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.

The fate of the carbon and nitrogen in dairy farm effluent (DFE) applied onto soil was investigated through laboratory experiments and field lysimeter studies. They resulted in the development and testing of a complex carbon (C) and nitrogen (N) simulation model (CaNS-Eff) of the soil-plant-microbial system. To minimise the risk of contamination of surface waters, regulatory authorities in New Zealand promote irrigation onto land as the preferred treatment method for DFE. The allowable annual loading rates for DFE, as defined in statutory regional plans are based on annual N balance calculations, comparing N inputs to outputs from the farming system. Little information is available, however, to assess the effects that these loading rates have on the receiving environment. It is this need, to understand the fate of land-applied DFE and develop a tool to describe the process, that is addressed in this research. The microbially mediated net N mineralisation from DFE takes a central role in the turnover of DFE, as the total N in DFE is dominated by organic N. In a laboratory experiment, where DFE was applied at the standard farm loading rate of 68 kg N ha⁻¹, the net C mineralisation from the DFE was finished 13 days after application and represented 30% of the applied C, with no net N mineralisation being measured by Day 113. The soluble fraction of DFE appeared to have a microbial availability similar to that of glucose. The low and gradually changing respiration rate measured from DFE indicated a semi-continuous substrate supply to the microbial biomass, reflecting the complex nature and broad range of C compounds in DFE. The repeated application of DFE will gradually enhance the mineralisable fraction of the total soil organic N and in the long term increase net N mineralisation. To address the lack of data on the fate of faecal-N in DFE, a ¹⁵N-labelled faecal component of DFE was applied under two different water treatments onto intact soil cores with pasture growing on them. At the end of 255 days, approximately 2% of the applied faecal ¹⁵N had been leached, 11 % was in plant material, 11 % was still as effluent on the surface, and 40% remained in the soil (39% as organic N). Unmeasured gaseous losses and physical losses from the soil surface of the cores supposedly account for the remaining ¹⁵N (approximately 36%). Separate analysis of the total and ammonium nitrogen contents and ¹⁵N enrichments of the DFE and filtered sub-samples (0.5 mm, 0.2µm) showed that the faecal-N fraction was not labelled homogeneously. Due to this heterogeneity, which was exacerbated by the filtration of DFE on the soil surface, it was difficult to calculate the turnover of the total faecal-N fraction based on ¹⁵N results. By making a simplifying assumption about the enrichment of the ¹⁵N in the DFE that infiltrated the soil, the contribution from DFE-N to all plant available N fractions including soil inorganic N was estimated to have been approximately 11 % of the applied DFE-N. An initial two-year study investigating the feasibility of manipulating soil water conditions through controlled drainage to enhance denitrification from irrigated DFE was extended a further two years for this thesis project. The resulting four-year data set provided the opportunity to evaluate the sustainability of DFE application onto land, an extended data set against which to test the adequacy of CaNS-Eff, and to identify the key processes in the fate of DFE irrigated onto soil under field conditions. In the final year of DFE irrigation, 1554 kg N ha⁻¹ of DFE-N was applied onto the lysimeters, with the main removal mechanism being pasture uptake (700 kg N ha⁻¹ yr⁻¹ removed). An average of 193 kg N ha⁻¹ yr⁻¹ was leached, with 80% of this being organic N. The nitrate leaching decreased with increasing soil moisture conditions through controlled drainage. At the high DFE loading rate used, the total soil C and N, pH and the microbial biomass increased at different rates over the four years. The long-term sustainability of the application of DFE can only be maintained when the supply of inorganic N is matched by the demand of the pasture. The complex simulation model (CaNS-Eff) of the soil-plant-microbial system was developed to describe the transport and transformations of C and N components in effluents applied onto the soil. The model addresses the shortcomings in existing models and simulates the transport, adsorption and filtration of both dissolved and particulate components of an effluent. The soil matrix is divided into mobile and immobile flow domains with convective flow of solutes occurring in the mobile fraction only. Diffusion is considered to occur between the micropore and mesopore domains both between and within a soil layer, allowing dissolved material to move into the immobile zone. To select an appropriate sub-model to simulate the water fluxes within CaNS-Eff, the measured drainage volumes and water table heights from the lysimeters were compared to simulated values over four years. Two different modelling approaches were compared, a simpler water balance model, DRAINMOD, and a solution to Richards' equation, SWIM. Both models provided excellent estimation of the total amount of drainage and water table height. The greatest errors in drainage volume were associated with rain events over the summer and autumn, when antecedent soil conditions were driest. When soil water and interlayer fluxes are required at small time steps such as during infiltration under DFE-irrigation, SWIM's more mechanistic approach offered more flexibility and consequently was the sub-model selected to use within CaNS-Eff. Measured bromide leaching from the lysimeters showed that on average 18% of the bromide from an irrigation event bypassed the soil matrix and was leached in the initial drainage event. This bypass mechanism accounted for the high amount of organic N leached under DFE-irrigation onto these soils and a description of this bypass process needed to be included in CaNS-Eff. Between 80 and 90% of the N and C leached from the lysimeters was particulate (> 0.2 µm in size), demonstrating the need to describe transport of particulate material in CaNS-Eff. The filtration behaviour of four soil horizons was measured by characterising the size of C material in a DFE, applying this DFE onto intact soil cores, and collecting and analyzing the resulting leachate using the same size characterisation. After two water flushes, an average of 34% of the applied DFE-C was leached through the top 0-50 mm soil cores, with a corresponding amount of 27% being leached from the 50-150 mm soil cores. Most of the C leaching occurred during the initial DFE application onto the soil. To simulate the transport and leaching of particulate C, a sub-model was developed and parameterised that describes the movement of the effluent in terms of filtering and trapping the C within a soil horizon and then washing it out with subsequent flow events. The microbial availability of the various organic fractions within the soil system are described in CaNS-Eff by availability spectra of multiple first-order decay functions. The simulation of microbial dynamics is based on actual consumption of available C for three microbial biomass populations: heterotrophs, nitrifiers and denitrifiers. The respiration level of a population is controlled by the amount of C that is available to that population. This respiration rate can vary between low level maintenance requirements, when very little substrate is available, and higher levels when excess substrate is available to an actively growing population. The plant component is described as both above and below-ground fractions of a rye grass-clover pasture. The parameter set used in CaNS-Eff to simulate the fate of DFE irrigated onto the conventionally drained lysimeter treatments over three years with a subsequent 10 months non-irrigation period was derived from own laboratory studies, field measurements, experimental literature data and published model studies. As no systematic calibration exercise was undertaken to optimise these parameters, the parameter set should be considered as "initial best estimates" and not as a calibrated data set on which a full validation of CaNS-Eff could be based. Over the 42 months of simulation, the cumulative drainage from CaNS-Eff for the conventionally drained DFE lysimeter was always within the 95% CI of the measured value. On the basis of individual drainage bulking periods, CaNS-Eff was able to explain 92% of the variation in the measured drainage volumes. On an event basis the accuracy of the simulated water filled pore space (WFPS) was better than that of the drainage volume, with an average of 70% of the simulated WFPS values being within the 95% CI for the soil layers investigated, compared to 44% for the drainage volumes. Overall the hydrological component of CaNS-Eff, which is based on the SWIM model, could be considered as satisfactory for the purposes of predicting the soil water status and drainage volume from the conventionally drained lysimeter treatment for this study. The simulated cumulative nitrate leaching of 4.7 g NO₃-N m⁻² over the 42 months of lysimeter operation was in good agreement to the measured amount of 3.0 (± 2.7) g NO₃-N m⁻². Similarly, the total simulated ammonium leaching of 2.7g NH₄- N m⁻² was very close to the measured amount of 2.5 (± 1.35) g NH₄- N m⁻² , however the dynamics were not as close to the measured values as with the nitrate leaching. The simulated amount of organic N leached was approximately double that measured, and most of the difference originated from the simulated de-adsorption of the dissolved fraction of organic N during the l0-month period after the final DFE irrigation. The 305 g C m⁻² of simulated particulate C leached was close to the measured amount of 224 g C m⁻² over the 31 months of simulation. The dissolved C fraction was substantially over-predicted. There was good agreement in the non-adsorbed and particulate fractions of the leached C and N in DFE. However, the isothermic behaviour of the adsorbed pools indicated that a non-reversible component needed to be introduced or that the dynamics of the de-adsorption needed to be improved. Taking into account that the parameters were not calibrated but only "initial best estimates", the agreement in the dynamics and the absolute amounts between the measured and simulated values of leached C and N demonstrated that CaNS-Eff contains an adequate description of the leaching processes following DFE irrigation onto the soil. The simulated pasture N production was in reasonable agreement with the measured data. The simulated dynamics and amounts of microbial biomass in the topsoil layers were in good agreement with the measured data. This is an important result as the soil microbial biomass is the key transformation station for organic materials. Excepting the topsoil layer, the simulated total C and N dynamics were close to the measured values. The model predicted an accumulation of C and N in the topsoil layer as expected, but not measured. Although no measurements were available to compare the dynamics and amounts of the soil NO₃-N and NH₄-N, the simulated values appear realistic for an effluent treatment site and are consistent with measured pasture data. Considering the large amount of total N and C applied onto the lysimeters over the 42 months of operation (4 t ha⁻¹ of N and 42 t ha⁻¹0f C), the various forms of C and N in dissolved and particulate DFE as well as in returned pasture, and that the parameters used in the test have not been calibrated, the simulated values from CaNS-Eff compared satisfactorily to the measured data.

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.

Soil P fractionation was used to examine changes in soil inorganic and organic P under grazed irrigated pasture in a long-term field trial at Winchmore in Mid-Canterbury. The soil P fractionation scheme used involved sequential extractions of soil with O.5M NaHCO₃ @ pH 8.5 (NaHCO₃ P), 0.1M NaOH (NaOH I P), 1M HCl (HCl P) and 0.1M NaOH (NaOH II P). The Winchmore trial comprised 5 treatments: control (no P since 1952), 376R (376 kg superphosphate ha⁻¹ yr⁻¹ 1952-1957, none since), 564R (564 kg superphosphate ha⁻¹ yr⁻¹ 1952-1957, none since) 188PA (188 kg superphosphate ha⁻¹ yr⁻¹ since 1952) and 376PA (376 kg superphosphate ha⁻¹ yr⁻¹ since 1952: Topsoil (0-7.5cm) samples taken from the different treatments in 1958, 1961, 1965, 1968, 1971, 1974 and 1977 were used in this study. Changes in soil P with time showed that significant increases in soil inorganic P occurred in the annually fertilised treatments (l88PA, 376PA). As expected, the overall increase in total soil inorganic P between 1958 and 1977 was greater in the 376PA treatment (159 µg P g⁻¹) than that in the 188PA treatment (37 µg P g⁻¹). However, the chemical forms of inorganic P which accumulated in the annually fertilised treatments changed with time. Between 1958 and 1971 most of the increases in soil inorganic P in these treatments occurred in the NaHCO₃ and NaOH I P fractions. On the other hand, increases in soil inorganic P in the annually fertilised treatments between 1971 and 1977 were found mainly in the HCl and NaOH II P fractions. These changes in soil P forms were attributed to the combined effects of lime addition in 1972 and increased amounts of sparingly soluble apatite P and iron-aluminium P in the single superphosphate applied during the 1970's. In the residual fertiliser treatments (376R, 564R) significant decreases in all of the soil inorganic P fractions (i.e. NaHCO₃ P, NaOH I P, HCl P, NaOH II p) occurred between 1958 and 1977 following the cessation of P fertiliser inputs in 1957. This was attributed to continued plant uptake of P accumulated in the soil from earlier P fertiliser additions. However, levels of inorganic P in the different soil P fractions in the residual fertiliser treatments did not decline to those in the control which indicated that some of the inorganic P accumulated in the soil from P fertiliser applied between 1952 and 1957 was present in very stable forms. In all treatments, significant increases in soil organic P occurred between 1958 and 1971. The overall increases in total soil organic P were greater in the annually fertilised treatments (70-86 µg P g⁻¹) than those in the residual fertiliser (55-64 µg P g⁻¹) and control (34 µg P g⁻¹) treatments which reflected the respective levels of pasture production in the different treatments. These increases in soil organic P were attributed to the biological conversion of native and fertiliser inorganic P to organic P in the soil via plant, animal and microbial residues. The results also showed that annual rates of soil organic P accumulation between 1958 and 1971 decreased with time which indicated that steady-state conditions with regard to net 'organic P accumulation were being reached. In the residual fertiliser treatments, soil organic P continued to increase between 1958 and 1971 while levels of soil inorganic P and pasture production declined. This indicated that organic P which accumulated in soil from P fertiliser additions was more stable and less available to plants than inorganic forms of soil P. Between 1971 and 1974 small (10-38 µg P g⁻¹) but significant decreases in total soil organic P occurred in all treatments. This was attributed to increased mineralisation of soil organic P as a result of lime (4 t ha⁻¹) applied to the trial in 1972 and also to the observed cessation of further net soil organic P accumulation after 1971. Liming also appeared to affect the chemical nature of soil organic P as shown by the large decreases in NaOH I organic P(78-88 µg P g⁻¹) and concomitant smaller increases in NaOH II organic P (53-65 µg P g⁻¹) which occurred in all treatments between 1971 and 1974. The chemical nature of soil organic P in the Winchmore long-term trial was also investigated using 31p nuclear magnetic resonance (NMR) spectroscopy and gel filtration chromatography. This involved quantitative extraction of organic P from the soil by sequential extraction with 0.1M NaOH, 0.2M aqueous acetylacetone (pH 8.3) and 0.5M NaOH following which the extracts were concentrated by ultrafiltration. Soils (0-7.5cm) taken from the control and 376PA annually fertilised treatments in 1958, 1971 and 1983 were used in this study. 31p NMR analysis showed that most (88-94%) of the organic P in the Winchmore soils was present as orthophosphate monoester P while the remainder was found as orthophosphate diester and pyrophosphate P. Orthophosphate monoester P also made up almost all of the soil organic P which accumulated in the 376PA treatment between 1958 and 1971. This indicated that soil organic P in the 376PA and control treatments was very stable. The gel filtration studies using Sephadex G-100 showed that most (61-83%) of the soil organic P in the control and 376PA treatments was present in the low molecular weight forms (<100,000 MW), although the proportion of soil organic P in high molecular weight forms (>100,000 MW) increased from 17-19% in 1958 to 38-39% in 1983. The latter was attributed to the microbial humification of organic P and indicated a shift toward more complex and possibly more stable forms of organic P in the soil with time. Assuming that the difference in soil organic P between the control and 376PA soils sampled in 1971 and 1983 represented the organic P derived from P fertiliser additions, results showed that this soil organic P was evenly distributed between the high and low molecular weight fractions. An exhaustive pot trial was used to examine the relative availability to plants of different forms of soil inorganic and organic P in long-term fertilised pasture soils. This involved growing 3 successive crops of perennial ryegrass (Lolium perenne) in 3 Lismore silt loam (Udic Ustochrept) soils which had received different amounts of P fertiliser for many years. Two of the soils were taken from the annually fertilised treatments in the Winchmore long term trial (188PA, 376PA) and the third (Fairton) was taken from a pasture which had been irrigated with meatworks effluent for over 80 years (65 kg P ha⁻¹ yr⁻¹). Each soil was subjected to 3 treatments, namely control (no nutrients added), N100 and N200. The latter treatments involved adding complete nutrient solutions with different quantities of N at rates of 100kg N ha⁻¹ (N100) and 200kg N ha⁻¹ (N200) on an area basis. The soil P fractionation scheme used was the same as that used in the Winchmore long-term trial study (i.e. NaHCO₃ P, NaOH I P, HCl P, NaOH II p). Results obtained showed that the availability to plants of different extracted inorganic P fractions, as measured by decreases in P fractions before and after 3 successive crops, followed the order: NaHCO₃ P > NaOH I P > HCl P = NaOH II P. Overall decreases in the NaHCO₃ and NaOH I inorganic P fractions were 34% and 16% respectively, while corresponding decreases in the HCl and NaOH II inorganic P fractions were small «10%) and not significant. However, a significant decrease in HCl P (16%) was observed in one soil (Fairton-N200 treatment) which was attributed to the significant decrease in soil pH (from 6.2 to 5.1) which occurred after successive cropping. Successive cropping had little or no effect on the levels of P in the different soil organic P fractions. This indicated that net soil organic P mineralisation did not contribute significantly to plant P uptake over the short-term. A short-term field experiment was also conducted to examine the effects of different soil management practices on the availability of different forms of P to plants in the long-term fertilised pasture soils. The trial was sited on selected plots of the existing annually fertilised treatments in the Winchmore long-term trial (188PA, 376PA) and comprised 5 treatments: control, 2 rates of lime (2 and 4 t ha⁻¹ ) , urea fertiliser (400kg N ha⁻¹ ) and mechanical cultivation. The above ground herbage in the uncultivated treatments was harvested on 11 occasions over a 2 year period and at each harvest topsoil (0-7.5 cm) samples were taken from all of the treatments for P analysis. The soil P fractionation scheme used in this particular trial involved sequential extractions with 0.5M NaHCO₃ @ pH 8.5 (NaHCO₃ P), 0.1M NaOH (NaOH P), ultrasonification with 0.1M NaOH (sonicate-NaOH p) and 1M HCl (HCl P). In addition, amounts of microbial P in the soils were determined. The results showed that liming resulted in small (10-21 µg P g⁻¹) though significant decreases in the NaOH soil organic P fraction in the 188PA and 376PA plots. Levels of soil microbial P were also found to be greater in the limed treatments compared with those in the controls. These results indicated that liming increased the microbial mineralisation of soil organic P in the Winchmore soils. However, pasture dry matter yields and P uptake were not significantly affected. Although urea significantly increased dry matter yields and P uptake, it did not appear to significantly affect amounts of P in the different soil P fractions. Mechanical cultivation and the subsequent fallow period (18 months) resulted in significant increases in amounts of P in the NaHCO₃ and NaOH inorganic P fractions. This was attributed to P released from the microbial decomposition of plant residues, although the absence of plants significantly reduced levels of microbial P in the cultivated soils. Practical implications of the results obtained in the present study were presented and discussed.

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.

Thesis (MScFor)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: A field trial of six replications was established to test the effect of various wood ash and fertilisers application rates on soil chemistry, tree nutrition and early growth rate of a clonal Eucalyptus grandis x urophylla stand. Wood ash from pulpmills is currently disposed of in landfills. Increasing costs and potential environmental risks have driven companies to investigate alternative disposal methods. Ash consists of a combination of carbonates, hydroxides and other calcium containing minerals that induce the liming effect if ash is applied to a soil. The trial was established near Richards Bay in October 2013 on a sandy soil with a low buffer capacity and a pH of approximately 5.5. The trial consists of four wood ash application rates in combination with three levels of fertiliser, viz. no fertiliser, 150 g conventional NPK fertiliser mixture, or 320g NPK controlled release mixture. Fertiliser mixtures and application levels were based on previous fertiliser trials in the region. Ash application rates for the field trial were based on a lab incubation study done with soil samples from Richards Bay, to which increasing amounts of lime were added. The study tested wood ash application rates of 0, 300, 600 and 1200 kg/ha. Field measurements were taken at 4 and 8 months after trial establishment. The primary objective was to investigate which application levels in combination with the type of fertiliser could be applied to soils without negatively affecting the stand nutrition or increase the levels of potentially harmful elements in the soil; thus investigating the feasibility of safely disposing wood ash on plantation soils as an alternative disposal method. Soil nutrient concentrations were not affected by individual wood ash treatments, but more a product of the time interval after the ash additions were made. Soil C, P, K+ and Mg2+ showed decreased concentrations from 4-8 months after establishment. Ca2+ concentrations increased in the same time interval. In addition, Na+ and B concentrations decreased from 4-8 months. Soil heavy metal concentrations for Cd, Hg, Cr and Pb, analysed for 0-1200 kg/ha ash rates, were well below toxic levels at both time intervals. Wood ash induced a temporary liming effect. Mean soil pH increased with 0.6 units for the period 0 - 4 months and decreased with 0.4 units at 4 - 8 months after trial establishment. Foliar nutrient analyses and assessment techniques revealed sub-optimal nutrient concentrations for P, K and Zn at 4 and 8 months of age. Concentrations were defined as sub-optimal, as none of the nutrients were below critical levels. Foliar heavy metal concentrations for Cd, Hg, Cr and Pb, measured at both time intervals, were less than 1mg/kg. The small concentrations found in this project were attributed to the low bioavailability of all four elements and were likely a product of the edaphic factors at Richards Bay, which was representative of a large greater portion of the Zululand coastal plain sites. The response in biomass index ranged between 13 % and 683 % relative to the control treatment (A0F0). Results showed that application of purely wood ash, or in combination with a supplementary N and P source increased growth up to 8 months after trial establishment for wood ash applications up to 1200 kg/ha. This project demonstrated that 1200 kg/ha wood ash can safely be disposed of on a typical Zululand coastal sand with little environmental risk and no supressed growth, provided that it is balanced with an appropriate NP fertiliser. / AFRIKAANSE OPSOMMING: ‘n Veldproef met ses herhalings is in Oktober 2013 uitgelê met die doel om die uitwerking van verskillende vlakke hout as en kunsmis toedienings op die grond-voedingstof status, boom-voedingstof status en die groei-tempo van ‘n Eucalyptus grandis x urophylla hibried plantasie te bestudeer. Hout as by pulpmeulens word tans weggegooi op stortingsterreine. Toenemende onkostes vir storting en die omgewingsrisiko’s gebonde aan stortingsterreine, dryf maatskappye om verbeterde en meer omgewingsvriendelike metodes te ondersoek om van die as ontslae te raak. Hout as bestaan uit ‘n reeks karbonate, hidroksiede en kalsium bevattende minerale en is verantwoordelik vir die bekalkingseffek op die grond na toediening. Die veldproef is geleë naby Richardsbaai op ‘n sanderige grond met n lae bufferkapasiteit en pH van ongeveer 5.5. Die proef het vier hout as vlakke getoets, gekombineer met drie vlakke van bemesting: geen, 150g konvensionele landbou kunsmis (CV) óf 320g beheerd-vrystellende kunmis (CRF). Die kunsmismengsels en vlakke van bemesting is gebaseer op bestaande of voltooide bemestingseksperimente in die streek. Hout as vlakke was bereken in gekontroleerde laboratorium toestande en gebaseer op ‘n inkubasie studie met grond monsters verkry vanaf Richardsbaai, waarby toenemende vlakke suiwer landboukalk gevoeg is. Die veldproef het hout as vlakke van 0, 300, 600 en 1200 kg/ha getoets. Veld metings is op 4 en 8 maande na behandeling geneem. Die primêre doelwit van die studie was om te bepaal watter vlak hout as en kunmis kombinasie toegedien kan word, sonder om die grond-voedingstof status negatief te beïnvloed of ‘n potensiële skadelike uitwerking op die plantasie groei te veroorsaak. Die uiteinde van die studie was om die haalbaarheid van hout as toedienings op plantasie gronde te bestudeer relatief tot die huidige praktyk van storting, insluitend die risiko van moontlike skadelike newe-effekte. Grondvoedingstatus was nie beduidend beïnvloed deur individuele hout as toevoegings nie, maar was eerder ‘n funksie van die tydsduur sedert behandeling. Grond koolstof, P anione, K+ en Mg2+ konsentrasies het beduidend afgeneem in die periode van 4 - 8 maande na behandling. Die Ca2+ konsentrasies het toegeneem tussen 4 en 8 maande en terselfdertyd het Na+ en B konsentrasies afgeneem. Die swaarmetaal status, spesifiek vir Cd, Hg, Cr en Pb, vir toevoegings van 0-1200 kg/ha hout as was beduidend laer as toelaatbare vlakke in gronde op albei tydsintervalle. Die hout as het ‘n tydelike toename in grond pH veroorsaak. Die gemiddelde pH het tussen 0 - 4 maande toegeneem met 0.6 eenhede en gedurende 4 - 8 maande afgeem met 0.4 eenhede. Blaarontledings en voedingstof assesseringsmetodes het sub-optimale konsentrasies vir P, K en Zn getoon op die ouderdom van 4 en 8 maande. Voedingstof konsentrasies is as sub-optimaal geklassifiseer, omdat konsentrasies nooit laer as kritieke waardes vir gebreksimptome was nie. Die inhoud van Cd, Hg, Cr en Pb in blare was aansienlik kleiner as 1 mg/kg op albei tydsintervalle. Die merkwaardige lae konsentrasies wat in die projek aangeteken is, word toegekryf aan die lae bio-beskikbaarheid van al vier elemente as gevolg van die edafiese faktore eie aan die Richardsbaai omgewing (en ook aan groot dele van die Zoeloelandse kusvlakte). Die groeireaksie (bepaal as biomassa indeks op ouderdom 8 maande) het gewissel van 13 % - 683 % groter as die kontrole behandeling (A0F0). Resultate het bewys dat toedienings van suiwer hout as, of hout as gekombineer met ‘n addisionele N en P kunsmisbron die groei postief beïnvloed tot op die ouderdom van 8 maande. Die studie het bewys dat 1200 kg/ha hout as veilig toegedien kan word op die sandgronde van die kusgebiede in Zululand, met minimale omgewingsrisiko en geen tekens onderdrukte groei nie, mits dit gebalanseer word met ‘n geskikte NP kunsmisbron.

Indiana University-Purdue University Indianapolis (IUPUI) / Long term no-till (NT) farming can improve the CH4 oxidation capacity of agricultural lands through creation of a favorable soil environment for methanotrophs and diffusive gas transport. However, limited data is available to evaluate the merit of that contention. Although the potential for biological CH4 oxidation may exist in NT soils, restricted diffusion could limit expression of that potential in fine-textured soils. A study was conducted to assess the CH4 oxidation potential and gaseous diffusivity of soils under plow till (PT) and NT for > 50 years. Intact cores and composite soils samples (0-10 and 10-20 cm) were collected from NT and PT plots located at a well-drained site (Wooster silt loam) and at a poorly-drained (Crosby silt loam) site in Ohio. Adjacent deciduous forest soils were also sampled to determine maximum rate expected in undisturbed soils in the region. Regardless of study sites and soil depth, CH4 oxidation rate (measured at near ambient CH4) and oxidation potential (Vmax, measured at elevated CH4) were 3-4 and 1.5 times higher in NT than in PT soils, respectively. Activity in the NT soils approached (66-80 %) that in the forest soils. Half saturation constants (Km) and threshold for CH4 oxidation (Th) were lower in NT (Km: 100.5 µL CH4 L-1; Th: 0.5 µL CH4 L-1) than in PT soils (Km: 134 µL CH4 L-1; Th: 2.8 µL CH4 L-1) suggesting a greater affinity of long-term NT soils for CH4, and a possible shift in methanotrophic community composition. CH4 oxidation rates were lower in intact soil cores compared to sieved soils, suggesting that CH4 oxidation was limited by diffusion, a factor that could lead to lower field-measured CH4 uptake than suggested by biological oxidation capacity measured in the laboratory. Regardless of soil drainage characteristic, long-term NT resulted in significantly higher (2-3 times) CH4 diffusivity (mean: 2.5 x 10-3 cm2 s-1) than PT (1.5 x 10-3 cm2 s-1), probably due to improved soil aggregation and greater macro-pores volume in NT soils. Overall, these results confirm the positive impact of NT on the restoration of the biological (Vmax, Km and Th) and physical (diffusivity) soil attributes essential for CH4 uptake in croplands. Long-term implementation of NT farming can therefore contribute to the mitigation of CH4 emission from agriculture.

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.