Biofumigation is being increasing used as alternative control method for soil borne pathogens. This method exploits toxic compounds, specifically isothiocyanates (ITCs), which are released during the breakdown of Brassica plant tissues. To date field and glasshouse experimentation assessing the potential for using biofumigation to control agricultural pests and pathogens have produced promising results. Yet large gaps still remain in the specifics of the biofumigation process. It is hoped that further research to analyse how specific toxic compounds produced during Brassica tissue breakdown, specifically ITCs, affect different pathogens. Additionally analysis of the specific isothiocyanates and concentrations produced by Brassica spp. will allow a more pathogen targeted approach to biofumigation to be generated. The importance of assessing the biofumigation process on different scales is also understood, and therefore this study has encompassed work carried out in vitro and using glasshouse experimentation to establish a comprehensive overview of the biofumigation process. Assessing the effects different agricultural treatments have on soil microbial communities has also been recognised and therefore was also be investigated in this study. This study aimed to determine the effects isothiocyanates, produced by Brassica spp., have on three economically important soil borne fungal pathogens, Colletotrichum coccodes, Rhizoctonia solani and Helminthosporium solani. Initial assessment was carried out using in vitro bioassays, allowing assessment of the overall toxicity of each ITC. Results identified that the pathogen response was dependent on both the structure of the ITC and the concentration of ITC present. The most significant pathogen suppression was observed with R. solani when exposed with benzyl or methyl ITC and H. solani when exposed to 2-phenylethyl ITC. To gain understanding of the naturally produced ITCs Gas-Chromatography Mass-Spectrometry analysis was used to analyse specific isothiocyanates produced by a range of different Brassica spp., at different development stages. Results identified Allyl, Benzyl and 2-Phenylthyl ITC as the most commonly produced by the Brassica cultivars used within this study. Overall the Allyl was found within the highest concentrations; however the specific ITCs and concentrations produced were dependent on both the development time and cultivar. Glasshouse experimentation was also carried out to assess both the effects of pure ITCs on R. solani and C. coccodes fungal inoculum within compost and diversity changes within the soil microbial community, in response to isothiocyanate incorporation and the biofumigation process. In order to examine changes in microbial communities‟ analysis was carried out using Terminal Restriction Fragment Length Polymorphism, a DNA fingerprinting method which allows bacterial diversity shift to be traced and statistically analysed. Overall incoproation of pure ITCs did not significantly reduce black scurf or black dot disease symptoms on daughter potato tubers. Additionally after 30 days soil microbial community diversity was not greatly altered by the addition of ITCs. Therefore as it is often suggested that biofumigation is influenced by the soil activity it is thought that this may be due to the addition of Brassica tissue. The increase of organic matter into agricultural soils may influence both biological and chemical processes which may in turn aid pathogen suppression. Overall this study provides a detailed insight into establishing the specific interactions that occur during biofumigation. Results produced findings of ITCs which significantly suppressed the growth of fungal potato pathogens. Development of a novel GC-MS assay revealed previously unknown data of levels and profiles produced by a number of different Brassica plants. Additionally study was also carried out to evaluate the effects of biofumigation of soil microbial communities, which is often ignored within other studies. Overall this study aimed to gain an increased level of knowledge of such processes in order for the methods and the results presented, to be used to establish effective, pathogen targeted biofumigation systems.

<p> The goal of my dissertation is to characterize the contribution of industrial food animal production to between-farm transmission of zoonotic influenza A viruses and transmission of these viruses from industrial food animals to humans. The intention of this research is to improve the capacity of public health policies in the United States to prevent the emergence of pandemic influenza viruses.</p><p> Preventing and controlling outbreaks within animal populations and avoiding human infection with zoonotic influenza A viruses can reduce the risk of emergence of pandemic influenza viruses in human populations. Industrial food animal production, which dominates the market in the United States and much of the developed world &ndash; and increasingly, the developing world as well &ndash; has long been considered biosecure. However, emerging research indicates that these industrial systems are vulnerable to disease incursions and suggests that they may play a central role in driving the emergence of zoonotic diseases. The implications of these industrial systems for human influenza risk, particularly the emergence of novel zoonotic influenza A viruses, remains largely unaddressed in the current literature and in health policy strategies in the United States. </p><p> Chapter 1 of this dissertation outlines my research goals and provides background on my central research themes and topics. Chapter 2 documents the limits of biosecurity within industrial systems, highlighting risks to food animal workers. Chapter 3 details a cross-sectional serology study of a cohort of industrial poultry workers and community members (n=99) in the Delmarva Peninsula, a tri-state area of intense poultry production in the Mid-Atlantic region of the United States. No evidence of infection with avian influenza viruses is observed in this population.</p><p> Chapter 4 contains a quantitative modeling study to estimates risk of between-farm transmission of avian influenza viruses among industrial poultry farms. This study concluded that company affiliation was a significant source of exposure risk from vehicular transmission. Chapter 5 is a policy analysis of the limitations of current pandemic preparedness policy in the United States to adequately incorporate primary prevention. The central results of this dissertation, their significance to public health and opportunities for further research are highlighted in Chapter 6.</p>

Ammonia is the most prevalent alkaline gas in the atmosphere and plays an important role in environmental pollution through acidification and eutrophication. Livestock are the largest source of ammonia in the UK, mainly originating during storage and spreading of animal manure. The aim of this study was to validate the collection efficiency of recurved passive ammonia flux (PAF) samplers and the flux frame method to provide a robust methodology for measurement of distributed agricultural sources of ammonia outdoors. The collection efficiency of recurved PAF samplers was determined in a wind tunnel under controlled conditions of ammonia flux (0.771 - 13.49 mg NH3 m-2 s-1), and at angles of orientation to the flow direction (0, 30, 60, 70, 80, 90°). The samplers were effective up to a wind speed of 7 m s-1 and an angle of 80°, with a mean collection efficiency of 71%. The flux frame method had a mean collection efficiency of 87.4% when used with ground level point sources under controlled conditions in the Atmospheric Flow Laboratory. However, in controlled field releases, the efficiency fell to 56.4%. The flux frame method was also suitable for line sources, although assumptions must be made about the source homogeneity and plume dispersion. ADMS modelling was used to predict the collection efficiencies for the flux frame method and these agreed with measured collection efficiencies to within 37.3%. A comparison of source strengths determined using a full size flux frame and portions of the flux frame showed that a full size flux frame was unnecessary as one column of samplers produced a very similar estimate to that of the whole frame. The validated method was then used to measure ammonia emissions from free-range pigs. The amount of ammonia emitted from this source was very low and less than 0.16 g (kg of sow)-1 day-1.

Relic periglacial solifluction features cover most of Britain, particularly the Midlands and the South, causing serious and continuing earthwork and construction problems. Although the engineering significance of the presence of periglacial solifluction deposits is widely appreciated, the mechanics of emplacement of these deposits has received surprisingly little attention. The principal objective of the research has been to investigate the freeze-thaw behaviour of some clay soils in Britain which have been exposed to periglacial conditions. The behaviour was examined using a Permafrost Oedometer or Permode, based on the apparatus used by Morgenstern and Smith, (1973). Tests have been carried out on Lias Clay, Weald Clay and Oxford Clay. In each test, a specimen was placed under an applied stress and subjected to 24 hour cycles of freezing and thawing. Freezing was mainly imposed from the top of the specimen downwards. The tests were carried out undrained. The pore water pressures were found to increase as a result of cyclic freeze-thaw conditions. Greater pore water pressures were generally recorded at the top than at the base of the specimen. This was considered to be due to moisture migration towards the freezing front during freezing, and impeded filtration, (due to underlying frozen material), during thaw. The significance of the additional pore water pressures in terms of slope stability was considered. A semi-infinite slope analysis model was used primarily, but reference was made to other, similar research. The analysis found that the predicted slope angle of failure is reduced significantly by relatively low increases in pore water pressure. Greater increases in pore water pressure are gained for soils of lower residual shear strength/higher plasticity. It was determined that the generation of excess pore water pressure and corresponding decrease in residual strength have considerable implications for the stability of slopes previously exposed to periglacial conditions.

Many authors have blamed African land tenure systems for the poor agricultural production and environmental degradation in sub-Saharan Africa, and therefore the resulting hunger, environmental refugees and the lack of socio-economic progress. The aim of this investigation was to investigate the customary and statutory tenure practices in north-east Ghana and their implications for agricultural production and environmental degradation and recommend ways of improving tenurial practices. The study revealed that contrary to the mainstream view that lack of security of customary land tenure is the main cause of the poor agricultural production and environmental degradation, stakeholders’ perceptions of their security of tenure was generally high. Stakeholders’ religious background, gender, levels of education, age, occupation and community membership status were important factors influencing their perceptions and attitudes to land tenure, and land and environmental management practices. Yet poor agricultural production and environmental degradation characterised the study area. Interviewees perceived the main causes to be due to non-tenurial factors including lack of finance, poor soil fertility, inadequate and unreliable rainfall, pests and diseases, inadequate farmlands, bush burning and excessive tree cutting. It was also shown in the study that women and strangers generally had little or no power and control over land use decision-making and management under customary land tenure. These findings have negative implications for tenurial conditions, environmental and livelihood sustainability in north-east Ghana since most women are involved in food production. Results of the investigation were used to develop a participatory and holistic approach to land use and management and developed an integrated framework of customary and statutory tenure as a way forward in sustainable land management and the provision of sustainable livelihoods in north-east Ghana in particular, and sub-Saharan Africa generally. The study has contributed to an understanding of the political ecology of north-east Ghana and concludes that the emerging changes in land resource access and use have conflicts as an inevitable element of the process, which broad-based stakeholder participation provides a useful solution.

This thesis focussed on assessing smallholder groundnut farmers and traders’ access to markets through quality improvement and also, determine the socio-economic factors that influence groundnut farmers when deciding to adopt quality management techniques and the extent/or level of involvement. The following research questions were tested: whether Malawi smallholder groundnut farmers have poor or limited access to markets; whether smallholder farmers face unequal bargaining relations with traders due perhaps to lack of competition in trading channels; whether belonging to a farmer organisation provides a framework whereby the prospects of higher prices could lead to higher quality regulated by the association? Qualitative analysis was used to map out the main processes, key actors and relationships within the various groundnut value chains. Price spread method was used to assess market efficiency in price for the various groundnut market channels. Finally, a Selective Tobit model was used to assess factors that influence smallholder farmers to adopt technologies on quality management and decide the extent of adoption. The study results indicated that smallholder farmers manage to sell all their groundnuts brought to the market. This means that smallholder farmers do not really have problems accessing the markets. However, there is a limited availability of structured groundnut markets that offer premium price as an incentive for farmers to invest in quality management. Another important finding is that belonging to an organised farmer organisation enabled smallholder farmers to access better agricultural services such as research, extension and quality certified seed. However, it was not enough to persuade the farmers to venture into collective marketing. The results suggest that the provision of economic incentives such as premium prices persuaded farmers to engage in collective action and also invest in quality management. There is convergence of prices for less quality sensitive regional markets and quality sensitive EU markets. As such, exporters have no incentive to invest more in quality management targeting EU markets. Selective Tobit model results showed that farmers value most profitability-related variables such as land allocated, structured markets and prices when deciding level of involvement in quality management. The study results also indicate that groundnut market in Malawi is efficient in price as demonstrated by the Market Efficiency Index of greater than one. Gross margin analysis also indicated that, on average, groundnuts producers have good returns to labour if compared to the current national minimum wage rate of US$1.2 per day.

abstract: Haiti has witnessed high deforestation rates in recent decades, caused largely by the fuel needs of a growing population. The resulting soil loss is estimated to have contributed towards a decline in agricultural productivity of 0.5% -1.2% per year since 1997. Recent studies show the potential of biochar use through pyrolysis technology to increase crop yields and improve soil health. However, the appropriateness of this technology in the context of Haiti remains unexplored. The three objectives of this research were to identify agricultural- and fuel-use-related needs and gaps in rural Haitian communities; determine the appropriateness of biochar pyrolyzer technology, used to convert agricultural biomass into a carbon-rich charcoal; and develop an action-oriented plan for use by development organizations, communities, and governmental institutions to increase the likelihood of adoption. Data were collected using participatory rural appraisal techniques involving 30 individual interviews and three focus-group discussions in the villages of Cinquantin and La Boule in the La Coupe region of central Haiti. Topics discussed include agricultural practices and assets, fuel use and needs, technology use and adoption, and social management practices. The Sustainable Livelihoods framework was used to examine the assets of households and the livelihood strategies being employed. Individual and focus group interviews were analyzed to identify specific needs and gaps. E.M. Rogers' Diffusion of Innovations theory was used to develop potential strategies for the introduction of pyrolysis technology. Preliminary results indicate biochar pyrolysis has potential to address agricultural and fuel needs in rural Haiti. Probable early adopters of biochar technology include households that have adopted new agricultural techniques in the past, and those with livestock. Education about biochar, and a variety of pyrolysis technology options from which villagers may select, are important factors in successful adoption of biochar use. A grain mill as an example in one of the study villages provides a model of ownership and use of pyrolysis technology that may increase its likelihood of successful adoption. Additionally, women represent a group that may be well suited to control a new local biochar enterprise, potentially benefiting the community. / Dissertation/Thesis / M.S. Sustainability 2011

Phytoremediation is a green technique used to restore polluted sites through plant-initiated biochemical processes. Its effectiveness, however, depends on the successful establishment of plants in the contaminated soil. Soils that are contaminated with polycyclic aromatic hydrocarbons (PAHs), especially low molecular weight, mobile PAHs such as naphthalene pose a significant challenge to this. Plant roots growing in these soils exhibit changes to their structure, physiology and growth patterns. Tall fescue (Festuca arundinacea) roots grown in sand contaminated with either petroleum crude oil (10.8g total extractable hydrocarbons kg-1 sand dw) or naphthalene (0.8g kg-1 sand dw) exhibited a temporary inhibition in elongation with accelerated lateral growth (p<0.01), whilst also showing a deviation from the normal root orientation responses to gravity. Scanning electron micrographs (SEM) revealed that the stele in the contaminated roots was located much further away from the root epidermis, because the cortex was larger (p<0.001) due to the cells being more isodiametric in shape. Once past the initial acclimatisation period of 2.5-3.0 months, no visual differences were observed between control and treated plants, but the root ultrastructural modifications persisted. The fluorescent hydrophobic probe „Nile red‟ was applied to the epidermis of a living root to mimic and visualise the uptake of naphthalene into the root through the transpiration stream. The root sections were also stained with 0.1% (w/v) berberine hemisulphate in order to stain Casparian bands. Overlaying images obtained with the use of Texas red HYQ filter (wavelength 589-615nm) and UV illumination (wavelength 345-458nm) revealed the presence of passage cells in the endodermis and uptake of Nile red into protoxylem vessels beyond the endodermis of control roots. On the other hand, the path of Nile red was blocked at the endodermis of naphthalene- treated roots. The cell walls in the endodermis of naphthalene-treated roots were prominently thickened (p<0.001) and lacked passage cells. The treated roots also possessed a well-formed exodermis (p<0.01). The results suggest that the well-formed endodermis lacking passage cells, the well-formed exodermis as well as the increased cortex zone provided an effective barrier to the flux of hydrophobic xenobiotics towards the inner core of the roots, if previously exposed to the contaminants. The SEM images of naphthalene-treated as well as crude oil-treated roots showed partial collapse in the cortex zone, presumably due to water stress, but the treated plants withstood drought stress better than the control plants. The underlying physiological changes responsible for the adaptive responses of tall fescue to the exposure to naphthalene contamination were studied through metabolic profiling of plant roots and shoots. The results indicated synergistic interactions between sugars or sugar- like compounds and phenolic compounds may assist to create an integrated redox system and contribute to stress tolerance in naphthalene-treated tall fescue. The signal for a compound speculated to be indole acetic acid (IAA) was either subdued or absent in the tissues of naphthalene-treated tall fescue, suggesting the existence of a detoxification mechanism/ defence pathway in the treated plants. The ultra-structural and molecular modifications, resulting from PAH stress enabled tall fescue to resist tougher challenges.

Plant performance under reduced water availability has traditionally been assessed as drought resistance and more recently as water use efficiency (WUE). An extensive body of work has been established over the past 15 years where the natural variation of water use efficiency has been studied in the model species Arabidopsis thaliana (Arabidopsis). At the same time, a substantial degree of criticism has arisen with respect to the use of drought resistance and WUE as measures of plant performance, due to the lack of relatedness of these parameters to reproductive performance, i.e. yield. The work in this thesis is centered on understanding the physiological and genetic basis of water use and water productivity as alternative measures of plant performance under the context of reduced water availability. The first part of this study describes an extensive assessment of the natural variation of water use and water productivity in Arabidopsis in relation to numerous key physiological, phenological, and developmental parameters. Furthermore, this work concisely relates plasticity of key traits to historical climatic variation. A fundamental aspect of this work was the clarification that it is possible to estimate long term water use to a high degree of accuracy based on short term water use, i.e. soil drying rate, and flowering time. Flowering time was demonstrated to be the predominant driver of vegetative performance and water use, however it appeared to be genetically uncoupled from reproductive performance. This is in contrast to previous work that suggests WUE, measured as the ratio of C12 to C13 isotopes (δ13C), is positively associated with flowering time. Additionally, it was demonstrated that multiple commonly employed proxies of reproductive performance including total biomass, WUE, and flowering time, were not sufficient at predicting seed yield in Arabidopsis across multiple environments. The second part of this study involved the genetic dissection of water use and productivity related traits in Arabidopsis through a quantitative trait loci (QTL) mapping study and a genome wide association study (GWAS). QTL mapping using a recombinant inbred line (RIL) population developed from the ecotypes Col-0 and C24 revealed two key flowering time genes, FLOWERING LOCUS C (FLC) and FRIGIDA (FRI), as key regulators of water use. It was demonstrated that a combination of non-functional alleles of both FLC and FRI reduced long term water use via a shorted life cycle, which is again in contrast to previous work relating to the genetic dissection of WUE in Arabidopsis. Crucially, it was observed that reduced water use mediated in this fashion did not detrimentally impact upon reproductive performance. GWAS was employed subsequent to the QTL mapping in order to identify candidate genes underlying the variation for productivity as a unique trait and also as a factor of water use, i.e. water productivity. GWAS identified multiple promising candidate genes that potentially underlie the heritable genetic variation for flowering time, water use, and water productivity.

With increasing prevalence of Wireless Sensor Networks (WSNs) in agriculture and hydrology, there exists an opportunity for providing a technologically viable solution for the conservation of already scarce fresh water resources. In this thesis, a novel framework is proposed for enabling a proactive management of agricultural drainage and nutrient losses at farm scale where complex models are replaced by in-situ sensing, communication and low complexity predictive models suited to an autonomous operation. This is achieved through the development of the proposed Water Quality Management using Collaborative Monitoring (WQMCM) framework that combines local farm-scale WSNs through an information sharing mechanism. Under the proposed WQMCM framework, various functional modules are developed to demonstrate the overall mechanism: (1) neighbour learning and linking, (2) low-complexity predictive models for drainage dynamics, (3) low-complexity predictive model for nitrate losses, and (4) decision support model for drainage and nitrate reusability. The predictive models for drainage dynamics and nitrate losses are developed by abstracting model complexity from the traditional models (National Resource Conservation Method (NRCS) and De-Nitrification-DeComposition (DNDC) model respectively). Machine learning algorithms such as M5 decision tree, multiple linear regression, artificial neural networks, C4.5, and Naïve Bayes are used in this thesis. For the predictive models, validation is performed using 12-month long event dataset from a sub-catchment in Ireland. Overall, the following contributions are achieved: (1) framework architecture and implementation for WQMCM for a networked catchment, (2) model development for low-complexity drainage discharge dynamics and nitrate losses by reducing number of model parameters to less than 50%, (3) validation of the predictive models for drainage and nitrate losses using M5 tree algorithm and measured catchment data. Additionally modelling results are compared with existing models and further tested with using other learning algorithms, and (4) development of a decision support model, based on Naïve Bayes algorithm, for suggesting reusability of drainage and nitrate losses.