In response to global climate change, many important earth-systems-oriented science programs have been established in the past. One such program, the Fluxnet program, studies the response of world forests and other natural ecosystems by measuring biospheric fluxes of carbon dioxide (CO2), water vapour, and energy with eddy-covariance (EC) techniques to assess the role of world ecosystems in offsetting increases in CO2 emissions and related impacts on global climate. The EC methodology has its limitations particularly when weather is inclement and during system stoppages. These limitations create non-trivial problems by creating data gaps in the monitored data stream, diminishing the integrity of the dataset and increasing uncertainty with data interpretation. This Thesis deals with the development of a parsimonious, semi-empirical approach for gap filling of net ecosystem productivity (NEP) data. The approach integrates the effects of environmental controls on diurnal NEP. The approach, because of its limited number of parameters, can be rapidly optimized when appropriate meteorological, site, and NEP target values are provided. The procedure is verified by applying it to several gap-filling case studies, including timeseries collected over balsam fir (Abies Balsamea (L.) Mill.) forests in New Brunswick (NB), Canada and several other forests along a north-south temperaturemoisture gradient from northern Europe to the Middle East. The evaluation showed that the model performed relatively well for most sites; i.e., r2 ranged from 0.68-0.83 and modelling efficiencies, from 0.89-0.97, demonstrating the possibility of applying the model to forests outside NB. Inferior model performance was associated with sites with less than complete input datasets.

This thesis explored the impacts of forest harvesting on gaseous elemental mercury emissions from forest soils in both field and laboratory studies, through novel use of enriched mercury isotope tracers. Forest floor Hg emissions, sourced from legacy deposition, increased proportionally to the vegetation quantity removed, with biomass harvesting most exacerbating emissions. Contemporary Hg deposition did not appear to be influenced by harvesting. Some of the tracer was rapidly lost to the atmosphere (~8%), but most was sequestered within the soil. Two regimes facilitating Hg emissions were observed in low-light conditions. Under extremely dry conditions deeper Hg sources (> 2cm depth) were as equally susceptible to emission as shallower sources. Following wetting to field capacity, emissions were elevated only from shallow sources, likely as a result of upward capillary transport. Impacts of vegetation removal and dry fluxes are previously uncharacterized and may constitute large additional sources to regional atmospheric Hg cycling.

This thesis explored the impacts of forest harvesting on gaseous elemental mercury emissions from forest soils in both field and laboratory studies, through novel use of enriched mercury isotope tracers. Forest floor Hg emissions, sourced from legacy deposition, increased proportionally to the vegetation quantity removed, with biomass harvesting most exacerbating emissions. Contemporary Hg deposition did not appear to be influenced by harvesting. Some of the tracer was rapidly lost to the atmosphere (~8%), but most was sequestered within the soil. Two regimes facilitating Hg emissions were observed in low-light conditions. Under extremely dry conditions deeper Hg sources (> 2cm depth) were as equally susceptible to emission as shallower sources. Following wetting to field capacity, emissions were elevated only from shallow sources, likely as a result of upward capillary transport. Impacts of vegetation removal and dry fluxes are previously uncharacterized and may constitute large additional sources to regional atmospheric Hg cycling.

Potatoes (Solanum tuberosum) were grown in a fine sandy loam soil in southern Manitoba in a three-year field study comparing four water management treatments: No Drainage with No Irrigation (NDNI), No Drainage with Overhead Irrigation (NDIR), Free Drainage with Overhead Irrigation (FDIR), and Controlled Drainage with Subirrigation (CDSI). The objectives of the study were (i) to evaluate the effect of the four treatments on yield and quality of potatoes, (ii) to evaluate the effect of water management on the environment, (iii) to estimate the shallow groundwater contribution to potato water requirement, and (iv) to simulate the shallow groundwater hydrology using the DRAINMOD and HYDRUS 1-D model. Subsurface drains were installed at 0.9 m depth and at spacings of 15 m (FDIR) and 8 m (CDSI). Subirrigation was done by pumping water back into the tiles through the drainage control structures. Overhead irrigation was carried out using a travelling gun. Water table depth, soil water content, drainage outflow, nutrient concentration in drainage water, irrigation rate, weather variables, potato yield and quality parameters, and biomass were measured. Compared to the NDNI treatment, the potato yield increase in the other treatments ranged between 15-32% in 2011 and 2-14% in 2012. In 2011, potato yield from FDIR was higher than CDSI (p = 0.011) and NDNI (p = 0.001), and yield from NDIR was higher than NDNI (p = 0.034). In 2012, potato yield was higher in FDIR in comparison to NDNI (p = 0.021). In 2012, the NDIR gave higher dark ends (p = 0.008) compared to other treatments. Under dry conditions, up to 92% of the potato crop water demand could be met by shallow groundwater contribution. Compared to free drainage, controlled drainage was able to lower the nitrate export by 98% (p = 0.033) in 2010 and by 67% (p = 0.076) in 2011, and the phosphate export decreased by 94% (p = 0.0117) in 2010. A major part of the drainage flow and nutrient export took place between April and June in southern Manitoba. DRAINMOD was able to accurately predict the shallow groundwater hydrology for this particular research site.

Near-surface soil moisture is a key state variable of the hydrologic cycle and plays a significant role in the global water and energy balance by affecting several hydrological, ecological, meteorological, geomorphologic, and other natural processes in the land-atmosphere continuum. Presence of soil moisture in the root zone is vital for the crop and plant life cycle. Soil moisture distribution is highly non-linear across time and space. Various geophysical factors (e.g., soil properties, topography, vegetation, and weather/climate) and their interactions control the spatio-temporal evolution of soil moisture at various scales. Understanding these interactions is crucial for the characterization of soil moisture dynamics occurring in the vadose zone. This dissertation focuses on understanding the spatio-temporal variability of near-surface soil moisture and the associated physical control(s) across varying measurement support (point-scale and passive microwave airborne/satellite remote sensing footprint-scale), spatial extents (field-, watershed-, and regional-scale), and changing hydro-climates. Various analysis techniques (e.g., time stability, geostatistics, Empirical Orthogonal Function, and Singular Value Decomposition) have been employed to characterize near-surface soil moisture variability and the role of contributing physical control(s) across space and time. Findings of this study can be helpful in several hydrological research/applications, such as, validation/calibration and downscaling of remote sensing data products, planning and designing effective soil moisture monitoring networks and field campaigns, improving performance of soil moisture retrieval algorithm, flood/drought prediction, climate forecast modeling, and agricultural management practices.

The last decade has been a period of great expansion and land use intensification for the New Zealand dairy farming industry with a 44% increase in national dairy cow numbers. Intensive dairy farming is now considered to be a major contributor to the deterioration in the quality of surface and ground water resources in some regions of New Zealand. Previous research has demonstrated intensive dairy farming is responsible for accelerated contamination of wateways by nutrients, suspended solids, pathogenic organisms and faecal material. A number of common dairy farming practices increase the risk of nutrient leaching. In particular, farm dairy effluent (FDE) has been implicated as a major contributor to the degradation of water quality. With the introduction of the Resource Management Act in 1991, the preferred treatment for FDE shifted away from traditional two-pond systems to land application. However, on most farms, irrigation of FDE has occurred on a daily basis, often without regard for soil moisture status. Therefore, it has been commonplace for partially treated effluent to drain through and/or runoff soils and contaminate fresh water bodies. The objectives of this thesis were to design and implement a sustainable land application system for FDE on difficult to manage, mole and pipe drained soils, and to assess the impacts of FDE application, urea application and cattle grazing events on nutrient losses via artificial drainage and surface runoff from dairy cattle grazed pasture. To meet these objectives a research field site was established on Massey University's No.4 Dairy farm near Palmerston North. The soil type was Tokomaru silt loam, a Fragiaqualf with poor natural drainage. Eight experimental plots (each 40 x 40 m) were established with two treatments. Four of the plots represented standard farm practice including grazing and fertiliser regimes. Another four plots were subjected to the same farm practices but without the fertiliser application and they were also irrigated with FDE. Each plot had an isolated mole and pipe drainage system. Four surface runoff plots (each 5 m x 10 m) were established as subplots (two on the fertilised plots and two on the plots irrigated with FDE) in the final year of the study. Plots were instrumented to allow the continuous monitoring of drainage and surface runoff and the collection of water samples for nutrient analyses. An application of 25 mm of FDE to a soil with limited soil water deficit - simulating a 'daily' irrigation regime - resulted in considerable drainage of partially treated FDE. Approximately 70% of the applied FDE left the experimental plots with 10 mm of drainage and 8 mm of surface runoff. The resulting concentrations of N and P in drainage and runoff were approximately 45% and 80% of the original concentrations in the applied FDE, respectively. From this single irrigation event, a total of 12.1 kg N ha-1 and 1.9 kg P ha-1 was lost to surface water representing 45% of expected annual N loss and 100% of expected annual P loss. An improved system for applying farm dairy effluent to land called 'deferred irrigation' was successfully developed and implemented at the research site. Deferred irrigation involves the storage of effluent in a two-pond system during periods of small soil moisture deficits and the scheduling of irrigation at times of suitable soil water deficits. Deferred irrigation of FDE all but eliminated direct drainage losses with on average <1 % of the volume of effluent and nutrients applied leaving the experimental plots. Adopting an approach of applying 'little and often' resulted in no drainage and, therefore, zero direct loss of nutrients applied. A modelling exercise, using the APSlM simulation model, was conducted to study the feasibility of practising deferred irrigation at the farm scale on No 4 Dairy farm. Using climate data for the past 30 years, this simulation exercise demonstrated that applying small application depths of FDE, such as 15 mm or less, provided the ability to schedule irrigations earlier in spring and decreased the required effluent storage capacity. A travelling irrigator, commonly used to apply FDE (a rotating irrigator), was found to have 2-3 fold differences in application depth and increased the risk of generating FDE contaminated drainage. New irrigator technology (an oscillating travelling irrigator) provided a more uniform application pattern allowing greater confidence that an irrigation depth less than the soil water deficit could be applied. This allowed a greater volume to be irrigated, whilst avoiding direct drainage of FDE when the soil moisture deficit is low in early spring and late autumn. A recommendation arising from this work is that during this period of low soil water deficits, all irrigators should be set to travel at their fastest speed (lowest application depth) to minimise the potential for direct drainage of partially treated FDE and associated nutrient losses. The average concentrations of N and P in both 2002 and 2003 winter mole and pipe drainage water from grazed dairy pastures were all well above the levels required to prevent aquatic weed growth in fresh water bodies. Total N losses from plots representing standard farm practice were 28 kg N ha-1 and 34 kg N ha-1 for 2003 and 2004, respectively. Total P losses in 2003 and 2004 were 0.35 kg P ha-1 and 0.7 kg P ha-1, respectively. Surface runoff was measured in 2003 and contributed a further 3.0 kg N ha-1and 0.6 kg P ha-1. A number of common dairy farm practices immediately increased the losses of N and P in the artificial drainage water. Recent grazing events increased NO3--N and DIP concentrations in drainage by approximately 5 mg litre-1 and 0.1 mg litre-1, respectively. The duration between the grazing and drainage events influenced the form of N loss due to a likely urine contribution when grazing and drainage coincide, but had little impact on the total quantity of N lost. Nitrogen loss from an early spring application of urea in 2002 was minimal, whilst a mid June application in 2003 resulted in an increased loss of NO3--N throughout 80 mm of cumulative drainage suggesting that careful timing of urea applications in winter is required to prevent unnecessary N leaching. Storage and deferred irrigation of FDE during the lactation season caused no real increase in either the total-N concentrations or total N losses in the winter drainage water of 2002 and 2003. In contrast, land application of FDE using the deferred irrigation system resulted in a gradual increase in total P losses over the 2002 and 2003 winter drainage seasons. However, this increase represents less than 4% of the P applied in FDE during the lactation season. An assessment of likely losses of nutrients at a whole-farm scale suggests that it is standard dairy farming practice (particularly intensive cattle grazing) that is responsible for the great majority of N and P loss at a farm scale. When expressed as a proportion of whole-farm losses, only a very small quantity of N is lost under an improved land treatment technique for FDE such as deferred irrigation. The management of FDE plays a greater role in the likely P loss at a farm scale with a 5% contribution to wholefarm P losses from deferred irrigation.

Bauxite mining is a major activity in the jarrah (Eucalyptus marginata Donn ex Sm.) forest of south-western Australia. After mining, poor tree growth can occur in some areas. This thesis aimed to determine whether soil constraints, including reduced depth and compaction, were responsible for poor tree growth at low-quality restored bauxite mines. In particular, this study determined the response of jarrah root morphology, leaf-scale physiology and growth/development to soil constraints at two contrasting (low-quality and high-quality) restored bauxite-mine sites. Jarrah root excavations at a low-quality restored site revealed that deep-ripping equipment failed to penetrate the cemented lateritic subsoil, causing coarse roots to be restricted to the top 0.5 m of the soil profile, resulting in fewer and smaller jarrah trees. An adjacent area within the same mine pit (high-quality site) had a kaolinitic clay subsoil, which coarse roots were able to penetrate to the average ripping depth of 1.5 m. Impenetrable subsoil prevented development of taproots at the low-quality site, with trees instead producing multiple lateral and sinker roots. Trees in riplines, made by deep-ripping, at the high-quality site accessed the subsoil via a major taproot, while those on crests developed large lateral and sinker roots. Bauxite mining is a major activity in the jarrah (Eucalyptus marginata Donn ex Sm.) forest of south-western Australia. After mining, poor tree growth can occur in some areas. This thesis aimed to determine whether soil constraints, including reduced depth and compaction, were responsible for poor tree growth at low-quality restored bauxite mines. In particular, this study determined the response of jarrah root morphology, leaf-scale physiology and growth/development to soil constraints at two contrasting (low-quality and high-quality) restored bauxite-mine sites. Jarrah root excavations at a low-quality restored site revealed that deep-ripping equipment failed to penetrate the cemented lateritic subsoil, causing coarse roots to be restricted to the top 0.5 m of the soil profile, resulting in fewer and smaller jarrah trees. An adjacent area within the same mine pit (high-quality site) had a kaolinitic clay subsoil, which coarse roots were able to penetrate to the average ripping depth of 1.5 m. Impenetrable subsoil prevented development of taproots at the low-quality site, with trees instead producing multiple lateral and sinker roots. Trees in riplines, made by deep-ripping, at the high-quality site accessed the subsoil via a major taproot, while those on crests developed large lateral and sinker roots.

[Truncated abstract] Self-filtration is here defined as particle detachment and re-deposition causing re-arrangement of the particles and therefore pore space which affects water flow in soil by decreasing hydraulic conductivity. This is of particular important in soils which are susceptible to structural breakdown. The objective of this thesis was to examine the dynamics of the self-filtration process in sodic sandy soils as affected by ionic strength and soil solution composition. The temporal changes of hydraulic conductivity and the elution of fine particles from soil columns were used as the main criteria to assess selffiltration. Two porous media exhibiting significantly different structural cohesion were examined, one a loamy sand (Balkuling soil) from agricultural land use and the second a mining residue from mineral sands operations . . . The effects of the composition of mixed calcium (Ca) and sodium (Na) ions in solution (sodium adsorption ratio (SAR)) on the exchange behaviour and saturated hydraulic conductivity were examined by carrying out batch binary exchange and saturated column transport experiments. A strong preference for Ca2+ ions in the exchange complex was observed for both soils. Generally K/Ko was found to decrease with increasing sodium adsorption ratio with the more structured Balkuling soil maintaining K/Ko for SARs 3 and 5 at an electrolyte concentration of 100 mmol/L. However measurements at the critical threshold and turbidity concentrations at a SAR of 15 revealed structural breakdown of the pore matrix system attributed to various extents of slaking, swelling, dispersion and decreases of pore radii as a result of selffiltration during leaching. These experiments illustrate the wide range of complex interactions involving clay mineralogy, solution composition and structural factors which can influence the extent of mobilization, transport and re-deposition of colloidal particles during the leaching process in soil profiles.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Exchanges of water in the soil-plant-atmosphere are controlled by physical-hydric soils, which in turn are highly variable in space and very sensitive to the use and soil management, especially in an agroecosystem. Precipitation, runoff, soil water storage and exchange of water vapor between the surface-atmosphere obtained from the eddy covariance and hydro-physical properties of soil were analyzed during the growing season (2009/2010) for no-till systems (NT) and conventional tillage (PC) in the cycle of soybean, in Cruz Alta, northwest of Rio Grande do Sul (RS). Most models that describe the interaction biosphere - atmosphere in agroecosystems has not efficiently represent physical differences for different soil management. In this sense, the study also will examine the response of the dynamic exchanges of water in the Agro-IBIS model when the soil physical properties in a system of management of PD (without revolution planting soil) and PC (with planting soil Revolution) are implemented. For this purpose, are used to soil properties of a long-term experiment in southern Brazil 2009/2010. Moreover, mathematical adjustments in leaf area index (LAI) is suggested to better represent the stage of leaf senescence. The results of the dynamics of soil water and evapotranspiration in the Agro-IBIS model for soybeans, when the implementation of soil properties and setting the IAF are compared with experimental data and with a simulation in which the soil property are described through the global database. The model represents satisfactorily the dynamics of soil water and evapotranspiration for both management systems, especially for wet periods. The results presented for the conventional management system are best correlated with the simulations, when the physical properties of this system are implemented and leaf senescence is corrected. Of the major changes that have been added, such as setting physical properties of soil, definition of the retention curve coefficients, and phenology of the crop, the main one was the consideration of a new factor of decline in leaf area index during senescence which greatly reduced the error in water balance components of the surface of soybean. / As trocas de água no sistema solo-planta-atmosfera são controladas pelas características físico-hídricas dos solos, que por sua vez são altamente variáveis no espaço e muito sensíveis ao uso e manejo do solo, principalmente em um agroecossistema. Precipitação, escoamento, armazenamento de água do solo e trocas de vapor de água entre superfície-atmosfera obtido a partir da covariância turbulenta e propriedades físico-hídricas do solo foram analisados durante a estação de cultivo (2009/2010) para os sistemas de plantio direto (PD) e plantio convencional (PC) no ciclo da cultura da soja, no município de Cruz Alta, região noroeste do Rio Grande do Sul (RS). A maioria dos modelos que descrevem a interação biosfera - atmosfera em agroecossistemas ainda não representam de forma eficiente às diferenças físicas para diferentes manejos do solo. Neste sentido, o estudo, também analisará a resposta da dinâmica das trocas de água no modelo Agro-IBIS quando as propriedades físicas do solo em um sistema de manejo de PD (plantio sem revolução do solo) e PC (plantio com revolução do solo) são implementadas. Para tanto, são usados às propriedades do solo de um experimento de longo prazo no sul do Brasil 2009/2010. Além disso, ajustes matemáticos no índice de área foliar (IAF) são sugeridos para melhor representar o estágio de senescência foliar. Os resultados da dinâmica da água no solo e evapotranspiração no modelo Agro-IBIS para a soja, quando da implementação das propriedades do solo e do ajuste no IAF são comparados com os dados experimentais e com uma simulação em que as propriedade do solo são descritas através do banco de dados globais. O modelo representa satisfatoriamente a dinâmica da água no solo e evapotranspiração para ambos os sistemas de manejo, especialmente para períodos úmidos. Os resultados apresentados para o sistema de manejo convencional estão melhores correlacionados com as simulações, quando as propriedades físicas deste sistema são implementadas e a senescência foliar é corrigida. Das principais mudanças que foram adicionadas, tais como o ajuste de propriedades físicas do solo, definição de coeficientes da curva de retenção, e fenologia da cultura, a principal foi à consideração de um novo fator de declínio do índice de área foliar na fase de senescência que reduziu sobremaneira o erro nas componentes do balanço de água da superfície de soja.

Eucalyptus plantations have increased significantly in recent times, but the productivity of forests are very sensitive to the availability of natural resources such as water, nutrients and light. In order to assess the water dynamics and characterize water flows in soil in a eucalyptus plantation in replacement of native grassland, there was a study in the city of São Francisco de Assis, RS, located in the “Bioma Pampa. Different densities were evaluated: 3,5x3,5m; 3,5x1,75m; 1,75x1,75m and 1,75x0,75m. The overall distribution of rainfall internal precipitation, straining the trunk interception losses of the canopy the and soil volumetric water content were evaluated during a period of one year. Three pluviometers were installed in the field area to measure and collect global precipitation. To measure the internal precipitation, 36 pluviometers were installed inside the plantation and 36 collectors were used (in selected trees) to determine the stemflow. The soil volumetric water content was monitored continuously to a depth of 2.10 m, using an automated TDR. The evapotranspiration was determined by the water balance equation, using the mass conservation method. The relationship between the biomass increase and the water amount transpired in different planting spacing, allow estimating the efficiency of water use by eucalyptus trees. The effective rainfall is higher in a narrower spacing plant, due to the increased water intake by stemflow, which results in lower treetop interception. The interception rate is lower in higher rainfall and decreases with increasing density of trees in the settement. The average evapotranspiration ranged from 4.0 to 4.5 mm day-1, with similar values among different planting spacings and is reduced in low-rainfall periods. There were no adverse effects on water resources and soil water regime due to the eucalyptus replacing natural herbaceous vegetation reforestation in Pampa Biome, evidenced by the soil water content that never was less than the value of permanent wilting point (1.5MPa). The water efficient use of Eucalyptus dunnii with 6 years old in the “Pampa biome” region varies from 3.27 to 2.40 g L-1. / As plantações de eucalipto vêm aumentando significativamente nos últimos tempos, porém a produtividade das florestas são muito sensíveis à disponibilidade de recursos naturais como água, nutrientes e luz. Com o objetivo de avaliar a dinâmica da água e caracterizar os fluxos hídricos no solo em uma povoamento de eucalipto em substituição à vegetação de campo nativo, realizou-se um estudo no município de São Francisco de Assis, Rs, localizado no Bioma Pampa. Foram avaliadas diferentes densidades populacionais: 3,5x3,5m; 3,5x1,75m 1,75x1,75m; 1,75x0,75m. Durante o período de um ano foram avaliados a distribuição da precipitação global em precipitação interna, o escoamento pelo tronco, as perdas por interceptação do dossel, bem como o conteúdo volumétrico de água no solo. Três pluviômetros foram instalados na área de campo para medir e coletar a precipitação global. Para medir a precipitação interna, 36 pluviômetros foram instalados no interior do plantio e 36 coletores foram utilizados (em árvores selecionadas) para determinar o escorrimento pelo tronco. O conteúdo volumétrico de água do solo foi monitorado continuamente até a profundidade de 2,10m, utilizando-se sondas e TDR automatizado. A evapotranspiração das árvores foi determinada pela equação do balanço hídrico, através do método da conservação de massas. A relação entre o incremento da biomassa aérea e o volume de água evapotranspirada nos diferentes espaçamentos de plantio, permitiu estimar a eficiência do uso da água pelas árvores de eucalipto. A precipitação efetiva é maior em espaçamentos mais adensados, em função da maior entrada de água pelo escoamento pelo tronco, o que resulta em menor interceptação pelas copas das árvores. A taxa de interceptação é menor em precipitações maiores e diminui com o aumento da densidade de árvores no povoamento. A evapotranspiração média variou de 4,0 a 4,5mm/dia, com valores muito próximos entre os diferentes espaçamentos sendo reduzida nas épocas de menor precipitação. Não houve nenhum efeito adverso sobre os recursos hídricos e o regime da água do solo em decorrência do reflorestamento de eucalipto em substituição da vegetação herbácea natural no Bioma Pampa, comprovado pelo conteúdo de água no solo, nunca foi inferior ao valor do ponto de murcha permanente (1,5Mpa). O uso eficiente da água para Eucalyptus dunnii de 6 anos de idade na região do Bioma Pampa varia de 3,27 a 2,40 g L-1, com os maiores valores no espaçamento mais amplo.