomeric mechanical behavior similar to grids made of poly(glycerol sebacate) (PGS), an established biomaterial. Multilayered PL32o scaffolds with regular, geometrically defined pore architectures support heart cell seeding and culture in a manner similar to multilayered PGS scaffolds. Subcutaneous implantation of multilayered PLT32o scaffolds with cultured heart cells provides long-term 3D structural support and retains the exogenous cells, whereas PGS scaffolds lose both their structural integrity and the exogenous cells over 31 d in vivo. PLT32o membrane implants retain their dry mass, whereas PGS implants lose 70 percent of their dry mass by day 31. Macrophages are initially recruited to PLT32o and PGS membrane implants but are no longer present by day 31. Facile synthesis and processing in combination with the capability to support heart cells in vitro and in vivo suggest that PLT32o can offer advantages for tissue engineering applications where prolonged in vivo maintenance of 3D structural integrity and elastomeric mechanical behavior are required., United States. National Institutes of Health (R01-HL107503)