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Item Water and solutes in soil : hydraulic characterisation, sustainable production, and environmental protection : application for the degree of Doctor of Science from Massey University, Palmerston North, New Zealand(Massey University, 2002) Clothier, Brent EThe soil of the rootzone, the fragile and fertile interface between the atmosphere and the subterranean realm, is characterised by massive transfers of water and solutes. Our understanding of the biophysical transport processes into, and through, soil has been enhanced by the research endeavours of the applicant, Brent Euan Clothier. Dr Clothier, a 1977 Ph.D. graduate of Massey University, has developed tools and techniques that increased the acuity of our vision of transport processes of water and solutes in soil, as well it has sharpened our ability to hydraulically characterise those mechanisms for the purpose of modelling and risk assessment. His research has also enhanced our understanding of how these biophysical processes affect sustainable agriculture, environmental protection, and the bioremediation of contamination. These endeavours are grouped, in this thesis, into four overlapping areas of research: • Processes and properties of water movement into and through soil • Processes and properties of solute movement through soil • Root uptake processes and sustainable irrigation • Plants, groundwater protection and bioremediation of contaminated soil. The key elements of these four themes, and their contribution to knowledge, form Chapters 2-5 of this thesis. Dr Clothier's awards, honours, and impact are discussed in Chapter 6.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 Impact of plantain (Plantago lanceolata) based pasture on milk production of dairy cows and nitrate leaching from pastoral systems : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Manawatu, New Zealand(Massey University, 2023) Nguyen, Truong ThiIn temperate dairy systems, the traditional perennial ryegrass (Lolium perenne)-white clover (Trifolium repens) (RGWC) pasture often has excessive nitrogen (N) content relative to the N requirement of animals, posing a risk of nitrate (NO₃⁻) leaching into the environment. Recently, incorporating plantain (Plantago lanceolata) with RGWC pasture has been increasingly used to improve economic and environmental benefits for dairy farms. However, the impact of plantain incorporation on farm productivity and NO₃⁻ leaching at the farm level has not been fully understood. The objectives of this thesis were to quantify the effect of incorporating increasing rates of plantain in grazing swards on pasture production, milk yield and composition of dairy cows, and NO₃⁻ leaching from pastoral dairy systems. To address the objectives of the thesis, a grazing trial was implemented at a research dairy farm between September 2019 and December 2021. Pasture treatments were RGWC (perennial ryegrass cv. ONE⁵⁰ and white clover cv. Tribute), RGWC + low plantain (cv. Agritonic) rate (PLL), RGWC + medium plantain rate (PLM), and RGWC + high plantain rate (PLH). Pastures were established with 20 experimental plots and four adaptation areas in April 2019 and were rotationally grazed by dairy cows over 22 grazing events during the experimental period. In each grazing, 60 or 80 cows were assigned to graze for 6 days in their adaptation areas and 1.5–3 days in the experimental plots. The experimental cows were managed under a typical practice, milking twice daily, offering grazing pasture and approximately 25% supplementary dietary feeds. Measurements were conducted to quantify the yield, botanical composition and nutritive value of the pasture, milk yield, milk composition and N excretion of dairy cows, and NO₃⁻ leaching from the pastoral system. The results showed that, over the first two lactation years after sowing, plantain-based pastures have a similar dry matter yield and contain higher water content, non-structural carbohydrates, minerals, and bioactive compounds than the RGWC pasture. The average plantain proportion in the swards over the first two years after sowing was 32% in PLL, 44% in PLM, and 48% in PLH, which increased in the first 15 months and declined to 20% in PLL and 30% in PLM and PLH at day 705 after sowing. Cows grazing the plantain-based pastures had a similar milk yield, composition and yield of solids, protein, fat, and lactose as those grazing the RGWC pasture. Furthermore, when 25% plantain was included in the diet of cows in late lactation, it resulted in a 44% increase in urine volume and a 29% reduction in urine N concentration by 29%. By incorporating an average of 30% and 50% plantain with RGWC pasture, NO₃⁻ leaching was reduced by 32 and 52%, respectively, over two drainage years after establishment, with a greater reduction in the first year than in the second year. Among sowing rates, PLM resulted in the greatest decrease in NO₃⁻ leaching, with 64% in the first year and 41% in the second year. The decreased NO₃⁻ leaching was associated with increased plantain content, enhanced herbage N uptake, reduced UN excretion of dairy cows and a lower N load in urine patches. In conclusion, in a typical practice, as in the present study, incorporating 30–50% plantain with RGWC pasture decreases NO₃⁻ leaching from pastoral systems without adversely impacting farm productivity for at least two years from sowing. However, the reduction of plantain content in the second year suggests further measurements to determine the effectiveness of plantain-based pasture in the longer term. In the conditions and time scale of the present study, the medium plantain rate treatment (PLM) is suggested to achieve a high effectiveness of plantain incorporation in reducing NO₃⁻ leaching.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 Nutrient leaching under intensive sheep grazing : a dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science at Massey University, Manawatu, New Zealand(Massey University, 2023) Maheswaran, SarminiThe use of some alternative forages may help sheep farmers to reduce nitrogen (N) leaching while increasing production. This thesis explores the effects of four forages (perennial ryegrass/white clover: RGWC; Italian ryegrass/white clover: IRWC; plantain/white clover: PWC; and a winter brassica) on sheep performance, urinary N excretion and N loss in drainage over two and a half years (Year 1: July to December 2019; Year 2: January to December 2020; Year 3: January to December 2021). This study was conducted on an artificially drained, fine textured Tokomaru silt loam soil at Massey University’s Keeble farm, near Palmerston North, Manawatu, New Zealand. The study design included four self-contained farmlets (each approximately 3.3 ha): three farmlets had 0.8 ha (24% of their grazing area) sown to include one of three alternative forages (IRWC or PWC or brassica), and the remaining 2.5 ha was sown in a perennial ryegrass/white clover sward. The entire area (100% of grazing area) of the fourth farmlet was sown in RGWC. Approximately 0.4 ha of each farmlet was located in a paddock where a series of 20 drainage plots (each 40 m by 20 m) were established to measure N leaching. Each of the alternative forages, and the RGWC, were sown on five of the drainage plots i.e., five replicates (combined area of 0.4 ha), which composed about one-half of the area of each alternative forage on each farmlet. The amount of N leached through a mole-pipe network on each drainage plot was also measured. Breeding ewe productivity including liveweight, condition score and lambing performance, as well as N excretion was also measured. In addition, forage growth and DM production were monitored along with chemical and botanical composition. The inclusion of alternative forages into the RGWC system did not affect animal performance. This was due, in part, to animal management. The N leached under various forages was, therefore, able to be compared without the confounding effects of differences in animal performance. The daily urinary N excretion per animal by sheep grazing PWC or brassica was lower (18 to 70%) than the daily urinary N excretion by sheep grazing RGWC or IRWC. It is likely that the diuretic effect of plantain and a lower N concentration in the brassica caused lower N concentrations in urine. Nitrate (NO₃⁻) leaching losses under RGWC, IRWC and PWC were very small in Years 1 and 2 (ranging from 0.4 to 0.8 kg N/ha). The poor persistence of IRWC and PWC at this site and the need to re-establish these forages on the plots resulted in greater NO₃⁻ leaching under these forages in Year 3, negating some of the advantages associated with these forages in Years 1 and 2. In contrast, NO₃⁻ leaching losses were greater under brassica forages (ranging from 0.4 to 6.4 kg N/ha) than under RGWC (ranging from 0.5 to 1.5 kg N/ha). Although sheep grazing brassica forages excreted less urinary N (on an individual animal basis), leaching losses under the brassica treatments were higher. In addition to the effect of cultivation, this increased leaching was likely because brassica plots were grazed for a more extended period during winter than other forages, and there was no crop (forage) cover until the spring resowing; therefore, the urinary N accumulated during winter grazing was displaced by subsequent drainage. With the assumption that the cropped area occupies a relatively small portion of the farm, grazing brassica is likely to result in a relatively small increase in whole farm NO₃⁻ leaching. Overall, NO₃⁻ leaching losses under sheep grazing forages were lower (ranging from 0.5 to 9.5 kg N/ha) than those reported under dairy cattle grazing forages, which suggests that sheep production may offer an alternative land use option for dairying areas where it is difficult to achieve the large reductions in NO₃⁻ leaching required to meet water quality objectives.Item Comparison of maize silage and traditional forage crops in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Science at Massey University, Manawatū Campus, New Zealand(Massey University, 2022) Thant, Aung MyoCattle wintering systems using crops including grazing kale, swede, and fodder beet crops in situ have resulted in soil and water quality deterioration. Nitrate leaching is the most common problem due to the high deposition of urine N driven by excess N intake. Alternative cropping systems offer a potential solution to reduce these environmental problems while maintaining or maximising productivity. We proposed maize silage as an alternative crop because it has high yield potential, flexible feeding requirements, compliments the nutritive value of pasture, and is potentially suitable for more regions in New Zealand in the future due to climate change. However, research needs to determine whether maize silage yield, feed quality and potential nitrate losses during production and utilisation means it is a viable alternative to in situ grazed forage crops in these areas. Field experiments were conducted at Massey University, Tokoroa and Kiwitea to determine forage yield and feed quality, management effects and site differences in 2018/19 and 2019/20. Crop yields and forage N content were utilised to simulate urine N loads from the feeding of these forage crops. The excreted N loads were analysed in APSIM (Agricultural Production Systems sIMulator) to predict nitrate leaching losses. Maize produced significantly higher yields compared with the winter forage crops at all Massey University trials while producing competitive yields at Tokoroa and Kiwitea. Yields ranged from 10,940 to 30,417 kg DM/ha for maize whilst wide and lower yield ranges were observed for the winter forage crops (4,579 to 22,928 kg DM/ha). Irrigation increased yields of forage crops by 29-63%. Similarly, nitrogen fertiliser increased yield by 30%, on average. The faster canopy development of maize has the advantage of intercepting more radiation in summer and suppressing weeds, contributing to greater growth and yield despite a shorter crop season. All forage crops produced forage with good metabolisable energy content (MJ/kg DM); higher values in swede (10.1-14.5) and fodder beet (10.8-14.9) whereas intermediate values in kale (8.9-12.7) and maize (9.9-12.2). However, maize was the highest energy-yielding crop, ranging from about 200-316 GJ/ha while other crops varied from 34 to 217 GJ/ha. Protein content in kale (7.5-16.6% DM) and swede (11.4-18.2% DM) were adequate for non-lactating cows whereas maize (5.4-9.2% DM) and fodder beet (7.6-11.2% DM) were lower than recommended protein levels for dairy cows but offering an opportunity to reduce urinary N excretion. Maize also had recommended fibre content. With higher sugar contents, swede and fodder beet were poor in fibre sources, potentially prone to rumen acidosis unless considered mixed diet with high fibre feed. APSIM modelling indicated that maize would produce the lowest urine N output while swede the highest in simulated feeding. Accordingly, N loads/ha was higher for winter forage crops especially when good yields were produced. When common feeding practices were considered, i.e., off-paddock maize feeding (no urine N deposition) and on-paddock grazing of winter forage crops (high urine N deposition), simulated nitrate losses from maize cropping systems were the lowest. Predicted nitrate losses were 21 and 32 kg N/ha for maize under irrigated and non-irrigated conditions. A ryegrass cover crop further reduced simulated nitrate losses by 20-30%. Predicted nitrate losses for fodder beet, kale, and swede crops were 126, 162, 154 kg N/ha under irrigated conditions and 72, 201, 199 kg N/ha under non-irrigated conditions, respectively in grazing systems.Item An investigation of pasture legume root and shoot properties that influence their rate of decomposition in soil : 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, 2021) Walker, HelenAgriculture is the largest source of GHG emissions (47.8 %) in New Zealand. Emissions are increasing annually, driven by increasing relative productivity. Irrespective of the climate regime, grassland soils have historically sequestered large amounts of atmospheric C into SOM (soil C) raising interest in the potential for agricultural emissions to be mitigated through acceleration of soil C sequestration. Soil C sequestration is a direct result of the rate of deposition (excreta, plant litter, and roots) exceeding the rate of decomposition and can be raised by: 1) increasing the rate of input (manipulating the drivers of vegetation); or 2) increasing the longevity of C in the system. This PhD study tests the hypothesis that C sequestration in pasture soils can be accelerated, by selecting pasture species that contribute slower decomposing litter to soil. A series of laboratory incubation studies were conducted to measure the decomposition rate (CO₂ emissions) of plant shoots and roots with high (Lotus pedunculatus) and low (Trifolium repens) tannin contents. In addition the effects of residue management (fresh and freeze dried), application to soil (fresh - surface, freeze dried - surface, and freeze dried - mixed) and rate of application (2, 5, 10 mg C. g⁻¹ soil) were evaluated. The effect of species, plant management, plant part, and rate of application on C emissions were all statistically significant (P < 0.05), with large variance in CO₂ emissions associated with all treatments. Plant species and plant part influenced the amount of C retained in the soil, although not entirely as expected. Lotus pedunculatus shoot material retained significantly more C than Trifolium repens shoot material at all rates of application (2, 5, 10 mg C. g⁻¹ soil); whereas Trifolium repens root material retained significantly more C than Lotus pedunculatus root material at all rates of application (P < 0.05). Notably plant roots and particularly Trifolium repens roots had slow decomposition rates compared to shoot materials. Research showed that soil and plant residue preparation greatly influenced the total amount of C retained for both shoot and root treatments, with more C retained under conventional incubation techniques (dried - mixed application) than with fresh applications. This indicates that CO₂-C retention in a field situation may be overestimated if predicted using conventional laboratory incubation techniques. However from a research perspective it is infinitely easier to work with pre-dried incubation materials (timing, handling, chemical analysis) so it is highly likely that this style of incubation practice will continue to be the preferred method of research. Care must therefore be taken when extrapolating the results from such incubation studies. A four compartment (2 soil C pools, persistent and labile; and 2 plant C residue pools, fast and slow) computer simulation model was developed and provided an excellent explanation of the CO₂ emissions from the incubation of fresh shoot and root material. The measurement of the metabolisable energy (ME) or lignin contents of plant shoot and root were successful in parameterising (allocating C to) the fast and slow plant residue pools. Plant tannin content was not able to explain CO₂ emission rates. The experimental and modelling studies provide evidence that grazed pasture rotations in mixed farming systems could be manipulated, by careful plant pasture species selection, to accelerate soil C sequestration. Litter and root metabolisable energy (ME) or lignin contents could be useful in species selection, but further research into other pasture species and pasture management techniques is required. Field studies should focus on the role of clover (Trifolium repens) roots in building pasture soil C content.Item Plant associated soil mechanisms of cadmium uptake and translocation in chicory and plantain : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) in Environmental Science at Massey University, Palmerston North, New Zealand(Massey University, 2021) Ubeynarayana, NilushaCadmium (Cd) is a non-essential trace element that is extensively distributed in the environment. Cadmium is effectively absorbed by plant roots and transported to its aerial parts and plants growing in soils with high Cd concentration can accumulate Cd in their roots and shoots to levels which can threaten human and animal health. Elevated Cd concentrations in New Zealand agricultural soils are a function of the country’s long-term history of using Cd-contaminated phosphate fertiliser. Recent studies have identified that two forage species chicory (Cichorium intybus L.) and plantain (Plantago lanceolata L.), which are increasingly used in New Zealand agriculture, accumulate a significantly higher shoot Cd concentration than traditional pasture species. The variation in Cd accumulation between forage species suggests that different plants have different abilities to absorb Cd in roots and translocate this trace element from roots to shoots. Thus, Cd uptake and the potential translocation of Cd to aerial tissues deserves more research, particularly for forage species of economic importance to countries such as New Zealand, where agriculture is dependent on pastoral grazing systems. Information from such studies will be useful in mitigating the continuing risk of Cd transfer into the food chain. The overall aim of this thesis is to better understand Cd uptake and translocation mechanisms in chicory and plantain. Cadmium uptake by plant roots is a function of rhizosphere soil chemistry and the interaction between plant roots and soil solution. Plants exude Low Molecular Weight Organic Acids (LMWOA) into soil solution and these play a key role in regulating Cd bioavailability. A pot trial was conducted to evaluate the influence of increasing soil Cd concentration on the secretion of LMWOAs by chicory and plantain roots and to analyse their impact on plant Cd uptake. Chicory and plantain were grown under increasing Cd levels and showed variable secretion of oxalic, fumaric, malic and acetic acids as a function of Cd treatment. Results revealed that the primary cause for the significant increase of shoot and root Cd concentration in both chicory and plantain, as a function of treatment level, is the significantly greater bioavailable Cd concentration in soil solution with increasing Cd treatment level. The significantly higher shoot Cd accumulation in chicory (18.63 mg Cd/kg DW) than plantain (4.22 mg Cd/kg DW) at the highest tested soil Cd concentration (1.6 mg Cd/kg) can be explained by increased acetic acid and reduced fumaric acid excretion from chicory relative to plantain. Increased understanding of Cd translocation mechanisms in plants requires knowledge of the free Cd2+ ion concentration in xylem saps. However, the determination of low concentrations of free Cd2+ ions in a low volume of xylem sap poses an analytical challenge. To overcome this limitation, a thiosalicylic-acid-modified carbon-paste electrode was developed as an alternative and reliable measurement tool for the detection of free Cd2+ ions in environmental samples, including xylem saps. Compared to other Cd2+ ion ligands used to develop Cd2+-ion-specific electrodes in literature, thiosalicylic acid is a readily available solid, which is stable to air, making it a conveniently handled ligand. The developed electrode showed a lower detection limit of 11 μg Cd/L (0.1 10-6 mol Cd/L) with a linear range from 20 to 100 μg Cd/L (0.18 10-6 to 0.88 10-6 mol Cd/L). To the best of my knowledge, this is the first time a Cd2+ ion-specific electrode was developed to determine free Cd2+ ion concentration in plant xylem sap. The modified electrode has the ability to distinguish between total Cd and free Cd2+ in solution and measure only the free Cd2+ ions in environmental samples, including xylem sap, with high precision (RSD<5%). Subsequent analysis using the thiosalicylic acid modified electrode showed that Cd is mainly in a complex form in chicory and plantain xylem sap. Therefore, a glasshouse experiment was set up with six increasing Cd concentrations in hydroponic solution to assess the impact of LMWOA on xylem sap Cd translocation and shoot accumulation in chicory and plantain. Results revealed that both chicory and plantain showed variable production of oxalic, fumaric, citric, malic and acetic acids with increasing Cd concentration in the hydroponic media. The higher shoot Cd accumulation (by 28-208%) in chicory compared to plantain can be explained in terms of variations in LMWOA production between chicory and plantain. Functional relationship analysis showed that the primary cause for higher shoot Cd concentration in chicory relative to plantain is fumaric acid production in chicory xylem sap which may bind with Cd in chicory and translocate the metal towards shoots. To explore the specific role of fumaric and acetic acids on Cd uptake and translocation in chicory, a glasshouse experiment was conducted with the external addition of fumaric and acetic acid into the hydroponic solution. Increasing fumaric acid concentration in the hydroponic solution showed the ability to reduce Cd uptake and translocation in chicory with a maximum reduction achieved at 10 mg/L and 50 mg/L fumaric acid treatment for root and shoot Cd accumulation, (respectively) for a solution concentration of 1 mg/L Cd. The shoot Cd concentration significantly increased at lower acetic acid treatment levels (1 mg/L) and reduced with increasing acetic acid concentrations from 10 mg/L to 50 mg/L in the presence of 1 mg Cd/L solution concentration. However, the root Cd accumulation increased as a function of acetic acid concentration in the hydroponic solution up to 50 mg/L acetic acid treatment. The root: shoot Cd concentration ratio showed a significant positive correlation (R=0.729 P<0.05) with acetic acid treatments (up to 50 mg/L treatment). Chicory biomass significantly reduced at all LMWOA treatments compared to the control treatment in the presence of 1 mg Cd/L Cd level, showing that there was a limited potential ameliorative effect of LMWOA on Cd toxicity at any concentration for the experimental conditions used in this study. This study highlights that variations in plant root LMWOA secretion and xylem sap LMWOA production between chicory and plantain can explain the different shoot Cd accumulation characteristics of these two forage species. This work shows that fumaric acid plays a fundamental role in both Cd uptake and translocation in chicory, while such a role is not clear for plantain. Low secretion of fumaric acid by roots and production of fumaric acid in chicory xylem sap aid to increase shoot Cd accumulation in chicory compared to plantain while low acetic acid secretion by chicory roots supports the high shoot Cd accumulation in chicory compared to plantain. Future work is recommended to develop a new cultivar of chicory which express traits of variations in fumaric acid production and acetic acid production. Such work may yield new cultivars of chicory which restrict the translocation of Cd from roots to shoots in this important forage species. The future application of this work is to help develop strategies which could assist in mitigating high Cd accumulation in offal to maintain the standards of New Zealand’s food production.