To date, there has been little research into the role of microbial community structure in the functioning of the soil ecosystem and on the links between microbial biomass size, microbial activity and key soil processes that drive nutrient availability. The maintenance of structural and functional diversity of the soil microbial community is essential to ensure the sustainability of agricultural production systems. Soils of the same type with similar fertility that had been under long-term organic and conventional crop management in Canterbury, New Zealand, were selected to investigate relationships between microbial community composition, function and potential environmental impacts. The effects of different fertilisation strategies on soil biology and nitrogen (N) dynamics were investigated under field (farm site comparison), semi-controlled (lysimeter study) and controlled (incubation experiments) conditions by determining soil microbial biomass carbon (C) and N, enzyme activities (dehydrogenase, arginine deaminase, fluorescein diacetate hydrolysis), microbial community structure (denaturing gradient gel electrophoresis following PCR amplification of 16S and 18S rDNA fragments using selected primer sets) and N dynamics (mineralisation and leaching). The farm site comparison revealed distinct differences between the soils in microbial community structure, microbial biomass C (conventional>organic) and arginine deaminase activity (organic>conventional). In the lysimeter study, the soils were subjected to the same crop rotation (barley (Hordeum vulgare L.), maize (Zea mais L.), rape (Brassica napus L. ssp. oleifera (Moench)) plus a lupin green manure (Lupinus angustifolius L.) and two fertiliser regimes (following common organic and conventional practice). Soil biological properties, microbial community structure and mineral N leaching losses were determined over 2½ years. Differences in mineral leaching losses were not significant between treatments (total organic management: 24.2 kg N ha⁻¹; conventional management: 28.6 kg N ha⁻¹). Crop rotation and plant type had a larger influence on the microbial biomass, activity and community structure than fertilisation. Initial differences between soils decreased over time for most biological soil properties, while they persisted for the enzyme activities (e.g. dehydrogenase activity: 4.0 and 2.9 µg g⁻¹ h⁻¹ for organic and conventional management history, respectively). A lack of consistent positive links between enzyme activities and microbial biomass size indicated that similarly sized and structured microbial communities can express varying rates of activity. In two successive incubation experiments, the soils were amended with different rates of a lupin green manure (4 or 8t dry matter ha⁻¹), and different forms of N at 100 kg ha⁻¹ (urea and lupin) and incubated for 3 months. Samples were taken periodically, and in addition to soil biological properties and community structure, gross N mineralisation was determined. The form of N had a strong effect on microbial soil properties. Organic amendment resulted in a 2 to 5-fold increase in microbial biomass and enzyme activities, while microbial community structure was influenced by the addition or lack of C or N substrate. Correlation analyses suggested treatment-related differences in nutrient availability, microbial structural diversity (species richness or evenness) and physiological properties of the microbial community. The findings of this thesis showed that using green manures and crop rotations improved soil biology in both production systems, that no relationships existed between microbial structure, enzyme activities and N mineralisation, and that enzyme activities and microbial community structure are more closely associated with inherent soil and environmental factors, which makes them less useful as early indicators of changes in soil quality.

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.

From the Proceedings of the 1972 Meetings of the Arizona Section - American Water Resources Assn. and the Hydrology Section - Arizona Academy of Science - May 5-6, 1972, Prescott, Arizona / Storm runoff from the Tucson metropolitan area is unsuitable for most uses without processing. A lysimeter comprised of a grass and soil filter was constructed and is being evaluated as a water-quality treatment facility. The lysimeter is 200 feet long, 4 feet wide and 5 feet deep, and contains homogeneous calcareous loam covered by common grasses. Experimental apparatus was installed to divert less than a cubic foot per second of runoff from urbanized Arcadia Watershed. Runoff flows by gravity over the lysimeter, where surface inflow, surface outflow and subsurface outflow are measured and sampled. Four trials, each associated with a discrete runoff event, were conducted in the fall of 1971. Water samples were analyzed for inorganic chemical constituents, chemical oxygen demand (COD), coliforms, turbidity and sediment contents. Subsurface-outflow samples from initial trials were high in COD and total dissolved solids, representing soil flushing or leaching. Concentrations of inorganics reached a maximum value within a few hours of initial seepage, and then decreased. The peaking represents a salt build-up between trials. Concentrations of COD, coliforms, turbidity and sediment in subsurface-outflow samples decreased significantly during each trial. Surface-outflow samples had lower turbidity, COD, bacteria and sediment contents than surface-inflow samples. Turbidity, suspended and volatile solids, coliforms and COD in runoff samples may be reduced by grass and soil filtration. Increased grass development and soil settling work to produce a better quality effluent. Quantification of the lysimeter's effectiveness will be useful for urban watershed management.