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Item Effect of increasing cow urine patch area on nitrogen losses from grazed pastures : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) in Soil Science at Massey University, Palmerston North, New Zealand(Massey University, 2024) Hedges, May TanaThe expansion and intensification of dairy farming in New Zealand (NZ) over the last few decades has made a major contribution to the country’s greenhouse gas emissions, and to the nitrogen (N) enrichment of its surface and ground waters. The environmental concerns associated with dairy farming have led researchers to investigate potential mitigations to reduce N losses from cow urine patches, which are the main source of N losses. However, there has been little research conducted on the effect of increasing the spread area of urine patches as a mitigation for N losses. The development of a prototype urine spreading device, intended to be worn by cows during summer and autumn, has made such a mitigation possible. The primary aim of this device is to provide a method to reduce nitrate (NO₃⁻) leaching, by directly reducing the N application rate in the urine patch. The impact of increasing the size of the urine patch on N emissions to the atmosphere is also an important consideration. Research was required to quantify the effects of increasing urine spread on N losses from urine patches. This research quantified the effect of increasing the urine patch spread area on ammonia (NH₃) and nitrous oxide (N₂O) emissions, and on NO₃⁻ leaching losses. The first field experiment was conducted in early autumn on Dairy Farm 1, Massey University, near Palmerston North, New Zealand. The soil at the site is a Manawatu silt loam. Three urine application depth treatments of 10 mm, 5 mm and 2.5 mm were applied to an area (0.018 m²) inside a series of 20 chambers (5 replicates). These treatments represented the depths that would result from applying 2.5 L of urine to three different patch areas: 0.25 m² (i.e. typical patch size), 0.5 m² and 1 m², respectively. A control treatment with no urine applied was also included. The concentration of total N in applied urine was 4.53 g N L⁻¹. Ammonia measurements were conducted over a period of 20 days using the Dynamic Chamber method. Soil samples were also collected periodically from adjacent treatment plots to measure mineral-N (nitrate and ammonium), soil moisture and pH. The results showed that increasing the urine patch area from 0.25 to 1 m² has increased total NH₃ emissions from 25 to 36% of the total urine-N applied and, consequently the emission factor also increased. This NH₃ increase also increases indirect N₂O emissions, which can have an influence on annual emissions. However, the loss of NH₃ from the urine patch also reduces the amount of urinary N that is available for subsequent direct N₂O emissions and NO₃⁻ leaching. The second and third field experiments were carried out on Dairy Farm 4, Massey University. The soil type at both sites is the Tokomaru silt loam soil. One of the field experiments involved urine application in early-autumn and the other in early-winter. Urine collected from lactating dairy cows was applied to small, mowed plots at application depths of 10 mm (applied to 0.25 m²), 5 mm (applied to 0.5 m²) and 2.5 mm (applied to 0.5 m² and results were extrapolated to a notional patch area of 1 m²). A control treatment with no urine applied was also included. All treatments were replicated five times. Gas sampling was conducted in the field using the static chamber method (chamber area of 0.50 m²). The results of these studies showed that increasing the size of the urine patches from 0.25 to 1 m² with the same volume of urine-N in early-winter did not significantly increase N₂O emissions and emission factors (EF₃). Although increasing the urine patch area increased N₂O emission by 39%, this difference was not large enough to be statistically significant (P>0.05). However, for the first 14 days of total N₂O emissions, the 1 m² urine patch treatment was statistically different (P<0.05) from the 0.25 m² urine patch treatment. In contrast, increasing the size of the urine patches from 0.25 to 1 m² in early-autumn decreased N₂O emissions and EF₃ by 56% (P<0.05). The different effect of increasing the urine patch area in these two different seasons, is likely to be attributed to the differences in soil moisture conditions at the time of urine application and the weeks that followed. To determine the overall effect on N₂O emissions, the reduction in N₂O emissions in autumn was compared with the increase in NH₃ emissions at this time using the N₂O inventory emission value of 0.1 for indirect emissions. These indirect N₂O emissions was estimated to be about 3.6 times higher than the reduction in direct N₂O emissions. Therefore, the use of a urine spreading device to increase the spread area of cow urine in autumn is expected to result in greater overall accumulation of N₂O in the atmosphere. The fourth experiment was conducted on Dairy Farm 4, Massey University. The experimental paddock consisted of twelve pasture plots measuring 800 m² per plot, with separate mole and pipe drainage systems. There were two treatments and six replicates of each treatment. The treatments were cows wearing urine-spreading devices (‘Device’ treatment) and without the device (‘Control’ treatment). The devices were used on four grazing events over the late summer and autumn period. Drainage water from the plots was monitored and analysed for total N and NO₃⁻-N, and pasture accumulation measurements were also conducted. Overall N leaching losses were low, and the differences in total N and NO₃⁻ leaching between the two treatments were small and not statistically significant (P>0.05). There were also no differences in pasture accumulation over a 9-month period. Further improvements to the device are required to consistently increase the spread area of urine patches and the uniformity of the spread. The improved device should then be evaluated over a number of years to assess its potential to reduce leaching of N and its impact on N gaseous emissions to the atmosphere.Item Phosphorus speciation in submerged agricultural soils : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Soil Science at Massey University, Palmerston North, New Zealand(Massey University, 2024) Palihakkara, JananiPhosphorus (P) management in submerged agricultural soils is challenging as release of P in such soils occurs due to complex hydrological and biogeochemical processes that are influenced by inherent soil characteristics and external factors such as climate and agronomic practices. Thus, in depth understanding of P speciation in submerged agricultural soils is crucial to optimise P management and mitigate environmental risks, ensuring the sustainability of agricultural systems in diverse climatic regions. This thesis explores the dynamics of P speciation in submerged agricultural soils via three studies: one focusing on transformation of P in inorganic P fertiliser applied tropical paddy soils under long-term (>2 months) submergence to provide fundamental understanding of P dynamics in those soils to support inconsistent response of rice yields for applied P, and the others focusing on the potential risk of dissolved P release in critical source areas (CSAs) in temperate soils under short-term (hours to few days) submergence during rainfall events. In tropical regions, long-term submergence of paddy soils leads to unique P dynamics due to the alternative oxic/anoxic conditions and high levels of iron (Fe) and aluminium (Al) oxy(hydr)oxides present in these soils. The challenge lies in understanding P dynamics in such soils to optimise fertiliser management strategies and enhance rice productivity sustainably. An incubation study was conducted in Sri Lanka to investigate P release and transformations in three contrasting paddy soils (Ultisols, Alfisols and Entisols) with applied two types of inorganic P fertilisers. This study revealed that the P fertilisers did not increase dissolved reactive P (DRP) into porewater in all soils, except immediately after fertiliser application because the P released by dissolution of calcium (Ca) phosphates and P associated ferrihydrite under reduced conditions were translocated to deeper soil layers and resorbed onto abundantly available Fe/Al oxy(hydr)oxides and reprecipitated as Ca minerals. Further, it was revealed that during submergence, moderately labile P pools (ie: sodium hydroxide extractable P) increased in P applied soils, which can be available for plant adsorption under unique micro-environment of the rice plant rhizosphere. Contrastingly, in temperate regions, short-term submergence events, such as heavy rainfall, or flooding, pose risks of dissolved P release from soils, and subsequently diffuse P loss to overlying floodwater leading to freshwater quality concerns. The CSAs are nutrient hotspots in a farm which have active hydrological connectivity to surface waters. These areas often saturated/submerged during rainfall events. Hence, P release from CSAs can contribute to eutrophication in nearby freshwater bodies, posing environmental and agricultural sustainability challenges. Two studies were conducted to explore P release and transformations from three contrasting soils upon short-term submergence of CSAs during rainfall in New Zealand. A glasshouse study revealed that two soils (Recent and Pallic soils) released P to porewater while the other soil (Allophanic soil) sorbed P during short-term submergence suggesting the potential use of the Allophanic soil as a P sorbing material to mitigate P loss. A field study conducted in two CSAs (Recent and Pallic soils) connected to the Manawatū River revealed elevated DRP in porewater and floodwater during winter aligned with the findings of the glasshouse study. The findings of these studies can be applied to mitigate P losses from these CSAs during periods of high-risk for surface runoff such as in winter and to select suitable sites/soils for edge of farm mitigation practices such as wetlands and detainment bund constructions.Item The long-term effects of elevated CO₂ on soil organic carbon sequestration, partitioning and persistence in a grazed pasture : a thesis presented in partial fulfilment of the requirements for the degree of Doctor in Philosophy in Soil Science at Massey University, Manawatu, New Zealand(Massey University, 2024-03-04) Gonzalez Moreno, Marcela AngelicaThe increased concentration of atmospheric carbon dioxide (CO₂) is a significant driver for climate change and also influences the cycling of soil organic carbon (OC) in ecosystems. Despite the importance of grassland soils as a sink for CO₂, the effect of long-term exposure to elevated CO₂ (eCO₂) on OC sequestration, partitioning and persistence in grazed grassland soils is poorly understood. This thesis aimed to investigate the effect of eCO₂ on soil OC stocks, the partitioning of OC in soil fractions and persistence in a grazed legume-based pasture at the New Zealand (NZ) Free Air CO₂ Enrichment (FACE) facility. The NZ-FACE, established in 1997, is the only FACE experiment worldwide that includes the influence of grazing practices on the above- and below-ground components of the OC cycle. The effect of eCO₂ on soil OC persistence and stability was assessed by measuring changes in soil OC stock, in the distribution of soil OC in the soil fractions by wet fractionation analysis and in the soil OC decomposition pathways by determining the molecular composition of soil organic matter (OM) by pyrolysis analysis followed by gas chromatography/mass spectroscopy (GC-MS) and thermally assisted hydrolysis methylation-GC-MS (THM-GC-MS) analysis to a soil depth of 250 mm. In Chapter 3, we assessed OC storage and persistence in the soil fractions in a grazed legume- based pasture exposed to eCO₂ for 22 years on Pukepuke soil (Mollic Psammaquent) at three soil depths. Our study revealed that after 22 years of exposure to eCO₂ there were no significant changes in the stocks of OC and N as well as the partitioning of OC within different soil fractions in the Pukepuke soil. Interestingly, in the last 10 years at the NZ-FACE facility, there has been a sharp reduction of OC and N stocks in the Pukepuke soil, independent of the CO₂ treatment. We suggest that in the sandy Pukepuke soil under conditions of warmer temperatures and a wetter system, the deficiency that has emerged in soil nutrient availability, the environmentally enhanced plant growth and the larger amounts of fresh OM input has caused a positive priming effect, mainly in the labile fraction. Even though eCO₂ did not change the soil OC stocks nor OC content in the soil fractions in any soil layer, it did modify the soil nutrient status (phosphate in particular) and did increase polysaccharides and aliphatic proportions in the coarse particulate organic matter and micro-aggregates indicating that the priming was further enhanced in eCO₂ soils with this effect being especially prominent in the 50 – 150 mm soil layer (Chapter 3). In Chapter 4, the hypothesis that grazing animals, by returning nutrients in urine, dung, and plant litter trampled into the soil surface, would contribute to an increase in soil OC and N stocks under eCO₂ was investigated and rejected. Despite not finding any interaction effect between eCO₂ and defoliation treatment on the soil OC stocks and partitioning in the soil fractions, the presence of an interaction effect in the soil OM molecular composition suggests that distinctly different OC decomposition pathways exist depending on pastures management under eCO₂. Our study showed that under grazing there was an accumulation of lignin-derived OM, which reveals a higher proportion of shoot-derived rather than root- derived OC under eCO₂. In Chapter 5, the influence of the inherent properties of a soil – which might enhance or limit the effects of eCO₂ on soil OC persistence and stability – was examined in two contrasting soils (Pukepuke and Stratford; a Entic Dystrandept) in mesocosms installed at the NZ-FACE in May 2005 and extracted after 15 years. Our results showed that over the course of the mesocosm study, OC and N contents and stocks (to 150 mm soil depth) in the Pukepuke soil declined by 16 t ha-1 under ambient CO₂ atmosphere, possibly as a result of soil disturbance during the establishment of the mesocosms. In the Stratford soil, with the ability to strongly preserve OM through mineral associations, the decline in soil OC was much smaller (5 t ha-1). Elevated CO₂ interacted with soil type and after 15 years of exposure to eCO₂, the Pukepuke soil had 6.5 t ha-1 more OC stocks, compared to the same soil under ambient CO₂ conditions, while no differences were found in the OC stocks of the Stratford soil (Chapter 4). These findings indicate that in the Pukepuke soil the eCO₂ treatment might have (i) helped overcome the impact of disturbance by favouring plant growth and generating a larger plant detritus input to the soil that enabled the partial replenishment of the OC loss at the time of mesocosm establishment, or (ii) limited the impact of disturbance, as eCO₂ often improves soil aggregation. It is crucial to consider that (i) the Stratford soil was subjected to ~50% less precipitation at the NZ-FACE compared to its original location and (ii) the mesocosm might have introduced new variables due to physical barriers. Thus, extrapolating the findings to field conditions at the NZ-FACE facility and elsewhere requires cautious interpretation. The findings presented in this thesis contribute significantly to enhancing our understanding of the mechanistic processes underlying the influence of eCO₂ on the stabilization and mineralization of soil OM. These insights have direct implications for the development of sustainable agricultural management practices in response to a changing environment.Item An investigation of soil carbon fluxes and pools in the thermo-sequence of Mt. Taranaki forest : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Soil Science at Massey University, Manawatu, New Zealand(Massey University, 2023) Siregar, Idri HastutyUnderstanding the relationship between temperature and soil carbon (C) pools and fluxes is a key aspect in determining the feedback of the global C balance to rising temperature. The overall objective of this thesis was to investigate the influence of rising temperature in the net change of soil C stocks and fluxes in a thermo-sequence of Mt. Taranaki and explore the mechanisms underlying this change if any. Taranaki region has a ca. 3.2°C mean annual temperature (MAT) gradient with identical parent material, moisture (constant plant-available moisture), and vegetation type. The soil type under this study is alu-andic Andosol, which is the mineral soil group with the largest C content worldwide and characterised by its abundance in aluminium (Al)-organic matter (OM) complexes (e.g., Al³⁺-OM and allophane-OM complexes). Yet, there is considerable uncertainty as to how rising temperatures will affect the stability of organo-mineral complexes and their formation. Together with the unique thermo-sequence available across the Taranaki slope, they offer an excellent benchmark for investigating the potential responses of soil C storage to long-term warming. Firstly, we hypothesised that: (i) temperature rise influences the forms of reactive Al (i.e., short range order (SRO) constituents vs. organo-Al complexes), with a greater abundance of SRO constituents at warmer elevation sites as opposed to organo-Al complexes at colder elevation sites, where the weathering rate is slower; (ii) in warmer conditions, microbial-derived C is favoured, while in cooler conditions, plant fingerprints are more evident; (iii) as a result, the C preservation mechanism along the transect differs, with SRO constituents (and microbial-derived C) being more prevalent at warmer elevation sites and Al cations (and plant-derived C) being more abundant at colder elevation sites. To reveal how climatic and geochemical properties regulate soil C preservation, we conducted a field survey to investigate the changes in: (i) soil geochemical properties including; soil pH, reactive Al and Fe (i.e., SRO constituents and organo-Al complexes); (ii) total C content, stocks, and fractions, as well as composition of OM along the gradient, in which soils at four elevation sites were sampled down to 85 cm depth. Four sampling sites were selected, with elevations ranging from 512 to 1024 m above sea level (asl) and and a mean annual temperature (MAT) of 7.3, 8.2, 9.1, and 10.5 °C ( referred to as T7, T8, T9, and T10, respectively). The results showed that: (i) at colder elevation sites (T7 and T8), soil profiles were richer in well-preserved plant material and in organo-Al complexes, as opposed to (ii) warmer elevation sites (T9 and T10), which had a more microbial processed C and a higher fraction of protected C forms, along with a greater abundance of SRO Al constituents. The results revealed that climate (particularly temperature rise) and soil geochemistry interacted to regulate soil C preservation. While the study has revealed that the mechanisms that protect OM (particularly at depth) differ across the thermogradient, C stocks do not change with temperature., models projecting soil C changes over time under various climate scenarios should also consider the existing interaction with soil geochemistry (Chapter 3). After understanding the interaction between soil geochemistry and temperature rise in relation to the soil C preservation mechanism, we investigated the long-term effect of rising temperatures on the soil C fluxes (input and output) in a mature native forest along the thermo-sequence in Mt. Taranaki. We used specific molecular markers to monitor the changes in soil C abundance and composition (i.e., carbohydrates) in order to gain a deeper understanding of the effect of temperature rise on the turnover of soil C. We hypothesised that, in the absence of a water shortage, an increase in temperature would increase forest productivity and litterfall, which in turn would increase soil C inputs; this increase in organic substrate along with higher temperatures would, in turn, generate an additional soil CO₂ efflux; however, no net C loss would occur as the increased in soil C input would offset the increased soil CO₂ efflux. To test this, soil C pools, plant biomass C pools, soil C fluxes, and soil OM composition (i.e., carbohydrate abundance and composition), at four elevation sites along the Taranaki thermo-sequence were quantified. The outcome of this investigation demonstrated that above- and below-ground biomass C increased ca. 32% (significant at P <.05) when temperatures rose (from T7 to T10). This led to an increase in aboveground litterfall (29%), belowground C input (15%), soil respiration rate (16%, significant at P <.05), and decay intensity (as inferred from the carbohydrate preservation index (CPI)). The study showss that the increase in temperature along this quasi-thermo-sequence at Taranaki increases plant C input through enhanced net primary production, which counteracts soil C loss, resulting in no apparent detrimental effect on soil C storage (Chapter 4). This study highlights the importance of considering plant C input of an entire ecosystem along with soil OM decomposition when investigating the response to temperature rise. To understand the effect of warming on the temperature sensitivity (Q₁₀) of soil organic matter (OM) decomposition rate along the Taranaki thermo-sequence, we collected soils from four distinct elevation sites with four different depths and incubated them in the laboratory at temperatures of 5, 15, 25, and 35°C for 330 days (Chapter 5). The incubation data were then fitted with a three-component model to generate three C pools with distinct decomposition rates, followed by the calculation of their respective Q₁₀ values. Using multivariate analysis, these values were then combined with a complete set of soil geochemical characteristics and OM molecular composition data to gain mechanistic insights into the biogeochemical causes of Q₁₀ variations. The results of this study revealed that: (i) Q₁₀ of soil OM decomposition is inclined to attenuate over a centennial scale under elevated MAT; and (ii) Q₁₀ values of the bulk soil OM and the distinct C pools were differentially regulated by soil C availability, OM molecular composition, and OM-mineral interactions (Chapter 5). These results suggest that temperature affects the distinct C pools differently; with Q₁₀ values having a trend to decrease as temperature increases.All the results obtained in this thesis contribute to provide a mechanistic understanding about the effect of rising temperatures on soil C fluxes, and stocks as well as the underlying mechanism governing them, in order to accurately anticipate soil C dynamics in response to global warming.Item Amplifying the power of proximal sensing techniques to assess the cadmium concentration in agricultural soils : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Soil Science at Massey University, Palmerston North, New Zealand(Massey University, 2023) Shrestha, GautamCadmium (Cd) accumulation in agricultural soils due to long-term phosphate fertiliser applications has raised concerns in New Zealand and globally due to the potential toxicity of Cd in food products. Elevated soil Cd concentration can enhance Cd availability for plant uptake, increasing the risk of food chain transfer. Cadmium management is generally achieved through reference laboratory methods to estimate Cd concentration in soil and plant samples. Reference laboratory methods of Cd analysis are precise; however, sample preparation and associated resource cost make them expensive. As a complementary method, proximal sensing techniques including visible-near-infrared (vis-NIR: 350–2500 nm), mid-infrared (MIR: 4000–400 cm-1) reflectance and portable X-ray fluorescence (pXRF: 0–40 keV) spectroscopy have been successfully used to monitor elevated Cd levels in mining areas and in plants showing stress or toxicity symptoms due to Cd. However, application of such technologies in agricultural soils with low Cd concentration are relatively understudied. Hence, this study was conducted to amplify the power of three proximal sensing techniques to quantify Cd in soil samples from diverse soil orders, climatic conditions, land uses, and vegetations and plant samples for cost-effective Cd monitoring at regional to farm scale. In this doctoral study, soil and plant samples were scanned using vis-NIR, MIR, and pXRF sensors. Topsoil samples were obtained from (1) the Otago-Southland regional survey (n=622), (2) a pastoral farm survey (n=87) including dairy and sheep and beef farms with long-term phosphate fertiliser application history, and (3) two independent glasshouse experiments using Pallic and Allophanic soils amended with increasing soil Cd concentrations, and with or without a model forage herb, chicory (Cichorium intybus L.). In both experiments, chicory aboveground biomass and root samples were scanned using the three sensors, along with a periodic collection of vis-NIR spectra from soil and plant in-situ. Total Cd was determined in all samples, while the distribution of Cd among geochemical fractions was studied in the pastoral farm survey samples only. Reference laboratory results and spectral information were combined to develop models for accurate Cd predictions. For regional survey samples (n=622, 0.01–0.56 mg Cd/kg) including agricultural soils (47%), validation (v) results (n=124, 0.01–0.43 mg Cd/kg) showed Granger-Ramanathan model averaging of outputs from models using individual pXRF, vis-NIR, and MIR data as input for partial least squares (PLS) – support vector machine regression performed optimally to quantify total soil Cd with normalised root mean square error (nRMSEv) of 37% and concordance correlation coefficient (CCCv) of 0.84. For agricultural soils (n=84, 0.10–1.20 mg Cd/kg), cross-validation (cv) results of models using individual vis-NIR, MIR, and pXRF data as input for PLS performed with nRMSEcv of 26%, 30%, and 31% and CCCcv of 0.85, 0.77, and 0.75 respectively. For acid soluble (0.01–0.27 mg Cd/kg) and organic matter bound (0.02–0.27 mg Cd/kg) Cd, models using vis-NIR data performed with nRMSEcv of 11% and 33% and CCCcv of 0.97 and 0.84, respectively. For exchangeable (0.003–0.25 mg Cd/kg) Cd, a model using MIR data as input performed with nRMSEcv of 40% and CCCcv of 0.57. Using the Otago and Southland regional survey soil samples spectra as a soil spectral library (SSL), Cd concentration in the local set (agricultural soil samples) were quantified. A model using MIR data from the regional SSL pastoral soil subset (n=283, 0.01–1.31 mg Cd/kg) spiked with selected local set samples (n=12) with weights (×4) as input for LOCAL algorithm quantified local soil Cd with nRMSE of 38% and CCC of 0.78. In the glasshouse experiments, Cd translocation factor (TF) values for chicory were calculated using proximal sensor data and the results showed a significant relationship (R2=0.74, p<0.001) between measured and predicted TF values. A model using in-situ leaf clip vis-NIR spectra showed optimal performance to assess Cd concentration in aboveground chicory biomass with nRMSEcv of 28% and CCCcv of 0.93. Among vegetation indices calculated ‘blue green index 2’ showed a significant (p<0.01) R2 value (0.19, 0.36) in both experiments. Models using pXRF spectra as input showed optimal performance to predict chicory root (n=28, 0.86–25.79 mg Cd/kg) and Allophanic soil (n=112, 0.41–4.81 mg Cd/kg) Cd with nRMSEcv of 16% and 9% and CCCcv of 0.95 and 0.99, respectively. A model using laboratory vis-NIR spectra showed optimal performance to quantify Pallic soil Cd (n=336; 0.17–5.45 mg Cd/kg) with nRMSEcv of 22% and CCCcv of 0.97. Optimal prediction models using proximal sensor data can potentially be used for rapid cost-effective analysis of Cd concentration in soil and plant samples. Quantitative models for soil Cd using a combination of complementary proximal sensors data and chemometrics could feasibly be deployed for long-term monitoring of soil Cd at concentrations below pXRF detection limits and with reduced matrix interference from organic matter when compared to the individual techniques alone. The use of proximal sensing techniques to determine total soil Cd concentration in New Zealand agricultural soils has the potential to improve the scale and scope of long-term repeated monitoring of soil Cd concentration required under the framework of the national Tiered Fertiliser Management System. Reflectance spectroscopy could potentially be implemented to monitor plant-available and potentially-available soil Cd fractions to minimise plant Cd uptake. The use of a large soil spectral library to assess the local Cd concentration in agricultural soils could reduce the analytical cost to the farmers and allow intensive spatial and temporal monitoring of pastoral farms based on spectral analysis only. The use of in-situ and laboratory proximal sensor data to calculate bioconcentration and translocation factors could potentially support the evaluation of Cd food chain transfer risks. The spectral library developed from this doctoral study, including soil and plant root and aboveground biomass pXRF, vis-NIR, and MIR spectra with a wide range of Cd concentration can be used as reference materials for field level and airborne remote sensing studies.Item Manipulating soil bioavailable copper as an innovative nitrate leaching mitigating strategy in New Zealand pastoral soils : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) in Soil Science, School of Agriculture and Environment, College of Sciences, Massey University, Palmerston North, New Zealand(Massey University, 2023) Matse, Dumsane ThembaUrine patches are the primary sources of nitrate (NO₃⁻ -N) leaching from pastoral dairy farms. Since NO₃⁻ -N is the product of nitrification, a clear understanding of the nitrification process is a vital step toward the development of effective and efficient mitigation approaches. The first step of ammonia (NH₄⁺) oxidation to hydroxylamine (NH₂OH) is catalyzed by the ammonia monooxygenase enzyme (AMO), and copper (Cu) is a co-factor in the activity of the AMO enzyme. Therefore, manipulating Cu bioavailability through the application of Cu-complexing organic compounds such as calcium lignosulphonate (LS) and co-poly acrylic-maleic acid (PA-MA) to soil could influence AMO activity and consequently limit the nitrification rate in soil. There are no published studies that have examined the effect of bioavailable Cu concentration changes on nitrification rate, ammonia-oxidizing bacteria (AOB) and archaea (AOA), and NO₃⁻ -N leaching. The overall aim of this thesis is to determine the significance of bioavailable Cu in the nitrification process in the context of developing novel Cu-complexing organic compounds to inhibit nitrification rate in pastoral soils. A soil incubation study was conducted to characterize the relationship between changes in soil bioavailable Cu concentration and nitrification rate. This study was conducted using three pastoral soils (Pumice, Pallic, and Recent soils) spiked with five Cu levels (0.1, 0.3, 0.5, 1, and 3 mg kg⁻¹). Treatments of Cu-complexing compounds were separately applied to each Cu level. The treatments were urea applied at 300 mg N kg⁻¹, urea + LS at 120 mg kg⁻¹, and urea + PA-MA at 10 mg kg⁻¹. Results show that increasing the added Cu concentration from 0.1 to 3 mg kg⁻¹ increased nitrification rate by 35, 22, and 33% in the Pumice, Pallic, and Recent soils, respectively. Application of LS and PA-MA significantly (P ˂ 0.05) decreased nitrification rate with the mean reduction being 59 and 56%, 32 and 26%, and 39 and 38% in the Pumice, Pallic, and Recent soils, respectively at Day 8 relative to the urea-only treatment. To further extend knowledge of the relationship between bioavailable Cu and the key nitrifying microorganisms in soils, a greenhouse-based pot trial using three soils (Pumice, Pallic, and Recent soils) planted with ryegrass and treated with synthetic urine applied at 300 kg N ha⁻¹ and three levels of Cu (0, 1, 10, 100 mg added Cu kg⁻¹) was established. Results show that AOB amoA gene abundance increased as a function of increasing added Cu from 1 to 10 mg kg⁻¹ but was inhibited at 100 mg added Cu kg⁻¹ in both Pallic and Recent soils. The effect of bioavailable Cu was not apparent in the Pumice soil. The increase in AOB amoA gene abundance positively correlated with nitrification rate in both the Pallic (r = 0.982, P < 0.01) and Recent soil (r = 0.943, P < 0.01) but not in the Pumice soil. There was no effect of increasing Cu concentration on AOA amoA gene abundance in all three soils. Results from both incubation and greenhouse pot trials provide strong evidence that Cu is an important trace element in the nitrification process and reducing Cu can reduce nitrification in soil. However, in order to definitively quantify this treatment effect, further field studies were necessary. Therefore, a field lysimeter study was conducted using Pumice soil (Manawatu climate) and Pallic soil (Canterbury climate). The following treatments were investigated to reduce NO₃⁻ -N leaching during late-autumn application; urine only at 600 kg N ha⁻¹, urine + PA-MA at 10 kg ha⁻¹, urine + LS at 120 kg ha⁻¹, urine + a split-application of calcium lignosulphonate (2LS at same rate, initial and after a month of first application), and urine + ProGibb SG (GA at 80 g ha⁻¹) + LS (GA + LS). Another set of treatment applications, urine only, urine + GA only, and urine + GA + LS, were applied mid-winter to both soils. The GA was applied to improve the effectiveness of these organic compounds during climatic periods of poor plant growth. Results showed that there was no significant reduction in mineral N leaching associated with the late-autumn application of both PA-MA and LS for the Pumice or Pallic soils. However, the application of 2LS reduced mineral N leaching by 16 and 11% in Pumice and Pallic soils, respectively, relative to urine-only. The late-autumn inclusion of GA increased the effectiveness of LS in both soils. This was confirmed by a significant reduction of mineral N leaching by 35% from both Pumice and Pallic soils. Mid-winter application of GA + LS significantly reduced mineral N leaching only in the Pumice soil (by 20%) but not in the Pallic soil relative to urine-only. In both late-autumn and mid-winter treatments application of the different Cu-complexing treatments did not have negative effects on pasture dry matter yield in either Pumice or Pallic soils. In this lysimeter study, the mechanistic effect of PA-MA and LS on reducing bioavailable, nitrification rate and AOB/AOA amoA gene abundance was not investigated. A second field lysimeter experiment was established using the Recent soil in Manawatu to explore the mechanism of Cu manipulation through the application of LS and PA-MA on nitrification rate, AOB/AOA amoA gene abundance, and mineral N leaching. The effect of combining organic inhibitors with GA on reducing mineral N leaching was also investigated. This study evaluated the same treatments used in the first lysimeter study and applications were again conducted at two different seasonal periods (late-autumn and mid-winter). The results showed that the effect of PA-MA and 2LS on bioavailable Cu corresponded with a reduction in nitrification rate and AOB amoA gene abundance. The effect of PA-MA and 2LS was associated with reduced mineral N leaching by values of 16 and 30%, respectively, relative to urine-only. The reduction in mineral N leaching induced by PA-MA and 2LS increased N uptake by 25 and 7.8% and herbage DM yield by factors of 11 and 8%, respectively, relative to the urine-only. The LS treatment did not induce a significant change of either bioavailable Cu or nitrification rate which corresponded to no significant effect on mineral N leaching. The late-autumn combination of GA + LS reduced mineral N leaching by 19% relative to urine-only, but there was no significant difference in mineral N leaching observed for the mid-winter application relative to urine-only. The overall results of this research show that bioavailable Cu is a vital trace element in the nitrification process and for AOB functioning in soil. Therefore, reduction in bioavailable Cu through the application of Cu-complexing compounds can inhibit nitrification. In this doctoral study, the application of Cu-complexing compounds (LS and PA-MA) showed potential to inhibit nitrification rate and subsequently reduce mineral N leaching in pastoral systems, but their efficacy depends on soil characteristics. Future work is recommended to investigate the effect of LS and PA-MA application on nitrous oxide emissions. Further research is recommended to investigate the short and long terms effects of these treatments on non-target soil microbiota.Item An incubation study to assess the effect of waste sludge additions on some chemical characteristics of mine spoils : a thesis presented in partial fulfilment of the requirements for the degree of Master of Horticulture in Soil Science at Massey University(Massey University, 1997) O'Reilly, Joanne LimpusIn 1985 a study undertaken by the New Zealand Soil Bureau identified a major shortfall in topsoils for mining rehabilitation works and the use of surrogate materials to overcome this shortfall was postulated (Wills, 1992). The Resource Management Act 1991 places constraints on the disposal of wastes and may act as a catalyst for research into the beneficial utilisation of once waste products for land rehabilitation. The most common problem reclaiming of derelict and degraded land is a shortage of organic matter (Pulford, 1991) in the growing medium. The overall objective of the research reported in this study was to investigate chemical interactions between various mine spoils and sludge materials as organic amendments and to determine the level of sludge application (based on organic matter content) that maximised the chemical benefit to the mine spoils. A controlled incubation study was used to achieve the objectives of the study. Six mine spoils from two sources (a gold mine and a coal mine) and three sludge amendments from two sources (municipal sewage sludge and paper sludge) were used. The sludge amendments were applied to the mine spoils to supply three different rates of organic matter (2, 5 and 10% in the amended spoils) and incubated for 38 weeks. The incubations were sampled every four weeks until week 20 and finally at week 38 for chemical analysis. Results of the study revealed that organic matter, total and mineral N, total and Olsen P levels of the amended spoils could be predicted directly from the characteristics of the sludge and spoil constituents but pH, EC, CEC could not. The benefit of sludge addition on many of the chemical characteristics of the mined spoil increased with increasing level of sludge addition. Manukau sewage sludge was the most beneficial sludge to apply with respect to P fertilisation. North Shore sewage sludge presented the greatest benefit for mine spoil rehabilitation with respect to N and it provided less risk of heavy metal contamination than Manukau sewage sludge. Paper sludge presented the most benefit with respect to pH and organic matter and the least risk of heavy metal contamination; however, nutritionally it was inferior to the sewage sludges.Item An investigation on the stability of biochar-C in soils and its potential use to mitigate non-CO₂ greenhouse gases using near-infrared (NIR) spectroscopy : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Soil Science at Massey University, Manawatu, New Zealand(Massey University, 2020) Mahmud, Ainul FaizahThe global interest in using biochar for C sequestration-climate mitigation and soil improvement has driven rapid expansion in biochar research to understand its properties and application impacts. The potential for biochar application to increase soil organic carbon (SOC) stocks and its potential agronomic and additional environmental benefits, such as reducing soil nitrous oxide (N₂O) emission, are determined by its stability in the soil, which is dependent on its intrinsic properties and the soil conditions. The inherent properties of biochar are highly influenced by feedstock type and pyrolysis temperature hence, the use of various types of feedstock and pyrolysis technologies leads to uncertainties in predicting the effect of biochar addition to soils. Previous research has established a general assumption that biochar stability is strongly influenced by the type of feedstock used and maximum pyrolysis temperature. Research is required, however, to produce practical and reliable techniques that can be used to verify the reported maximum pyrolysis temperature, regardless of the type of feedstock used and predict the likely stability of the biochar. In addition to the pyrolysis process, the final particle size of the biochar and the method of incorporation into the soil may also influence the ability of the biochar to moderate soil properties and function. With previous research, there is general lack of attention given to these potentially influential parameters when assessing the impact of biochar application to soil. Therefore this thesis evaluates (i) the use of near-infrared (NIR) spectroscopy technique for predicting the maximum pyrolysis temperature of biochar as it is a well-known, non-destructive, and rapid technique for analyzing organic material; (ii) the effect of biochar application, with special attention to biochar particle size and depth of placement, on N₂O soil emission and SOC stocks; and (iii) the integrated use of NIR spectroscopy for SOC measurement. In the first study, we hypothesized that NIR spectroscopy can be used to predict the maximum pyrolysis temperature achieved during biochar production. Eighty-two carbonized materials produced from various feedstock types and pyrolysis conditions with the reported pyrolysis temperature ranged between 220 to 800 °C, were scanned using NIR spectrometer and were used as the calibration set. The NIR calibration model was built by correlating the NIR spectral data with the reported pyrolysis temperature using partial least squares regression (PLSR). A separate sample set (n=20) was compiled using laboratory-produced biochar made from pine wood at pyrolysis temperature ranged from 325 to 723 °C. The calibration model validated using (i) leave-one-out cross-validation (LOO-CV) and (ii) the prediction set, yielded good accuracy (LOO-CV: r²=0.80 and RMSECV:48.8 °C; prediction: r²=0.82 and RMSEP: 57.7 °C). Results obtained in this study have shown that NIR spectroscopy can be used to predict the maximum pyrolysis temperature of biochar and has the potential to be used as a monitoring tool for biochar production. In addition to the first study, the predictive ability of the NIR model was evaluated further. We hypothesized that the variation in feedstock types and pyrolysis processes may affect the predictive performance of the NIR model in predicting the maximum pyrolysis temperature of biochar. Therefore, three sample sets were generated from a total of 82 carbonized materials and its subsets (Set A: n=82; Set B: n=68; Set C: n= 48) and were used for developing three calibration models. The selection of samples for Set B and C was made by reducing the variability associated with production conditions and feedstock type i.e. Set B consist of samples produced by slow pyrolysis and using the same pyrolyzer unit, while for Set C (a subset of Set B), samples produced from “processed feedstocks” were excluded. A separate sample set (n=18) consists of samples produced from animal manure, crop residue, and woody materials were used as the prediction set. This biochar was produced using the slow pyrolysis technique in a laboratory or under relatively high production controlled conditions at temperature ranged from 250 to 550 °C. These calibration models were validated using (i) leave-one-out cross-validation (LOO-CV) and (ii) a prediction set, with the model based on set C gave the best prediction (R2: 0.941; RMSEP: 27.3 °C), followed by the model based on set A (R2: 0.896; RMSEP: 35.6 °C), and set B (R2: 0.928; RMSEP: 37.3 °C). These results indicate that feedstock types have a considerable effect on the performance of the NIR model while the effect of pyrolysis conditions was less pronounced. Thus, data variability from samples needs to be taken into account in developing the NIR calibration model for predicting the maximum pyrolysis temperature of biochar. Before studying the effect of biochar on N₂O soil emission and SOC stocks, the maximum pyrolysis temperature of biochar to be used in the experiment was predicted using the NIR spectroscopy technique. The estimated pyrolysis temperature – after scanning the 3-year old pine wood biochar and using the NIR model developed – was 500 °C, while the reported temperature was 550 °C. A controlled glasshouse study was conducted to investigate the effect of biochar particle size and the impact of soil inversion (through simulated mouldboard ploughing) on N₂O emissions from soils to which cattle urine was applied. We hypothesized that the application of biochar may (i) affect N₂O emissions through changes in soil physical properties, specifically soil aeration and water retention; and (ii) the effects of biochar addition on these properties may differ depending on their particle size (e.g., a larger particle size may increase soil aeration whereas a smaller particle size may clog pores), and their placement in soil (e.g., the incorporation of a large particle size-biochar at depth may promote water movement from the top layer and increase the overall drainage of the soil). Pine biochar (550 °C) with two different particle sizes (<2 mm and >4 mm) was mixed either into the top soil layer at the original 0–10 cm depth in the soil column or at 10–20 cm depth by inverting the top soil to simulate ploughing. Nitrous oxide emissions were monitored every two to three days, up to seven weeks during the summer trial, and measurements were repeated during the autumn trial. The use of large particle size biochar in the inverted soil had a significant impact on increasing the cumulative N₂O emissions in the autumn trial, possibly through changes in the water hydraulic conductivity of the soil column and increased water retention at the boundary between soil layers. Thus, the importance of the role of biochar particle size and the method of biochar placement on soil physical properties and the implications of these on N₂O emissions was highlighted. In the same glasshouse study, the effect of biochar particle size and depth of placement was further evaluated in relation to soil organic C. We hypothesized that (i) the large-particle size biochar may affect soil aeration and accelerate soil C decomposition rate with increased oxygen availability, and this effect is greater when biochar is incorporated at depth due to the more compacted soil at deeper layer with poorer aeration compared to the surface layer; and (ii) the NIR spectroscopy technique can be used to predict the SOC concentration and SOC stocks in biochar-amended soil. Carbon stocks were estimated using NIR spectroscopy coupled with partial least-squares regression analysis (NIR/PLSR) and direct organic C measurements using an elemental analyzer. The NIR spectra of the soil were acquired by scanning intact soil cores using the NIR spectrometer. By the end of the glasshouse trial (327 days), the large-particle size biochar applied at depth had induced significant soil C loss (9.20 Mg C ha⁻¹ (P < 0.05), possibly through the combination of enhanced soil aeration, and the interrupted C supply from new plant inputs at that depth due to soil inversion. This C loss did not occur in the treatment with the small-particle size biochar. Near-infrared (NIR) spectroscopy was able to predict the SOC concentration, however, the prediction accuracy may be negatively affected by an increasing biochar particle size and soil inversion, thus may affect the subsequent SOC estimates. The information obtained in this thesis will inform the future use of biochar and contribute to the knowledge of possible factors affecting soil N₂O emission from biochar-amended soil, the mineralization of native SOC, and the changes in SOC stocks over time, particularly in the pastoral soils of New Zealand. Also, based on this study, the use of NIR spectroscopy technique may potentially be integrated as part of the methodology for SOC estimation.Item Study of the effect of temperature on the cycling of carbon in a forest ecosystem at Mount Taranaki : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Soil Science, School of Agriculture and Environment, Palmerston North, New Zealand(Massey University, 2020) Osei-Asante, ErnestSoil organic matter (OM) represents one of the largest reservoirs of carbon (C) on the global scale. It is therefore crucial to understand the potential response of these C stocks to global warming. Global mean surface temperature is likely to increase by between 1.4 °C and 3.1 °C by the end of the 21st century (2081–2100), relative to 1986–2005 range, and it is anticipated that any warming-induced C emissions from soils will further drive planetary warming. However, there is disagreement on the potential feedbacks of soil organic C to climate warming, due to the complexity of the relationship between climate warming and soil C. The objective of this study was therefore to assess how changes in temperature affects the cycling of soil OM in a thermo-sequence at the Egmont National Park in Taranaki. Soil samples were collected at four sites (in a transect of increasing altitudes, ranging from 512 m to 1024 m asl) down to 40 cm depth, at depth increments of 5 cm, using PVC pipes of 5 cm Ø. Additional soil samples were taken for a general chemical characterisation of the soils at time 0. The soil columns were incubated for 190 days at four different temperatures (5°C, 15°, 25°C and 35°C) using a 0.25 M NaOH solution to trap CO₂ with soil moisture maintained at field capacity. A three-pool C model was used to determine the rate of C decay in the C fractions/pools. The results showed that, in general, altitude did not have a significant effect on either C stocks or cumulative C efflux at the end of the laboratory incubation. Cumulative C efflux was ~3 times larger (significant at P<0.05) at the highest temperature (e.g., 0.015 t C/ha/day for topsoil layer) compared with the lowest temperature (0.005 t C/ha/day for topsoil layer). At all temperatures and sites, the topsoil layer had the largest C efflux (ranging from 0.015 to 0.005 t C/ha/day) compared with the deeper layers (averaged between 0.006 to 0.002 t C/ha/day). The Q₁₀ values (averagely 1.47-1.35) revealed that all soil layers were temperature sensitive. All three C pools considered (fast, intermediate, slow) were temperature sensitive, though C efflux in the slow pool was very small (< 0.00006 t C/ha/day). We attributed the higher C efflux in the topsoil to the presence of more labile C enriched in necromass, weaker interaction of organic ligands with mineral components and high microbial abundance. Our findings showed that a rise in temperature enhanced the decomposition of soil OM even at the deepest layer, where mineral protection is largest. Also, the organic C at all C pools, soil layers, and altitudes were shown to be temperature sensitive.