There is an extensive debate on the potential environmental impact of dairy farms and in particular the effect of dairy farms on the nitrogen cycle and the effect that this has on ecosystems. Within New Zealand and in particular in the South Island, the expansion of dairying and the adoption of new dairy systems has led to this becoming an increasingly important issue, locally through its effect on water quality and the environment and nationally and internationally through the production of green house gases. Increases in nitrogen usage at the expense of clover nitrogen fixation, irrigation, stocking rate and the introduction of dairy cows onto light free draining soils previously the preserve of arable or sheep farming has led to concern as to the effect intensive pastoral dairying may have on the nitrogen dynamics of the farm and the environment. This study is designed to assess how changes in grazing management in particular changes in pre-grazing and post-grazing residuals alter the clover/ryegrass balance on the farm and the effect that this has on the farm’s nitrogen dynamics. The effects of qualitative changes in grazing management on pasture composition are well established but little is known of the effect of quantitative changes in pasture management on composition, in particular the effect of grazing residuals. There are a number of detailed models of the physiological processes in the energy and nutrient cycling in plants, animals and the soil. There are a smaller number of whole farm models that through integration and simplification of component models attempt to represent the flux of nutrients though a dairy farm. None of these whole farm models is currently able to model the nitrogen flux through a dairy farm at a sufficient level of resolution to capture differences in pasture composition as these occur spatially, temporally and in response to grazing management. This project sought to better understand the nitrogen dynamics on a dairy farm by constructing and then linking component models – a pasture composition and growth model, a cow model, an excretal return model, a soil model and a water balance model – within a whole farm management schedule. The formal null hypothesis is that the mechanistic, mathematical model constructed for this PhD cannot capture and explain the full range of the changes in soil water content, soil nitrogen status, pasture production and composition and animal production, following the alteration in management of the dairy farm between 2002 and 2004. Individual component models were constructed by the author using the computer software package (Matlab) and validated against data extracted from the literature. The models were then converted into one simulation package using C-sharp as the source code language by Elizabeth Post, Senior Computer Scientist at Lincoln Ventures Ltd, Lincoln, New Zealand and the author. This model was then used to investigate the nitrogen dynamics of a dairy farm: the relationship with pasture composition and whether small changes in pasture residuals make a difference to pasture composition and nitrogen dynamics. Two different simulations were run based on the management practice of Lincoln University Dairy farm (LUDF) over two dairy seasons (2002-03 and 2003-04) and validated against the data recorded on this farm. In 2002-03, 50 cows were over wintered and 580 cows were subsequently milked on 200ha. Post grazing residuals where maintained at 1600-1750KgDM/ha. In 2003-04, 125 cows were overwintered and 635 cows were milked on 200ha with post grazing residuals maintained at 1400KgDm/ha. All models operate on a daily time step. Within the pasture model composition is described by 9 state variables describing different components of the pasture and pasture growth is modelled mechanistically from a calculation of component photosynthesis. A further 9 state variables describe the nitrogen composition of the pasture components. The soil model is a variable two layer, mechanistic representation, parametised for the shallow, stony soils of LUDF. Soil water status is an input for the pasture model while water uptake by the growing plants affects the soil water balance within the soil model. Animal intake and production are modelled mechanistically with model cows described in terms of their age, genetic merit, body weight, breed, pregnancy status, conception date and body condition score. Each cow type produces a different quantity of urinary and faecal excretion which varies with dry matter intake, milk yield and the sodium and potassium status of the pasture. Excretal nitrogen composition is predicted within a separate model which calculates daily nitrogen excretion in faeces, urine and milk. Excretions are deposited randomly over the grazed area and account is taken of overlapping excretions that are created on the same day and overlaps that occur with older excretal patches deposited in previous grazing rounds. Each excretal patch has its own associated pasture, water and soil model reflecting the differences in nitrogen status between patches. Grazing preference is expressed within the model between different classes of excretal patch and between excretal patches and the base pasture and between clover and grass. Supplementary silage is conserved and fed according to the management schedule of LUDF. Cows calve, become pregnant and are dried off within the model according to the relevant records from LUDF. Cows are deemed to arrive on the farm on the day of calving and to leave on the day that drying off is finished (a 5 day procedure within the model), except for those cows that are overwintering which remain on the farm. The soil model has multiple nitrogen/carbon pools and is dynamically linked to all the other models. External nitrogen losses from the system are modelled as volatilisation, leaching and denitrification, with pasture nitrogen uptake from the soil model and fixation by clover from the atmosphere. Both the individual component models and the final assembled composite model were successful in matching the available data in terms of pasture and animal production, pasture composition, soil water balance and nitrogen status and external losses. The model indicates that the low residual, high stocking rate farm returns more excreta to the soil. However, this is countered by a reduction in the amount of dead material returned to the paddock and this reduces the relative size of the pool of nitrogen in the dead organic matter. This produces a relative lack of substrate for the soil microbes which are thus unable to exploit all of the nitrogen in the available pool. Soil ammonium and nitrate pools are also increased from the increase in faecal and urinary return so precipitating an immobilising flux from these larger pools to the smaller pool of nitrogen available to the soil microbes. However, the relative inability of the soil bacteria to fully exploit this means that the production of soil organic live matter and the resulting mineralising flux from the dead organic matter pool through the available pool to the ammonium and nitrate pools is reduced. The larger ammonium and nitrate pools will also be associated with increased external losses from the system as denitrification, leaching and volatilisation are increased. The increase in the clover percentage within the sward in 2003-04 led to greater nitrogen fixation and the model suggests that some of the extra nitrogen is effectively captured by the animals in increased production. However, the reduction in the return of dead matter coupled with an increase in excretal return and the consequent increase in the mineral nitrogen pools within the soil lead to greater losses of nitrogen from the soil.

It is widely accepted that bioavailability, rather than total soil concentration, is preferred when assessing the risk associated with metal contamination. Despite this, debate continues on what constitutes a bioavailable pool and how to best predict bioavailability, especially in relation to crop plants. The overall aim of this thesis was to assess and validate measures of cadmium (Cd), copper (Cu), nickel (Ni) and zinc (Zn) bioavailability in a range of soils amended with metal salts and biosolids. Six potential measures of bioavailability were investigated and compared: total metal; 0.04 M EDTA extraction; 0.05 M Ca(NO₃)₂ extraction; soil solution extracted using rhizon probes; effective solution concentration (CE) determined using diffusive gradients in thin films (DGT); and modelled free ion activities (WHAM 6.0). These were compared to shoot metal concentrations obtained from plants grown in three soils with contrasting properties treated with biosolids and metal salts. The first study involved a wheat seedling (Triticum aestivum) assay carried out under controlled environmental conditions on incubated soils treated with metal salts and biosolids. Results showed that the presence of biosolids resulted in increases of DOC, salinity, Ca and Mg in soil solution as well as total concentrations of Cu and Zn, dry matter was also adversely affected by increased levels of salinity. The addition of biosolids did not significantly alter the extractability or solubility of Cd, Cu, Ni and Zn although concentrations of Cd in shoots were significantly lower in plants grown in biosolids amended soils compared with unamended soils. The second study involved a field experiment that used 20 cm diameter by 30 cm deep soil monoliths of the same three soils treated with metals and biosolids, and perennial ryegrass (Lolium perenne) was grown for 24 months. Results revealed the addition of biosolids significantly increased the amount of DOC, salinity, Ca and Mg in solution. The presence of biosolids also significantly altered the bioavailability of Cd, Cu, Ni and Zn, as measured by soil solution, CE and free ion activity. However, this change had little effect on plant metal uptake. The length of time following treatment application had the greatest effect on soil chemistry and metal availability, resulting in pH decreases and increases in DOC, soil solution salinity, Ca and Mg. The free ion activities of each metal increased with time, as did soil solution Cd and Zn and CE-Cu, with results for Zn indicative of migration through the soil profile with time. Plant uptake of Ni and Zn also changed with time. Nickel concentrations in shoots decreased, while concentrations of Zn in shoots increased. The findings from the two studies demonstrated that biosolids increased the amount of DOC, salinity, Ca and Mg present in soil solution. In the lysimeter study measures of metal availability were affected in soils amended with biosolids, but this did not effect shoot concentrations. The overall predictive strengths of the six potential measures of bioavailability was investigated using results from the previously described experiments and related studies carried out by ESR and Lincoln University using nine different soils amended with combinations of biosolids and metal salts. Of the four metals Ni provided the strongest correlations between metal bioavailability and shoot concentrations, with 0.05 M Ca(NO₃)₂ extraction giving the strongest relationship for Ni concentrations in shoots (r² = 0.73). This suggests that the solubility of Ni is highly indicative of shoot concentrations and that Ca(NO₃)₂ is a robust measure of Ni bioavailability. In addition Ca(NO₃)₂ provided the best estimate of Zn bioavailability (r² = 0.65), and CE-Cd provided the best measure of Cd bioavailability, although it could only describe 47 % of shoot Cd concentration. Results for Cu were typical of previously described studies as assays of Cu availability are almost always poorly correlated with shoot concentrations, with total Cu having the strongest relationship (r² = 0.34). Methods based on the extractability and solubility of Cu in soils were poor indicators of Cu concentration in shoots. Overall, the addition of biosolids did not alter the outcome of these bioavailability assays, and results indicated that total metal concentrations present in the soils and biosolids matrix, plus length of time since soil treatment, had a greater affect on metal bioavailability.

Changes brought about by chemical and physical weathering were investigated in a chronosequence of terrace soils near Reefton, New Zealand. The parent materials of the soil, which ranged in age from about 1000 to over 130,000 years were outwash gravels, sands and silts derived from granite (dominant) and indurated sandstone. Variations in pH, organic matter, particle size, cation exchange properties, total Mg, Al, Si, K, Ca, Fe and Ti, poorly-ordered and organic-complexed forms of Al and Fe, and mineralogy caused by increasing duration of weathering and by short range, short term variations in the intensity of the biotic factor were determined. It was concluded that the younger soils represented dynamic systems in which alternative weathering cycles could replace each other as the growth, death and eventual disappearance of individual red beech trees caused localised fluctuations in pH. It was further concluded that these processes would lead ultimately to the formation of gley podzols as are now found on the two oldest surfaces p and that podzolisation preceded gleying. Attempts were made to determine if minerals of the plumbogummite group were responsible for the high proportion of soil phosphate from these soils that, on fractionation, appeared in the residual P fraction. It was found that attempts to concentrate these minerals by prolonged digestion with HF resulted in their solution, and in precipitation of complex fluorides that yielded diffraction spacings that have been mistaken for minerals of the plumbogummite group.

A series of glasshouse and laboratory experiments was carried out to enable comparison of two woody perennial legumes, gorse and broom, with other legumes, nodulated non-legumes and other biological nitrogen fixing systems. Both species had distinct juvenile phases in which broom closely resembled herbaceous species in appearance, but adult plants of both species bore little resemblance to each other or to other legume species. Nodule development was similar to that of other legumes, but mature nodules exhibited structural adaptations to longevity - meristematic activity, a well developed vascular system and numerous cytoplasmic granules in cortical cells. Acetylene reduction and ¹⁵N₂ fixation continued for much longer following excision than has been observed in other legumes. In all experiments, broom nodules exhibited higher rates of acetylene reduction and nitrogen fixation than did gorse nodules. The first detectable product of nitrogen fixation in excised nodules - ammonia - was rapidly incorporated into amide and ∝ amino groups and another unidentified fraction. The principle free amino acid in nodules and sap was asparagine. Its preponderance increased as plants aged. Whole nodulated plants and excised nodules of both species exhibited a relatively low temperature optimum for growth and nitrogen fixation (22°C). They were very sensitive to elevated temperatures. Results indicated that gorse and broom have relatively low light requirements. When aeration was sufficient, combined nitrogen had little effect on growth of nodulated plants. Nodulation in both species was reduced by increasing amounts of combined nitrogen. High levels (100 mg/1) of nitrate and ammonia caused considerable inhibition of nitrogen function. Both species showed large responses to phosphate, but were able to grow and fix nitrogen when supplied with low amounts of phosphate. Boron deficiency reduced nitrogen fixation. Nodulation was increased to compensate for this. Considerable amounts of nitrogen can be contributed to the ecosystem in gorse end broom litter. Direct transfer between gorse or broom and Pinus radiate is likely to be small and may be masked by competition for other nutrients. These findings are discussed with respect to the use of gorse and broom to overcome nitrogen deficiency in reafforestation on the Moutere Gravels, in Nelson, N.Z.

It is widely accepted that bioavailability, rather than total soil concentration, is preferred when assessing the risk associated with metal contamination. Despite this, debate continues on what constitutes a bioavailable pool and how to best predict bioavailability, especially in relation to crop plants. The overall aim of this thesis was to assess and validate measures of cadmium (Cd), copper (Cu), nickel (Ni) and zinc (Zn) bioavailability in a range of soils amended with metal salts and biosolids. Six potential measures of bioavailability were investigated and compared: total metal; 0.04 M EDTA extraction; 0.05 M Ca(NO₃)₂ extraction; soil solution extracted using rhizon probes; effective solution concentration (CE) determined using diffusive gradients in thin films (DGT); and modelled free ion activities (WHAM 6.0). These were compared to shoot metal concentrations obtained from plants grown in three soils with contrasting properties treated with biosolids and metal salts. The first study involved a wheat seedling (Triticum aestivum) assay carried out under controlled environmental conditions on incubated soils treated with metal salts and biosolids. Results showed that the presence of biosolids resulted in increases of DOC, salinity, Ca and Mg in soil solution as well as total concentrations of Cu and Zn, dry matter was also adversely affected by increased levels of salinity. The addition of biosolids did not significantly alter the extractability or solubility of Cd, Cu, Ni and Zn although concentrations of Cd in shoots were significantly lower in plants grown in biosolids amended soils compared with unamended soils. The second study involved a field experiment that used 20 cm diameter by 30 cm deep soil monoliths of the same three soils treated with metals and biosolids, and perennial ryegrass (Lolium perenne) was grown for 24 months. Results revealed the addition of biosolids significantly increased the amount of DOC, salinity, Ca and Mg in solution. The presence of biosolids also significantly altered the bioavailability of Cd, Cu, Ni and Zn, as measured by soil solution, CE and free ion activity. However, this change had little effect on plant metal uptake. The length of time following treatment application had the greatest effect on soil chemistry and metal availability, resulting in pH decreases and increases in DOC, soil solution salinity, Ca and Mg. The free ion activities of each metal increased with time, as did soil solution Cd and Zn and CE-Cu, with results for Zn indicative of migration through the soil profile with time. Plant uptake of Ni and Zn also changed with time. Nickel concentrations in shoots decreased, while concentrations of Zn in shoots increased. The findings from the two studies demonstrated that biosolids increased the amount of DOC, salinity, Ca and Mg present in soil solution. In the lysimeter study measures of metal availability were affected in soils amended with biosolids, but this did not effect shoot concentrations. The overall predictive strengths of the six potential measures of bioavailability was investigated using results from the previously described experiments and related studies carried out by ESR and Lincoln University using nine different soils amended with combinations of biosolids and metal salts. Of the four metals Ni provided the strongest correlations between metal bioavailability and shoot concentrations, with 0.05 M Ca(NO₃)₂ extraction giving the strongest relationship for Ni concentrations in shoots (r² = 0.73). This suggests that the solubility of Ni is highly indicative of shoot concentrations and that Ca(NO₃)₂ is a robust measure of Ni bioavailability. In addition Ca(NO₃)₂ provided the best estimate of Zn bioavailability (r² = 0.65), and CE-Cd provided the best measure of Cd bioavailability, although it could only describe 47 % of shoot Cd concentration. Results for Cu were typical of previously described studies as assays of Cu availability are almost always poorly correlated with shoot concentrations, with total Cu having the strongest relationship (r² = 0.34). Methods based on the extractability and solubility of Cu in soils were poor indicators of Cu concentration in shoots. Overall, the addition of biosolids did not alter the outcome of these bioavailability assays, and results indicated that total metal concentrations present in the soils and biosolids matrix, plus length of time since soil treatment, had a greater affect on metal bioavailability.

A two-year lysimeter study was undertaken to compare the environmental effects (e.g. nitrate leaching and nitrous oxide emissions) of soil applied lactose-depleted dairy factory effluent (LD-DFE) with lactose-rich DFE. The aim of this experiment was to determine the fate of nitrogen from LD-DFE and dairy cow urine applied to a Templeton fine sandy loam soil (Udic Ustrochrept), supporting a herbage cover of ryegrass (Lolium perenne) and white clover (Trifolium repens). Measurements were carried out on the amount of nitrogen lost from the soil via leaching, lost by denitrification, removed by the pasture plants, and immobilized within the soil organic fraction. Further, a comparison between the fate of nitrogen in LD-DFE irrigated onto land under a "cut and carry" system, as opposed to a "grazed" pasture system was undertaken. Lactose-depleted dairy factory effluent was applied at three-weekly intervals during the summer months at rates of 25 and 50 mm, until nitrogen loading targets of 300 and 600 kg N ha⁻¹ yr⁻¹ had been achieved. Measured leaching losses of nitrogen averaged 2 and 7 kg N ha⁻¹ yr⁻¹ for Control 25 and Control 50 treatments; 21, 20 and 58 kg N ha⁻¹ yr⁻¹ for 25 and 50 mm "cut and carry" treatments respectively; and 96 kg N ha⁻¹ yr⁻¹ for the 25 mm "grazed" treatment. The range of nitrate-N leaching loss from LD-DFE plus urine is no different from the lactose-rich DFE nitrate leaching loss. Uptake of nitrogen by the growing pasture averaged 153, 184,340,352,483, and 415 kg N ha⁻¹ yr⁻¹ for Control 25, Control 50, LD-DFE 25 and LD-DFE 50 mm "cut and carry" treatments, and the LD-DFE 25 mm "grazed" treatment, respectively. Denitrification losses were 0.06, 4.4, 1.69, 19.70, and 7.4 kg N ha⁻¹ yr⁻¹ for Control 25, the LD-DFE 25 "cut and carry" treatments, the LD-DFE 25 mm "grazed" treatment, and calculated "paddock losses", respectively. Isotopic nitrogen studies found that 29.4 and 25.8% of applied LD-DFE nitrogen was immobilised in the LD-DFE 25 and LD-DFE 50 "cut and carry" treatments. The results of this experiment confirm the findings of the previous lactose-rich DFE study, in that the effects of grazing stock are of greater environmental concern than the removal of lactose from the effluent waste stream.