<p>Northern peatlands (>45°N) mostly initiated during the Holocene and have been a large C sink to the atmosphere. Northern peatland formation prefers wet and cold condition where the productivity persistently exceeds decomposition and thereby C accumulates. As the northern high latitude region is likely to be warmer in the future, whether northern peatlands will continue being C sinks or switch to C sources is uncertain. To address this issue, I revise and apply a process-based model designed for describing peatland biogeochemical processes, Peatland Terrestrial Ecosystem Model (PTEM), to simulate the C dynamics at both site and regional level, from 15 ka BP-2300. For the site-level simulation, PTEM 1.0 is substantially revised into PTEM 2.0 in terms of peat accumulation process, plant functional types, productivity and decomposition, and soil thermal properties. A simulation from peat initiation to 2300 is conducted for three northern peatland sites. I found PTEM 2.0 can effectively capture the historical C accumulation progress, when compared with the observation. The future simulation indicates northern peatlands have reduced C sink capacity or switch to a C source under N insufficiency and water table deepening. </p> <p>Afterwards, a historical pan-Arctic simulation during 15ka BP-1990 is conducted. PTEM 2.0 is revised into PTEM 2.1 by adding spatially-explicit run-on and run off processes. The spatially-explicit peat initiation dataset is derived from neural network approach and a spatially-explicit peat expansion trend is established on top of it. My estimated pan-Arctic peatland C storage is 396-421 Pg C with the long-term C accumulation rate (CAR) of 22.9 g C∙m-2 yr-1. The simulated spatial distribution of peat C and the temporal pattern of CAR both agree with literature values. I analyzed northern peatlands’ response to historical climate change since 0.5 ka BP and found decreased CAR in the warmer non-permafrost and permafrost-thaw region, while the opposite was found in the colder permafrost region. The results indicate warmer southern peatlands will first switch to a C source under warming while more northern peatlands will become larger sinks. </p> <p>Based on the result of historical simulation, a future simulation is conducted for 1990-2300 with peatland expansion/shrinkage considered. PTEM 2.1 is revised into PTEM 2.2 such that the water table depth, run-on and run-off are estimated from a TOPMODEL approach. In the 21st century, northern peatlands are projected to be a C source of 1.2-13.3 Pg C under five out of six climate scenarios. During 2100-2300, northern peatlands under all scenarios are a C source under all climate scenarios. Northern peatlands switch to C sources due to deepening water table depth, insufficient N availability, and plant functional type shift. I found that northern peatlands remain as a C sink until a mean pan-Arctic peatlands annual temperature reaches -2.09 - -2.89°C. This study predicts a northern peatland sink to a source shift around 2050, earlier than previous estimates of after 2100, and emphasizes the vulnerability of northern peatlands to climate change. </p>

In Peru, nearly 32 million people rely heavily on human-made coastal irrigation agricultural hubs that rely on water from melting glaciers, snowpack, and rain transported by rivers and canals from high in the Andes. However, Peru’s water resources are in a vulnerable state as climate change has shifted rainfall patterns causing glacier retreat affecting nearly the loss of one-third of the glaciers. In recent decades, an increase and expansion of irrigation projects in Peru require agriculture practices to consider environmental impacts directly. Now is the time to explore the sustainability of the desert agroecosystems and understand how different water management practices influence the supporting soil’s health so decision-makers can plan for future change in water resources and any feedbacks to the productivity of the soils. Over the past 40 years, Peru has led some of the largest scale water management projects on earth to convert infertile coastal desert soils into irrigated agricultural land. Still, these efforts can come at a severe local cost with impacts to groundwater quality, salination of the soil, toxic concentrations of trace metals due to evaporation, and overuse of fertilizer and pesticides. This thesis presents a study to assess how drip irrigation impacts desert soil chemistry within one of Peru’s desert irrigation projects in Arequipa’s southern district. We explored a chronosequence of drip irrigation in vineyards of 9-, 16- and 35- years. Results showed that both soil carbon and salinity accumulated progressively over time but that spatial accumulation patterns were influenced by proximity to the irrigation drip line. By 35 years, salinity levels exceeded what would be tolerances for most crops. Trace metals, such as Mn, Zn, and Ni, increased with time under drip irrigation and have significant relationships with Fe, present in the highest concentrations, seemingly controlling the patterns due to co-precipitation. However, no trace metals were found in quantities that would exceed Peru’s limits for agricultural soils. While drip irrigation is considered a water conservation strategy and widely promoted in the region over other irrigation techniques like high water volume furrow irrigation, its use may accelerate localized negative impacts to surface soil health. These progressive changes highlight the need for effective monitoring and salinity mitigation strategies in the region. This project is part of the bilateral technical program between Purdue University and Universidad Nacional San Agustín (UNSA) called the Arequipa Nexus Institute for Food, Water, Energy, and the Environment.

<div>In fire-prone forests, tree taxa and burn temperature are the major controllers of the chemical and physical properties of pyrogenic organic matter (PyOM), the aromatic carbon-rich product of the incomplete combustion of plant biomass, that accumulates in soil in such settings. These controls also dictate how soil microbes can degrade plant C once it enters into soil as previous studies demonstrate that increased fire temperature results in low PyOM degradability but also impacts the decomposition of the original soil. However, we know little about how taxa and temperature of C-inputs impact the production and accumulation of cellular residues from soil microbes, which can be the dominant source of stabilized soil organic matter in many ecosystems. </div><div>This work presents the results of the analysis of soil microbial amino sugars, as proxies for soil microbial necromass, from long-term soil incubation experiments, 180 and 600 days, that were amended with jack pine (JP) and red maple (RM) wood or their PyOM produced at 300°C or 450°C. Both wood taxa amendments resulted in an increase in microbial sugar residues compared to non-amended soils but RM, the taxa with the highest proportion of soluble sugars and low tannin content, exhibited the highest percentage increase. Soils amended with PyOM exhibited lower amino sugar content as compared to their wood but no difference compared to controls (non-amended soils). There was no difference in soil amino sugars observed between the PyOM derived from the two taxa nor between the temperature of pyrolysis, possibly due to only small amounts of bioavailable C and N in the PyOM. Total amino sugar concentrations varied significantly between PyOM and fresh wood treatments, with PyOM treatments yielding 659 – 730 μg/ g soil while wood treatments yielded 757 – 930 μg/ g soil early in incubations. While fungal-derived amino sugars were dominated in all treatments, longer soil incubation time, 600 days vs 180 days, resulted in a proportionately greater decrease bacterial-derived amino sugars. Overall, at 180 days, PyOM treatments exhibited 19-27% of soil N and 4-5% of soil C quantifiable as amino sugars while wood treatments exhibited 27-28% of total soil N and 6-7% of total soil C as amino sugars. This work shows, for the first time, that on a per C or per N basis, PyOM versus fresh wood addition to soils will result in a net depletion of microbial residues. The variable response in amino sugars between treatments and incubation time highlights the importance and dynamic nature of the physicochemical characteristics of organic matter input to soil in controlling the contribution of soil microbial residues to that soil. </div><div><br></div>

<p dir="ltr">Globally, soils hold more carbon than both the atmosphere and aboveground terrestrial biosphere combined. Changes in land use and land cover have the potential to alter soil carbon cycling throughout the soil profile, from the surface to meters deep, yet most studies focus only on the near surface impact (< 25 cm deep). This research bias toward shallow soil carbon cycling has ramifications for understanding the full impacts of agricultural and restoration management practices on soil organic and inorganic carbon dynamics. The primary objective of my thesis research is to evaluate the factors controlling the impact of deep-rooting perennial grass on soil carbon cycling during prairie restoration of soil following long term, row crop agriculture. Paired soil pits were established to compare the effects of restoration on soil C dynamics in a corn-soy cropping system (minimal tillage) and restored prairie sites in Nebraska and Illinois. At each site, soil organic carbon (SOC) and inorganic carbon (SIC) content, stock, and stable carbon isotope analysis were preformed to ~2 m depth to assess long term integrated C dynamics. Estimating the contribution of prairie carbon inputs to the SOC in the soil profile was examined using stable carbon isotopic signatures in the SOC in relation to the above ground vegetation changes in C₃ and C₄ photosynthetic pathway plant community composition. Comparative analysis of edaphic properties and soil carbon suggests that deep loess deposits in Nebraska permit enhanced water infiltration and SOC deposition to depths of ~100 cm in 60 years of prairie restoration. In Illinois, poorly drained, clay/lime rich soils on glacial till and a younger restored prairie age (15 years) restricted the influence of prairie restoration to the upper 30 cm. Comparing the δ¹³C values of SOC and SIC in each system demonstrated that SIC at each site is likely of lithogenic origin. This work indicates that the magnitude of influence of restoration management is dependent on edaphic properties inherited from geological and geomorphological controls. Future work should quantify root structures and redox properties to better understand the influence of rooting depth on soil carbon concentrations. Fast-cycling C dynamics can be assessed using continuous, in-situ CO₂ and O₂ soil gas concentration changes. The secondary objective of my thesis was to determine if manual, low temporal resolution gas sampling and analysis are a low cost and effective means of measuring soil O₂ and CO₂, by comparing it with data from in-situ continuous (hourly) sensors. Manual analysis of soil CO₂ and O₂ from field replicates of buried gas collection cups resulted in measurement differences from the continuous sensors. Measuring CO2 concentration with manual methods often resulted in higher concentrations than hourly, continuous measurements across all sites. Additionally, O₂ concentrations measured by manual methods were higher than hourly values in the restored prairie and less in agricultural sites. A variety of spatial variability, pressure perturbations, calibration offsets, and system leakage influences on both analysis methods could cause the discrepancy.</p>

This thesis investigates the abiotic control of carbon (C) and water vapour fluxes (FCO₂ and E, respectively) in a New Zealand Pinus radiata D. Don plantation and a nearby clearcut. It concentrates on the limitation of these fluxes imposed by growing season soil water deficit. This results from low precipitation (658 mm a⁻¹) in combination with a limited root zone water storage capacity of the very stony soil (> 30% by volume). The thesis analyses results from seven eddy covariance flux measurement campaigns between November 1994 and March 1996. The study site was located in Balmoral Forest, 100 km north-west of Christchurch (42° 52' S, 172° 45' E), in a (in November 1994) 8-year-old stand. One set of measurements was conducted in an adjacent clearcut. Ecosystem flux measurements were accompanied by separate measurements of ground fluxes and of the associated environmental variables. Flux analysis focussed on the underlying processes of assimilation (Ac), canopy stomatal conductance (Gc) and respiration (Reco), using biophysical models coupled to soil water balance and temperature subroutines. Aiming to link time inegrated net ecosystem C (NEP) to tree growth, sequestration in tree biomass (NPP) was quantified by regular measurements of stem diameter using allometric relationships. Average rates of FCO₂ and E were highest in spring (324 mmol m⁻² d⁻¹ and 207 mol m⁻² d⁻¹, respectively) when the abiotic environment was most favourable for Gc and Ac. During summer, fluxes were impeded by the depletion of available soil water (θ) and the co-occurrence of high air saturation deficit (D) and temperature (T) and were equal or smaller than during winter (FCO₂ = 46 mmol m⁻² d⁻¹ in summer and 115 mmol m⁻² d⁻¹ in winter; E = 57 and 47 mol m⁻² d⁻¹, respectively). With increasingly dry soil, fluxes and their associated ratios became predominantly regulated by D rather than quantum irradiance, and on particularly hot days the ecosystem was a net C source. Interannually, forest C and water fluxes increased strongly with rainfall, and the simultaneously reduced D and T. For two succeeding years, the second having 3 % more rain, modelled NEP was 515 and 716 g C m⁻² a⁻¹, Ac 1690 and 1841 g C m⁻² a⁻¹ and Reco 1175 and 1125 g C m⁻² a⁻¹. NEP / E increased in wetter (and cooler) years (1.3 and 1.5 g kg⁻¹), reflecting a relatively larger gain in NEP. Responding mainly to increased rainfall during commonly dry parts of the year (ie summer), and reflecting the otherwise benign maritime climate of New Zealand, NEP during the winter months could exceed NEP during the middle of the notional tree growing season. Annual Ac, NEP, and NPP were strongly linearly related. This relation did not hold during bi-weekly periods when the processes of intermediate C storage were influential. Separate knowledge of tree growth and C fluxes allowed quantification of autotrophic, and heterotrophic respiration (Rhet≈ 0.4 NEP), as well as fine-root turnover (≈0.2 NEP). The ratio of NEP and stem volume growth was conservative (0.24 t C m⁻³) and allows a direct connection to be made between ecosystem carbon fluxes and forest yield tables. In the absence of living roots, the clearcut flux measurements demonstrated the expected limitation of Rhet by soil temperature (Ts) and θ. However, an additional 'pumping effect' was discovered at the open site whereby turbulence increased CO₂ efflux considerably when the soil surface was wet. Accounting for the combined effects of Ts, θ and turbulence, annual Rhet at the clear-cut site (loss to the atmosphere) was »50 % of NEP (C sequestered from the atmosphere) in the nearby forest. Clearly, there is an important contribution of C fluxes during early stages of ecosystem development to the total C sequestered over the lifetime of a plantation.

<p>Methane (CH₄) is the second most powerful greenhouse gas (GHG) behind carbon dioxide (CO₂), and is able to trap a large amount of long-wave radiation, leading to surface warming. Carbon monoxide (CO) plays an important role in controlling the oxidizing capacity of the atmosphere by reacting with OH radicals that affect atmospheric CH₄ dynamics. Terrestrial ecosystems play an important role in determining the amount of these gases into the atmosphere. However, global quantifications of CH₄ emissions from wetlands and its sinks from uplands, and CO exchanges between land and the atmosphere are still fraught with large uncertainties, presenting a big challenge to interpret complex atmospheric CH₄ dynamics in recent decades. In this dissertation, I apply modeling approaches to estimate the global CH₄ and CO exchanges between land ecosystems and the atmosphere and analyze how they respond to contemporary and future climate change.</p> <p>Firstly, I develop a process-based biogeochemistry model embedded in Terrestrial Ecosystem Model (TEM) to quantify the CO exchange between soils and the atmosphere at the global scale (Chapter 2). Parameterizations were conducted by using the CO <i>in situ</i> data for eleven representative ecosystem types. The model is then extrapolated to global terrestrial ecosystems. Globally soils act as a sink of atmospheric CO. Areas near the equator, Eastern US, Europe and eastern Asia will be the largest sink regions due to their optimum soil moisture and high temperature. The annual global soil net flux of atmospheric CO is primarily controlled by air temperature, soil temperature, SOC and atmospheric CO concentrations, while its monthly variation is mainly determined by air temperature, precipitation, soil temperature and soil moisture. </p> <p>Secondly, to better quantify the global CH₄ emissions from wetlands and their uncertainties, I revise, parameterize and verify a process-based biogeochemical model for methane for various wetland ecosystems (Chapter 3). The model is then extrapolated to the global scale to quantify the uncertainty induced from four different types of uncertainty sources including parameterization, wetland type distribution, wetland area distribution and meteorological input. Spatially, the northeast US and Amazon are two hotspots of CH₄ emissions, while consumption hotspots are in the eastern US and eastern China. The relationships between both wetland emissions and upland consumption and El Niño and La Niña events are analyzed. This study highlights the need for more in situ methane flux data, more accurate wetland type and area distribution information to better constrain the model uncertainty.</p> <p>Thirdly, to further constrain the global wetland CH₄ emissions, I develop a predictive model of CH₄ emissions using an artificial neural network (ANN) approach and available field observations of CH₄ fluxes (Chapter 4). Eleven explanatory variables including three transient climate variables (precipitation, air temperature and solar radiation) and eight static soil property variables are considered in developing the ANN models. The models are then extrapolated to the global scale to estimate monthly CH₄ emissions from 1979 to 2099. Significant interannual and seasonal variations of wetland CH₄ emissions exist in the past four decades, and the emissions in this period are most sensitive to variations in solar radiation and air temperature. This study reduced the uncertainty in global CH₄ emissions from wetlands and called for better characterizing variations of wetland areas and water table position and more long-term observations of CH₄ fluxes in tropical regions.</p> <p>Finally, in order to study a new pathway of CH₄ emissions from palm tree stem, I develop a two-dimensional diffusion model. The model is optimized using field data of methane emissions from palm tree stems (Chapter 5). The model is then extrapolated to Pastaza-Marañón foreland basin (PMFB) in Peru by using a process-based biogeochemical model. To our knowledge, this is among the first efforts to quantify regional CH₄ emissions through this pathway. The estimates can be improved by considering the effects of changes in temperature, precipitation and radiation and using long-period continuous flux observations. Regional and global estimates of CH₄ emissions through this pathway can be further constrained using more accurate palm swamp classification and spatial distribution data of palm trees at the global scale.</p>

<p>This thesis is a collection of three research articles to quantify carbon fluxes and isotopic signature changes across global terrestrial ecosystems. Chapter 2, the first article of this thesis, focuses on the importance of an under-estimated methane soil sink for contemporary and future methane budgets in the pan-Arctic region. Methane emissions from organic-rich soils in the Arctic have been extensively studied due to their potential to increase the atmospheric methane burden as permafrost thaws. However, this methane source might have been overestimated without considering high affinity methanotrophs (HAM, methane oxidizing bacteria) recently identified in Arctic mineral soils. From this study, we find that HAM dynamics double the upland methane sink (~5.5 TgCH₄yr^-1) north of 50°N in simulations from 2000 to 2016 by integrating the dynamics of HAM and methanogens into a biogeochemistry model that includes permafrost soil organic carbon (SOC) dynamics. The increase is equivalent to at least half of the difference in net methane emissions estimated between process-based models and observation-based inversions, and the revised estimates better match site-level and regional observations. The new model projects double wetland methane emissions between 2017-2100 due to more accessible permafrost carbon. However, most of the increase in wetland emissions is offset by a concordant increase in the upland sink, leading to only an 18% increase in net methane emission (from 29 to 35 TgCH₄yr^-1). The projected net methane emissions may decrease further due to different physiological responses between HAM and methanogens in response to increasing temperature. This article was published in <i>Nature Climate Change</i> in March 2020.</p> <p>In Chapter 3, the second article of this thesis, I develop and validate the first biogeochemistry model to simulate carbon isotopic signatures (δ¹³C) of methane emitted from global wetlands, and examined the importance of the wetland carbon isotope map for studying the global methane cycle. I incorporated a carbon isotope-enabled module into an extant biogeochemistry model to mechanistically simulate the spatial and temporal variability of global wetland δ¹³C-CH₄. The new model explicitly considers isotopic fractionation during methane production, oxidation, and transport processes. I estimate a mean global wetland δ¹³C-CH₄ of -60.78‰ with its seasonal and inter-annual variability. I find that the new model matches field chamber observations 35% better in terms of root mean square estimates compared to an empirical static wetland δ¹³C-CH₄ map. The model also reasonably reproduces the regional heterogeneity of wetland δ¹³C-CH₄ in Alaska, consistent with vertical profiles of δ¹³C-CH₄ from NOAA aircraft measurements. Furthermore, I show that the latitudinal gradient of atmospheric δ¹³C-CH₄ simulated by a chemical transport model using the new wetland δ¹³C-CH₄ map reproduces the observed latitudinal gradient based on NOAA/INSTAAR global flask-air measurements. I believe this study is the first process-based biogeochemistry model to map the global distribution of wetland δ¹³C-CH₄, which will significantly help atmospheric chemistry transport models partition global methane emissions. This article is in preparation for submission to <i>Nature Geoscience</i>.</p> <p>Chapter 4 of this thesis, the third article, investigates the importance of leaf carbon allocation for seasonal leaf carbon isotopic signature changes and water use efficiency in temperate forests. Temperate deciduous trees remobilize stored carbon early in the growing season to produce new leaves and xylem vessels. The use of remobilized carbon for building leaf tissue dampens the link between environmental stomatal response and inferred intrinsic water use efficiency (iWUE) using leaf carbon isotopic signatures (δ¹³C). So far, few studies consider carbon allocation processes in interpreting leaf δ¹³C signals. To understand effects of carbon allocation on δ¹³C and iWUE estimates, we analyzed and modeled the seasonal leaf δ¹³C of four temperate deciduous species (<i>Acer saccharum, Liriodendron tulipifera, Sassafras albidum, </i>and <i>Quercus alba</i>) and compared the iWUE estimates from different methods, species, and drought conditions. At the start of the growing season, leaf δ¹³C values were more enriched, due to remobilized carbon during leaf-out. The bias towards enriched leaf δ¹³C values explains the higher iWUE from leaf isotopic methods compared with iWUE from leaf gas exchange measurements. I further showed that the discrepancy of iWUE estimates between methods may be species-specific and drought sensitive. The use of δ¹³C of plant tissues as a proxy for stomatal response to environmental processes, through iWUE, is complicated due to carbon allocation and care must be taken when interpreting estimates to avoid proxy bias. This article is in review for publication in <i>New Phytologist</i>.</p> <p> </p>

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.

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.

<p>Current watershed-scale, nonpoint source (NPS) pollution models do not represent the processes and impacts of agricultural best management practices (BMP) on water quality with sufficient detail. To begin addressing this gap, a novel process-based, watershed-scale, water quality model (WEPP-WQ) was developed based on the Water Erosion Prediction Project (WEPP) and the Soil and Water Assessment Tool (SWAT) models. The proposed model was validated at both hillslope and watershed scales for runoff, sediment, and both soluble and particulate forms of nitrogen and phosphorus. WEPP-WQ is now one of only two models which simulates BMP impacts on water quality in ‘high’ detail, and it is the only one not based on USLE sediment predictions. Model validations indicated that particulate nutrient predictions were better than soluble nutrient predictions for both nitrogen and phosphorus. Predictions of uniform conditions outperformed nonuniform conditions, and calibrated model simulations performed better than uncalibrated model simulations. Applications of these kinds of models in real-world, historical simulations are often limited by a lack of field-scale agricultural management inputs. Therefore, a prototype tool was developed to derive management inputs for hydrologic models from remotely sensed imagery at field-scale resolution. At present, only predictions of crop, cover crop, and tillage practice inference are supported and were validated at annual and average annual time intervals based on data availability for the various management endpoints. Extraction model training and validation were substantially limited by relatively small field areas in the observed management dataset. Both of these efforts contribute to computational modeling research and applications pertaining to agricultural systems and their impacts on the environment.</p>