Pesticides are used worldwide and exhibit a plethora of different modes of action against a wide spectrum of organisms. Therefore, before they can be marketed they have to be tested against certain standardised regulations. These include the Food and Environment Protection Act 1985 (FEPA), the Control of Pesticides Regulations 1986 (COPR), and more recently the European Council Directive 1991 91/414 and the Plant Protection Products Regulations 1991 (PPPR). However, the current tests used to determine pesticide impacts on microorganisms as detailed by the OECD focus on only broadscale analytical methods that may mask more subtle effects that may still be ecologically significant. Therefore, this project aimed to determine the effects of a widely-used model pesticide, azoxystrobin on both target and non-target microbial communities across different trophic levels. The techniques used to perform this included broad- (soil microbial biomass and soil dehydrogenase activity) and fine-scale (T-RFLP, cloning/sequencing, and qPCR) analytical methods. The results of these analyses showed that the application of azoxystrobin had a significant, concentration-dependent impact on soil dehydrogenase activity whilst biomass was unaffected. The molecular analyses showed that azoxystrobin significantly impacted fungal community structure, diversity and gene copy number. Additionally, pesticide application significantly altered nematode community structure and general eukaryotic diversity. Soil and liquid culture enrichments showed that azoxystrobin degradation can be enhanced following repeated applications and enabled the isolation of two degrader organisms with sequence homologies to a Cupriavidus sp. and a Rhodanobacter sp. Further work showed that sequential enrichments with azoxystrobin also conferred cross-enhanced degradative abilities for three other strobilurin fungicides: pyraclostrobin, kresoxim methyl and trifloxystrobin. The work performed in this thesis served to illustrate how the current OECD test procedures may benefit from the incorporation of finer-scale molecular methods into its tests, as well as how difficult the task can be to produce compounds that persist in the environment long enough to perform their required function, but do not have significant deleterious impacts on non-target organisms when present.

Upland heather moorland is often subjected to wildfires, particularly in drought years, which destroy all vegetation, seed bank and surface peat. Post-fire management of liming, fertilising and seeding with grass species and Calluna vulgaris (ling heather), in addition to natural regeneration, often fails to fully re-vegetate the bare burnt peat, leading to erosion and degraded sites. Here, two sites were under investigation: Darwen Moor that suffered a severe fire in 1995, and a moor overlooking Stalybridge, Tameside, burnt in 1980. Both burnt areas received similar post-fire management. After a full vegetation survey of Darwen Moor, with data analysed using Two-way species indicator analysis (Twinspan), permanent quadrats were established within representative areas of identified vegetation sub-communities. Twice yearly surveys (spring and autumn) were undertaken within areas defined by these quadrats. Results of vegetation survey showed regeneration of C. vulgaris on burnt sections of Darwen moor had increased from 18% to 38%, (2000-2005), and had become the dominant species, with only 3% of the burnt moor remaining unvegetated. Vegetation succession was not advancing unidirectionally with increasing variation between samples of the same sub-community. This was in contrast to the Stalybridge site that remained unvegetated (77%) twenty-five years after wildfire. Survey data were collected using both digital photography and point quadrat survey. Pre-monitoring investigation showed no significant difference between data collected by these techniques. Experiments were undertaken to assess aspects of C. vulgaris seed dispersal and viability. Seed-trap experiments using transplanted C. vulgaris suggested that few seeds are being dispersed into degraded sites, whilst datalogger evidence showed poor germination opportunity for C. vulgaris seeds on moorland post-wildfire. C. vulgaris seeds were shown to germinate and grow on moorland peat in controlled conditions, although they rapidly became unviable when exposed to drought conditions. Use of a polyacrylamide gel to enhance environmental conditions for sown grass species showed early increased ground cover but failed to show any significant increase after 14 months. Accepted upland moorland revegetation management post-wildfire is reviewed and from experimental results, additional management techniques are suggested.

Firstly, increasing true stem RN capacity as means to increase the maximum rate of N uptake (kg N per day) during stem elongation may be feasible through optimisation of traits such as stem length and wall thickness. Secondly, modifying true stem RN unloading by increasing storage N in relation to accumulation N may offer a realistic mechanism for improving crop BPE and thus UTE. Such an increase in true stem NRE might be achieved through manipulation of key N assimilation enzymes. Thirdly, it may be possible to select for ‘stay-green’ traits associated with lower leaf lamina NRE and lower grain N% to boost UTE. However, in each case further phenotyping studies are required to characterise genetic variability, identify the most appropriate germplasm resources for genetic studies, and to identify appropriate genetic sources of variation for breeding.

Soil is one of the most complex ecosystems in the environment and changes to microbial diversity are thought to affect the physical structure (and vice versa). A fundamental question addressed in this research, is how microbial communities influence the functioning of soil, particularly with respect to the development and maintenance of a soil’s physical structure. Using micro- and macrocosms of sieved (and therefore structureless) soil, the effects of time, soil texture, manipulated background microbial diversity, and Plantago lanceolata (± mycorrhizal fungi) on the development of soil structure were determined. Background microbial diversity was manipulated using the dilution technique to give a low (101) dilution or a high (106) dilution of the original soil. This resulted in greater bacterial diversity in the lower (101) dilution than in the higher (106) dilution when in the presence of mycorrhizal plants. However, background diversity was the same irrespective of dilution in soils with non-mycorrhizal plants (and reversed within the bare soil). Micro- and macrocosms were continually assessed during controlled incubation periods ranging from 7 weeks to 15 months. Of the soil textures analysed (clay loam, loamy sand and sandy loam), loamy sand displayed the highest overall porosity as well as a noteworthy development in porosity throughout the incubation period. Mycorrhizal and nonmycorrhizal plants increased the speed of soil structural development by 5 months relative to unplanted soils. Although mycorrhizal fungi stunted root growth initially, aggregates within mycorrhizal planted treatments were smaller but nonetheless more stable than those in bare soil. Increasing mycorrhizal fungal species richness enhanced root and shoot biomass and reduced aggregate size and total porosity. There was a positive relationship between total porosity and numbers of culturable bacteria and fungi. In soils containing a lower microbial diversity, an increase in porosity, mean pore size, aggregate size and pore perimeter was observed. Results obtained were dependent on incubation conditions, planting regime and mycorrhizal status. Therefore, the effects of reducing microbial species diversity on soil structure parameters are idiosyncratic, with the presence of plant roots acting as a key factor.

A key aspect of the condition of soil as a medium for growing plants is the soil physical environment under which germination, growth and establishment occur. Crucially this affects factors such as water content, oxygen availability and soil strength. The dynamics of soil physical properties, and in particular soil structure, of a range of soils and how they relate to plant establishment are considered in this thesis. By engineering a variety of seedbeds and contrasting soil structures using different cultivation techniques, from intensive (plough) to reduced (disc) strategies, significant differences in the physical properties of the soils in terms of volumetric water content, soil strength and bulk density and interactions with plant establishment were identified. A model for Soil Quality of Establishment (SQE) was developed to predict plant establishment based upon soil bulk density and cultivation practices which significantly accounted for c. 50% of the variation occurring across contrasting soil types and environmental conditions. It was hypothesized from this that the precise porous architecture (i.e. soil structure) plays a crucial role in plant establishment given soil bulk density was a significant factor in the SQE model. Utilizing X-ray Computed Tomography (CT) both at a macro (c.300μm) and meso (c.65μm) scale soil structure (in terms of: porosity, pore area and perimeter, elongation, nearest neighbour distance, ECD and pore distribution) were determined in a quantitative manner. Results showed significant decreases in plant populations with associated increases in the soil porosity, with strong links to the pore size, roughness and spatial distribution (accounting for soil-seed contact, water storage / flow and ease of plant / root movement within the soil). Preferred porosity conditions for establishment and yield occurred between 12 - 20 % porosity (at the meso scale). SQE prediction was significantly improved with the addition of structural properties accounting for c. 70 % variation in crop establishment across soil texture and seasonal variation. The further 30 % variation in crop establishment may be explained by unforeseen circumstances such as disease and weather but equally this may also be related to crop genetics, soil chemistry and or the biological activities within the soil.

The aim of this work was to investigate the effect of soil properties on soil iodine dynamics and uptake to plants. Soil and vegetation samples were collected from across eastern Northern Ireland (NI) to form the basis of most experimental work; samples from the Rothamsted Park Grass archive were used to investigate the role of changing soil chemistry through time and due to selected fertiliser applications; and iodine dynamics in humic acid (HA) were studied to improve understanding of the role of organic matter in soils. Input of iodine in rainfall was considered in the context of samples from both locations, and the additional influences of coastal proximity, soil type and underlying geology were reviewed for the NI samples. Total iodine analysis was carried out using extraction with TMAH and quantification by ICP-MS; aqueous iodine speciation was determined using HPLC and SEC coupled with ICP-MS. The most important iodine inputs to both soil and vegetation were found to be directly from the sea in coastally-exposed locations, and from rainfall in other cases. Soil organic matter (measured as soil organic carbon, SOC) was determined to be involved in both retaining a portion of recalcitrant iodine in soil and HA, and in promoting sorption of both iodide and iodate in highly organic soils. Metal oxides (Fe, Mn and Al) were found to be important in rapid sorption of iodate to soils with SOC ≤ 38 %, and there was an indication that they may be involved in promoting the reaction of iodide with organic matter. Replenishment of a transient phyto-available pool was essential for provision of iodine to vegetation. The availability of recently added iodine (as 129IO3-) in the pot experiment was controlled by its sorption onto the solid phase, and near-constant input from irrigation water was the major source of vegetation iodine in most cases. Rainfall was shown to be important in controlling vegetation iodine concentrations in field situations. In soils collected from very coastally-exposed locations, the soil iodine concentration was extremely high and therefore a greater proportion of labile native iodine was available for uptake; irrigation sources were much less important. This work improves understanding of soil iodine dynamics and the important factors controlling iodine speciation and availability to plants. Results can be used to inform practices regarding provision of iodine to crops for both humans and grazing animals.

Conservation tillage is generally considered as an important component of sustainable agriculture. The benefits of conservation tillage have been presented as reducing runoff, enhancing water retention and preventing soil erosion. There is also general agreement that it can be used to conserve and enhance soil organic carbon levels to some extent. However, its applicability in mitigating climate change has been extensively debated, especially when the whole profile of carbon in soil is considered along with a reported risk of enhanced N2O emissions under conservation tillage. The suitability of conservation tillage in mitigating climate change and enhancing carbon sequestration is addressed in this research in an integrated approach combining characterisation of the soil porous architecture and other chemical and biological properties. Novel analytical tools such as X-ray Computed Tomography were used to characterise the 3-D soil pore network under conservation tillage for the first time. The study indicated zero tilled soils had a lower net emission of greenhouse gases on a CO2 equivalent basis indicating potentially zero tillage can be used to mitigate climate change. The net global warming potential under conventional tillage was 20% higher than zero tilled soil. A model developed to predict the greenhouse gas emissions from soil found that soil pore characteristics such as porosity played a significant role in the emission of greenhouse gases such as CO2 and CH4 among other factors such as microbial biomass carbon, bulk density and shear strength. Soil porosity alone accounted for 39.7% of the total variation for CO2 flux which was larger than any other parameter including microbial biomass carbon and soil carbon. Soil pore characteristics were revealed as one of the important determinant in aiding the GHG flux in soil. However N2O emission from soil was mainly dependent on soil moisture, microbial biomass carbon and microbial biomass nitrogen. It was also found that zero tilled soils contained 9% more soil carbon and 30% higher microbial biomass carbon than the tilled soil. It was found that tillage mediated aggregate changes could bring changes in carbon storage in soil depending on texture of soil. Increased microbial activity was evident at zero tilled soils as observed from the increased activities of hydrolysing and oxidising enzymes. The preservation of aromatic structures during residue decomposition might have contributed to enhanced sequestration of carbon under zero tilled soils as revealed by the FTIR data. The study indicates that soil management practices strongly influence other properties and by making a suitable choice of the tillage system, a comparative reduction in greenhouse gas emissions could be achieved at the same time enhancing sequestration of carbon.

An evaluation of the effectiveness of a training course is very difficult to implement, but it is necessary if the course is to achieve the objectives set out by the course designers. When the participants have completed their training, they should be equipped with the knowledge of the latest developments in their discipline, the skills to be able to put them into practice and the attitude to utilise this training experience to the full in the farm or unit situation. This study assesses the techniques available for evaluation and has selected one method of appraising Adult Short Courses, designed specifically for experienced agriculturalists from a particular farm discipline. The Agricultural Training Group Officer established the training needs of group members and organised a programme based at a central location and staffed by A. T. B. or external instructors. A questionnaire was administered to the population of course attenders at the end of each training day. The levels of knowledge, skills and attitudes were measured using a range of question designs and rating scales. The "before" level was valued at the same time as the "after" score. This is a departure from the more commonly used Pretest, Posttest design. Unit or farm physical performance data, related to stockperson control, was collected over the relevant years. A commercial psychological test was also used to evaluate the trainability of the course attenders. A comparative group of experienced agriculturalists, who were not involved in any A. T. B. training related to their unit attachment, were contacted to provide similar information and reduce any maturation, historical and local errors. The data collected showed significant increases in knowledge, skills and attitude levels with some degree of improvement in unit physical performance. The correlations between the objective criteria, unit physical data, and the subjective criteria, self-assessment ratings, were very mixed for the course attenders. The psychological tests tended to support independent unit manager valuations of the trainees. The training courses were effective and the evaluation has shown that trained staff can improve unit physical performance. The analysis supported the methodologies employed and further testing, with some modifications, using a larger population involved in a range of farm disciplines would be useful.

The use of peri-urban fenlands for agriculture usmg urban waste as manorial treatments is increasingly common worldwide, particularly in developing countries. The risk to human health from the use of these contaminated materials for crop production has been studied using two historically contaminated fenlands in NW England. The GBASE survey carried out by the British Geological Survey identified two areas of metal contaminated fenland; west of Manchester (Chat Moss) and north of Liverpool (Halsall Moss). The two areas are used for arable agriculture, and current demand for locally sourced food is increasing pressure on farmers to move to vegetable horticulture. The effect of the metal contamination on the soils and crops is of key importance to monitor any risk to the food chain. Historical research identified the two mossland areas as contaminated with urban wastes, Halsall Moss contaminated with urban organic wastes such as manure and Chat Moss contaminated with urban organic and mineral wastes. Waste disposal on Chat Moss was carried out by the Manchester Corporation to dispose of city waste and generate farmland from the peat. During the drainage up to 1.92 Mt of waste was incorporated into the soil, representing 38% of the topsoil today. Profiles of contaminated and control sites on Chat Moss and a contaminated site on Halsall Moss were collected, with pH, organic matter content and trace metal content measured. Trace metal content was elevated over subsoil levels in the topsoil of all sites, for example arsenic showed topsoil concentrations of 45 mg kg-I in the most contaminated site (CM-3) compared to 3 mg kg-I in the subsoil. The elevation of trace metals in the historically uncontaminated sites indicated possible atmospheric deposition of metals at the control site. Contamination levels were found to be less than originally identified in the GBASE survey, possibly due to differing sample preparation methods and survey size. The GBASE survey measured an average lead concentration in contaminated sites of 1985 mg kg-I compared to 378 mg kg-I measured by the current study. Arsenic and cadmium concentrations exceeded Soil Guideline Values in the most contaminated site, 43 mg kg-I and 1.8 mg kg-I respectively, but all other metals were within guideline limits. Halsall Moss was found to be less contaminated than Chat Moss, due to the mainly organic nature of the waste disposed at Halsall Moss. The mobility and fractionation of the contamination at the most contaminated site on Chat Moss were studied to understand the behaviour of the metals and assess potential risk to ecological or human health. Using sequential extractions, most metals were identified as hosted by organic, Fe/Mn oxide or residual phases. There was no difference observed in fractionation between control and contaminated sites, indicating that soil properties such as organic matter and Fe/Mn oxide content were more important in controlling fractionation than the source of metals. A comparison of Chat Moss with three soils of known contamination history also identified soil properties as key in controlling fractionation. Lability of Pb in the contaminated Chat Moss soil was assessed using 204Pb stable isotope dilution, it was found that 65% of lead was labile. This was the highest out of the four soils studied, and again most likely controlled by soil properties such as organic matter content and pH. The impact of flooding events on the Chat Moss soils was assessed, and it was found that under redox conditions of -200 mY, large quantities of arsenic, lead, molybdenum and manganese were released to soil solution, and drinking water limits for these metals were violated, for example As solution concentration reached 308 J.1g L-1 and the drinking water limit is 10 Ilg L-1. Environmental quality standards for freshwater were also violated by arsenic, copper, lead and zinc showing potential ecological hazard under these reducing conditions, with lead concentrations reaching 137 J.1g L-1 in contrast to the environmental quality standard of 4 - 20 J.1g L-1. The effect of soil contamination on vegetables grown on Chat Moss was also investigated, EU limits for Cd were exceeded by lettuce and onion, and EU limits for Pb were exceeded by parsley, carrot, radish and onion. Hazard Quotients used to assess the impact of plant contamination in the context of human intake showed that only cadmium and molybdenum were potentially hazardous. Thus it is not recommended to grow lettuce (high Cd), parsley, cabbage, radish and onion (all high molybdenum) at contaminated sites on Chat Moss. To minimise risk, conducting liming to raise the pH and immobilise the metals could be used, and careful selection of cultivars that do not accumulate metals is recommended.

The principal aim of this investigation was to understand the transformation and reaction kinetics of iodide and iodate added to soil in relation to soil properties. In addition, to integrate the data into a predictive model of iodide and iodate sorption kinetics parameterised by soil properties. Solid phase fractionation coupled with solution phase speciation (HPLC-ICPMS) was used to follow the assimilation of 129I- and 129IO3- spikes into ‘steady state’ soil microcosms. The extraction efficiency of tetra-methyl ammonium hydroxide (TMAH) for soil iodine, and the effects of experimental procedures and conditions on the speciation of extracted iodine were tested. Moreover, the possibility of extracting ‘reactive’ inorganic iodine forms sorbed on soil metal oxides by competition with PO43- ions was investigated. Results showed that changing TMAH concentration, extraction time, extraction temperature or soil particle size did not generally affect the concentrations of total iodine extracted. The ratio of iodide to total iodine in the TMAH extracts varied with the extraction conditions which led to the conclusion that part, or all, of the measured iodide is possibly produced by hydrolysis of organic iodine forms. This conclusion was also confirmed by the detection of high concentrations of iodide in TMAH extracts of a humic acid. Only iodide was measured in the phosphate extracts of soil and it constituted up to 33% of the total iodine in the KH2PO4 extracts which indicates that most of the iodine mobilised by KH2PO4 is organically bound. When soil / KH2PO4 suspensions were spiked with 129I- and 129IO3-, at least 50% of 129I- and 15% of 129IO3- were recoverable after 72 hours of reaction. The lowest recoveries were observed with the highest concentration of KH2PO4, which also mobilised the greatest concentrations of DOC, indicating that although KH2PO4 is capable of releasing sorbed iodide and iodate in soil, it may also promote iodide and iodate reaction with soil organic matter. Iodine content of soil biomass was determined following chloroform fumigation of soil. The concentrations of total iodine in fumigated soil samples were only marginally higher than iodine concentration in the control samples indicating that microbial biomass iodine constitutes only a small fraction of total soil iodine (0.01 – 0.25 %). The change in iodine (129I) solubility and speciation in nine soils with contrasting properties (pH, Fe/Mn oxides, organic carbon and iodine contents), incubated for nine months at 10oC and 20oC, was also investigated. The rate of 129I sorption was greater in soils with large organic carbon contents, low pH and at higher temperatures. Loss of iodide (129I-) from solution was extremely rapid, apparently reaching completion over minutes-hours; iodate (IO3-) loss from solution was slower, typically occurring over hours-days. In all soils an apparently instantaneous sorption reaction was followed by a slower sorption process for IO3-. For iodide a faster overall reaction meant that discrimination between the two processes was less clear. Instantaneous sorption of IO3- was greater in soils with high Fe/Mn oxide content, low pH and low organic content, whereas the rate of time dependent sorption was greatest in soils with higher organic contents. Phosphate extraction (0.15 M KH2PO4) of soils, ~100 h after 129I spike addition, indicated that concentrations of sorbed inorganic iodine (129I) were very low in all soils suggesting that inorganic iodine adsorption onto oxide phases has little impact on the rate of iodine assimilation into humus. Transformation kinetics of dissolved inorganic 129IO3- and 129I- to sorbed organic forms was modelled using a range of reaction and diffusion based approaches. Irreversible and reversible first order kinetic models, and a spherical diffusion model, adequately described the kinetics of both IO3- and I- loss from the soil solution but required inclusion of a distribution coefficient (Kd) to allow for instantaneous adsorption. A spherical diffusion model was also collectively parameterised for all the soils studied by using pH, soil organic carbon concentration and combined Fe + Mn oxide content as determinants of the model parameters (Kd and D/r2). From the temperature-dependence of the sorption data the activation energy (Ea) for 129IO3- transformation to organic forms was estimated to be ~43 kJ mol-1 suggesting a reaction mechanism slower than pore diffusion or physical adsorption, but faster than most surface reactions.