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The Department of Agricultural Sciences consists of animal science, plant science and farm management and agribusiness staff members.
The range of research conducted is quite extensive including: conversion of forests into pasture, alternative dryland pasture species, grain legume agronomy, sustainability in farming systems, nitrogen fixation and nitrogen cycling, shelter on dairy farms, economic viability of NZ farming systems, animal nutrition, immunology etc.
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Item Open Access Introduction to plant diseases(Lincoln College, 1975) Department of Agricultural MicrobiologyThis introduction to plant diseases has been based on, and uses material from, an earlier publication on this topic by Dr I.D. Blair. However, there has been some revision of the text and a number of new illustrations have been included. The aim has been to present information on general principles important in the study of plant diseases, and then to include details on a number of diseases of crops and pastures.Item Open Access Efficacy of dual intracerebroventricular and intravitreal CLN5 gene therapy in sheep prompts the first clinical trial to treat CLN5 Batten disease(Frontiers Media S.A., 2023-10-23) Murray, Samantha; Wellby, MP; Barrell, GK; Russell, KN; Deane, AR; Wynyard, JR; Gray, SJ; Palmer, DN; Mitchell, NadiaMutations in the CLN5 gene cause the fatal, pediatric, neurodegenerative disease CLN5 neuronal ceroid lipofuscinosis. Affected children suffer progressive neuronal loss, visual failure and premature death. Presently there is no treatment. This study evaluated dual intracerebroventricular (ICV) and intravitreal (IVT) administration of a self-complementary adeno-associated viral vector encoding ovine CLN5 (scAAV9/oCLN5) into CLN5 affected sheep (CLN5−/−) at various disease stages. CLN5 disease progression was slowed in pre-symptomatic sheep who received a moderate dose of scAAV9/oCLN5, whilst a higher ICV dose treatment in early and advanced symptomatic animals delayed or halted disease progression. Intracranial (brain) volume loss was attenuated in all treatment cohorts, and visual function was also sustained in both the early and advanced symptomatic treated sheep over the 24-month duration of the study. Robust CLN5 protein expression was detected throughout the brain and spinal cord, and improvements in central nervous system and retinal disease correlates were observed. These findings hold translational promise for extending and improving the quality of life in both pre-symptomatic and symptomatic CLN5 patients, and prompted the initiation of the first in-human Phase I/II clinical trial testing ICV/IVT administration of scAAV9 encoding human CLN5 (https://clinicaltrials.gov/; NCT05228145).Item Open Access Developing an approach to select nitrogen loss mitigations for temperate pasture-based dairy farms(Taylor & Francis Group, 2025) Kok, JC; Amer, PR; Beukes, PC; Al-Marashdeh, Omar; Edwards, P; Glassey, CB; Ledgard, SF; Bryant, RachealThe purpose of this study was to identify intensive pastoral farming practices with high nutrient inputs that contribute to nitrogen (N) loss to the environment, with a focus on New Zealand dairy systems. Barriers to adoption of N mitigation strategies include uncertainty regarding the impact and complementarity of the mitigations. The purpose of this study was to identify and develop a process for determining which N leaching mitigations are likely to complement each other when stacked together in a grazed pastoral dairy farm system and could thereby provide additive benefits towards achieving substantial reductions in N leaching. A list of mitigations for reducing N loss are presented and discussed. The review highlights the importance of the mechanism of N loss, and that by adopting N mitigations with different mechanisms, users can combine practices with complementary effects on reducing N loss. The review also acknowledges that successful N mitigation requires knowledge at tactical and operational levels. There are limited decision support tools available for farmers to assist them with the use of N mitigations that are suitable for individual circumstances. Consequently, the review suggests opportunities for provision of tactical and operational indicators.Publication Open Access Quantification of vernalisation for six forage brassica crops : A dissertation submitted in partial fulfilment of the requirement for the Degree of Bachelor of Science (Honours) at Lincoln University(Lincoln University, 2024) Jamie, CallumThe vernalisation response of six forage brassica crops was studied. The experiment examined phyllochron, days and thermal time to bud, and the thermal time between bud and flower over 0, 3, 6, 9 and 12 weeks of duration of vernalisation treatments of 4°C, 8.1°C, 12°C and 18°C. There was a range of phyllochron values for each crop, where lower vernalisation temperatures and longer durations of exposure resulted in a shorter phyllochron. For ‘Mainstar’ rape, the range was 35.2 to 88.4°Cd/leaf. For ‘Hawkestone’ swede, the range was 55.8 to 137°Cd/leaf. For ‘Firefly’ kale, the range was 75.2 to 178°Cd/leaf. For ‘Endurance’ radish, the range was 48.3 to 133°Cd/leaf. For ‘Hunter’ leafy turnip, the range was 22.0 to 80.8°Cd/leaf. For ‘CC Pallaton’ raphanobrassica, the range was 116 to 149°Cd/leaf. Rape, swede and kale had an obligate vernalisation requirement. A minimum of six weeks at 4°C was required for all plants to develop buds in rape and swede, while kale required the same treatment for any amount of plants to develop buds. Radish, leafy turnip and raphanobrassica indicated a facultative vernalisation response. Buds formed in all radish plants, and in some leafy turnip and raphanobrassica plants, without vernalisation. Three weeks at 4°C were required for all leafy turnip plants to develop buds, while no vernalisation treatment resulted in all raphanobrassica plants with buds. The thermal time to bud decreased with longer durations of colder vernalisation treatments. However, the effect diminished as thermal time approached a crop-specific minimum threshold for bud development. The 18°C temperature treatment did not reduce the thermal time to bud, so it could be beyond the range of inductive temperatures for vernalisation. The thermal time between bud and flower was consistent among durations within the same temperature treatment in kale (303°Cd), leafy turnip (163°Cd), and raphanobrassica (275°Cd). Variation was observed in rape, swede and radish and was likely attributable to the location of temperature measurements and the frequency of data collection. There is an indication that if vernalisation and photoperiod requirements are saturated, raphanobrassica may not have an overlap in flowering time with rape or leafy turnip and could be planted without isolation.Publication Embargo Metabolisable protein supply and diurnal rumen nitrogen management and use in beef steers grazing fodder beet : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2024) Prendergast, SophieThe winter feeding period in New Zealand presents a significant challenge for beef farmers to provide adequate feed for stock to maintain live weight (LWT) gains. The recent development of the fodder beet (Beta vulgaris subsp vulgaris L.) grazing system has enabled high LWT gains over this period. Commercial beef finishing operations have repeatedly reported ~1kg LWT gain per day, with dietary CP of <13%, and high sucrose and water content. Experiments were developed to investigate rumen and plasma nitrogen use and movement in the fodder beet diet, to better understand the mechanisms enabling high daily LWT gains. Experiment 1 of Chapter 3 quantified the daily and diurnal (1, 3, 6 and 24-hour) dry matter (DM) and nitrogen intake of steers grazing industry standard fodder beet diets (90% fodder beet, 10% supplement), to match intakes with LWT gain of the steers, on a commercial farm. A single group of 69 steers (LWT 352kg) grazed fodder beet in situ for >120 days, with average LWT gain 1.0kg per day. Measured DM intakes and in sacco derived coefficients of rumen nitrogen disappearance were used to estimate metabolisable protein supply, compared with the estimated metabolisable protein demand, and then altered to reduce rumen nitrogen losses and increase bypass nitrogen, to provide new estimates of metabolisable protein supply. These data were used to model rumen nitrogen release across the diurnal period. The diurnal DMI was non-uniform, and with a greater proportional intake of leaf and pasture components in the early grazing period. The diurnal nitrogen intake was then strongly non-uniform, with 47, 66 and 77% of daily nitrogen intake by 1, 3 and 6-hours. The feed nitrogen release was also strongly non-uniform, with 28% released in the first hour, then progressively declining to 24-hours. There was a 2.8kg WSC intake in the first 6-hours, and 0.97kg of WSC intake in the final 18-hours, with reduced nitrogen supply. It was concluded this diet was markedly asynchronous in rumen supply of energy and nitrogen. Despite a dietary CP content of 9.4%, the estimated metabolisable protein supply was adequate to meet the estimated metabolisable protein demand according to the AFRC feeding reference standard, but not for the NRC, for the observed LWT gain. Altering quickly degradable protein losses maximally from 0.8 to 0.95 increased the estimated metabolisable protein supply by 7%, and maximally altering undegraded dietary protein by 12%. It was concluded that the non-uniform pattern of nitrogen intake and asynchronous supply of energy and nitrogen to the rumen did not significantly adversely reduce production in steers grazing this diet, as high LWT gains were observed. The strongly non-uniform rumen nitrogen release and high LWT gains suggested nitrogen recycling would be required. Finally, it was therefore concluded that there may be additional nitrogen management strategies in operation, as well as the traditional rumen and whole-animal nitrogen use in steers fed this diet, perhaps due to the novel characteristics of the diet, evidenced by the high LWT gains observed. The strongly non-uniform, asynchronous intakes and high LWT gains observed in Experiment 1 led to the development of Experiment 2 in Chapter 4. This compared the DM and nitrogen intakes, LWT gains, rumen and plasma urea and ammonia concentrations, and plasma amino acids of steers on a fodder beet diet or a synchronous total mixed ration (TMR) on a commercial farm. A total of 938 steers in six mobs of ~150 steers, mobs grazed a diet of ad libitum fodder beet in situ or an ad libitum TMR. The diurnal DM and nitrogen intake of steers on the fodder beet and TMR diet treatments were measured at 1, 3, 6 and 24-hours, and rumen and plasma samples were obtained at two times during the grazing period. The LWT gains were similar (0.98kg per day; P>0.05) between treatment groups, despite the different dietary characteristics. The fodder beet diet treatment displayed a greater non-uniform pattern of DM and nitrogen intake than the TMR diet treatment (P<0.05), with 47 and 75% DMI, and 45 and 78% nitrogen intake, at 1 and 6-hours, respectively, and the TMR 20 and 45% DM and nitrogen intake at 1 and 6-hours, respectively. The fodder beet diet treatment had lower mean rumen ammonia concentrations (86mg /L) and higher mean rumen urea concentrations (992mg /L) (P<0.05) than the TMR diet. Plasma ammonia concentrations were 2.13 and 2.46mg /L at the Mid-Winter (P=0.091) and 1.98 and 2.41mg /L at the Late Winter (P=0.022) sampling for the fodder beet and TMR diet treatments, respectively. Plasma urea concentrations were 75.9 and 254.8mg /L at the Mid-Winter (P<0.001) and 180.6 and 318.92mg /L at the Late Winter (P<0.001) sampling for the fodder beet and TMR diet treatments, respectively. Plasma amino acid concentrations were similar (P>0.05) between the two diet treatments, with no apparent differences in glucogenic or ketogenic amino acid groups. While the TMR diet treatment estimated metabolisable protein supply was higher, both diet treatments supplied adequate metabolisable protein to meet demand despite the lower CP content of the fodder beet diet treatment (11.6 vs. 14.1%). It was concluded that there were important differences in rumen and whole-animal nitrogen use between the two diet treatments, despite the observed LWT gains being similar. Experiment 3 in Chapter 5 was designed to investigate rumen nitrogen use and export across the diurnal period in fodder beet diets. A comparison of fodder beet and pasture feeding in treatment groups of eight pen-fed sheep (LWT: 34.1 and 39.3kg) with total urinary collection was used. Rumen nitrogen loss and microbial protein (MCP) outflow via sub-diurnal urinary nitrogen and purine excretion patterns were quantified. Measurements of total DMI and total urine production were undertaken at periods of 1, 3, 6 and 24-hours, to correspond with measurements conducted in Chapters 3 and 4. At 1 and 3-hours, the fodder beet diet treatment had 2-fold higher (P<0.001) nitrogen intakes (5.38 and 5.73g vs 2.28 and 2.92g, respectively). The urinary nitrogen excretion at 1 and 3-hours was not different between the two diet treatments (P>0.05), with 0.36 and 0.71g nitrogen excretion for the fodder beet diet treatment, and 0.23g and 0.47g nitrogen excretion for the pasture diet treatment. The urinary purine excretion was also similar between the two diet treatments at 1, 3 and 6-hours (P>0.05). The low DM content and heterogeneous nature of the fodder beet diet resulted in greater non-uniform diurnal intake of feed water for the fodder beet diet treatment. The feed water intake was ~3-fold and ~2-fold higher for the fodder beet diet treatment at 1 and 3-hours, respectively, and 48% higher for the fodder beet diet treatment at 6-hours (P=0.001, P=0.001, P=0.002). While urine production was higher for the fodder beet diet treatment at 1, 3 and 6-hours (P=0.001, P=0.004, P=0.017), this was not proportionate to the increase in feed water intake compared to the pasture diet treatment. From the comparatively greater water intake against urinary output in the early (1 and 3-hour) feeding period for the fodder beet diet treatment it was concluded that there was a net water retention, most likely an increased GIT volume as rumen digesta volume. It was concluded the proportionately lower rumen export of nitrogen in the fodder beet than the pasture diet treatment in the early (1 and 3-hour) period of the diurnal cycle to urinary nitrogen or to purines was likely due to greater nitrogen retention in the rumen in the early (1 and 3-hour) feeding period, and this may be a mechanism of nitrogen use and movement in the fodder beet diets that may explain the strong production observed with comparatively low CP content. The results of Experiment 3 suggesting reduced rumen nitrogen export in the early feeding period and with this a net water retention were further examined in Chapter 6 in two experiments. Experiment 4a was designed to quantify the proportion of rumen nitrogen exported from the rumen, or recycled to the rumen, in ad libitum fodder beet fed steers, using infusions of isotopically labelled 15N15N urea to either the plasma or the rumen. Experiment 4b quantified the diurnal rumen volume fluctuations in fistulated rising-one-year-old beef steers fed fodder beet or pasture. Four rising-one-year-old steers in metabolism crates (Experiment 4a) had feed intake measured and total faecal and urinary collection, in a 2 x 2 crossover experimental design. In each of two 76-hour periods separated by an 18-day washout, two steers were infused with the stable isotope of 15N15N urea into the rumen, and two steers were infused with 15N15N urea into the jugular and blood and rumen digesta samples were then obtained from steers at 4-hour intervals for 24-hours to determine abundance of 15N in rumen fluid and plasma, and also in daily urine and faeces. Experiment 4b used complete rumen evacuations every 16-hours for 48-hours to determine rumen digesta volume across the diurnal cycle (0, 8, 24-hours after feeding) in steers grazing ad libitum pasture or fodder beet. Diurnal rumen fluid abundance of 15N for the rumen infusion treatment displayed substantial diurnal variation (P<0.001), with the highest abundance observed (488 δ15N ‰) at morning feeding time, but reaching a nadir (223 δ15N ‰) 12-hours after feeding. The jugular infusion treatment did not vary across the diurnal cycle for rumen fluid 15N abundance (P=0.137), with <20 δ15N ‰ difference from the nadir at 12-hours post-feeding. The rumen and jugular infusion treatment abundances were different at 0, 4 and 20-hours after feeding (P<0.05). Plasma 15N abundance for the jugular infusion treatment did not vary across the diurnal cycle (P=0.182), whereas, the rumen infusion treatment did vary (P=0.006). However, the two infusion treatments were not different in plasma 15N abundance (P>0.05) at any measurement period throughout the diurnal cycle. Mean daily urinary excretion of 15N was 3701 for the rumen 15N infusion compared with 9842 for the jugular 15N infusion (P=0.004). The mean abundance of 15N in faeces was higher (P=0.037) for the rumen (238 δ15N ‰) than the jugular infusion (137 δ15N ‰) treatment. These results indicated low transfer of rumen nitrogen to the plasma, with little diurnal variation in this transfer, and that rumen import of nitrogen was more substantial, and greater at diurnal phases associated with higher rumen activity. Experiment 4b demonstrated that rumen volume increases at 8-hours were greater in fodder beet fed steers, compared to pasture fed steers, and the rumen urea pool was significantly greater at 8 and 16-hours after feeding (P<0.05) for the fodder beet diet treatment, and the rumen ammonia pool significantly greater for the pasture diet treatment, across the entire diurnal cycle (P<0.05). From the results of this series of experiments, it was concluded that, in addition to nitrogen recycling strategies previously described, rumen retention of nitrogen in the early post-prandial period, by these several mechanisms identified in this study, was a possible novel rumen nitrogen management approach which may have influenced the high LWT gains observed with this diet by reducing rumen nitrogen losses. The role of rumen adaptation to a diet of low CP and NDF, but high WSC and water content, in any rumen nitrogen management mechanism should be an important consideration in further research.Item Open Access Impact of implementing female genomic selection and the use of sex-selected semen technology on genetic gain in a dairy herd in New Zealand(Multidisciplinary Digital Publishing Institute (MDPI), 2025-02-01) Mckimmie, Craig; Forutan, Mehrnush; Tajet, Håvard Melbo; Ehsani, Alireza; Hickford, Jonathan; Amirpour, HamedGenomic selection (GS) has changed cattle breeding, but its use so far has been in selecting superior bulls for breeding. However, its farm-level impact, particularly on female selection, remains less explored. This study aimed to investigate the impact of implementing GS to identify superior cows and using artificial mating of those cows with sex-selected semen in a New Zealand Holstein-Friesian (HF) dairy herd (n = 1800 cows). Heifers (n = 2061) born over four consecutive years between 2021 and 2024 were genotyped and their genomic breeding values (GBVs) were estimated. These heifers were ranked based on the Balanced Performance Index (BPI; DataGene, Dairy Australia) Lower-performing cows producing less than 15 L/day (or 20 L/day for older cows) and those with severe mastitis were culled. Cows were mated with HF genetics based on production and udder breeding values, while lower-performing cows were mated to beef genetics. Milking adult cows were mated to bulls with similar BPI value. Annual genetic change was measured using Australian breeding values (ABVg) for milk fat production (FAT), protein production (PROT), fertility (FER), Mastitis Resistance (MAS), and BPI. The genetic merits of the heifers improved annually, with BPI increasing from 136 to 184 between 2021 and 2023, corresponding to a financial gain of NZD 17.53 per animal per year. The predicted BPI gain from 2023 to 2026 is expected to rise from 184 to 384, resulting in a financial gain of NZD 72.96 per animal per year. Using sex-selected semen on the top 50% of BPI-rated heifers in 2024 further accelerated genetic gain. Predicted BPI values for progeny born in 2025 and 2026 are 320 and 384, respectively. These findings revealed that the female GS, combined with sex-selected semen from genomically selected bulls, significantly accelerates genetic gain by improving the intensity and accuracy of selection. The approach achieves genetic progress equivalent to what traditionally would have required eight years of breeding without female GS, and has potential to improve dairy herd performance and profitability.Publication Embargo Reducing nitrogen loss from cow urine patches: Strategies for pasture-based dairy systems : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2024) Kok, Jacobus ChristiaanIn dairy grazing systems, intensive farming practices with high nutrient inputs contribute to environmental pollution with nitrogen (N) loss from farmland, a key contributor to water quality degradation. The New Zealand dairy industry aims to reduce N leaching by 40-60% by 2030. Achieving this target may require transitioning from moderate to lower input systems and implementing mitigation strategies focused on managing high N sources, such as cow urine patches, to improve N use efficiency and reduce leaching risk. While cow urine patches present a primary source of N loss from pasture-based dairy farms, there is limited information on how the relationship between urine volume per urination event and urine patch area affect the N leaching risk. The aim of the thesis is to investigate this relationship and how grazing management strategies influence urine N load and plant N uptake following a regrowth period to mitigate N leaching risk. Additionally, it aims to develop a tool for predicting the impact of management strategies on N loss from urine patches. A key finding of the literature review was that successful N mitigation requires tactical and operational knowledge of implementing mitigation strategies, which has slowed adoption due to uncertainty in implementation. Additionally, the review also identified mitigations centred around the transfer of N, specifically relating to the urine patch, urine N load, or plant N uptake, to improve N use efficiency within a farm system. The review identified a lack of decision support tools for farmers to tailor N mitigations to individual circumstances. One finding was the opportunity to provide tactical and operational tools, such as a urine patch model, to understand urine distribution variation and develop management strategies that target urine and urine patch characteristics to reduce leaching risk. Using a modelling approach (Chapter 3), the aim was to determine if reducing N input alone could achieve the required N leaching reduction with minimal impact on farm operating profit, or if additional mitigation practices targeting N transfer from high N sources, such as cow urine patches, are needed to improve N use efficiency and reduce the risk of leaching. A two-year dairy farmlet study was conducted comparing two farm systems: moderate stocking rate (MSR, 3.9 cows/ha); and lower stocking rate (LSR, 2.9 cows/ha); with a benchmark, high-performing commercial demonstration farm (Lincoln University Dairy Farm [LUDF]; 3.4 cows/ha). Milk yield, pasture production, and quality data were collected, and modelled in FARMAX and OverseerFM to estimate the financial and environmental performance of each farm system. The LSR system produced the best environmental outcome across the two years (2018/19 and 2019/20), leaching an estimated 31% less N compared with MSR and LUDF, but at the cost of profitability. The average, annual milk solid production per ha was 28% less for LSR relative to MSR and LUDF. Correspondingly, the average annual operating profit per ha was 35% less for LSR compared with LUDF. A low N input system reduces production and operating profit to the extent that these mitigation strategies may not be adopted. Therefore, the next step was to target sources of high N input, such as cow urine patch areas, and improve N use efficiency from these areas to reduce the risk of leaching. In Chapter 4, we investigated the effects of grazed pasture canopy characteristics (using plant species and height) on urine patch area. The experiment was conducted during autumn in Canterbury, New Zealand. Warm water was used to simulate urine events, ranging in volume from 1 to 8 L, onto either partially (Lenient, 6-15 cm) or fully (Hard, <6 cm) grazed perennial ryegrass and white clover or pure plantain pastures. A thermal digital camera and imaging software were used to calculate the wetted area of each urine event. When a mid-range volume (4 L) was poured onto lenient grazed pastures, plantain had a greater wetted area than perennial ryegrass/white clover pasture (0.30 m2 ± 0.11 m2 and 0.16 m2 ± 0.08 m2, respectively; mean ± standard deviation). However, the wetted area was similar for plantain and perennial ryegrass/white clover pasture under hard grazing (0.36 m2 ± 0.16 m2 and 0.31 m2 ± 0.13 m2, respectively). Irrespective of pasture treatments and grazing intensity, the relationship between water volume and wetted area was curvilinear, with no significant increase in wetted area for simulated urine events greater than 4 L. Our results indicated that both pasture treatments and grazing intensity (i.e., residual pasture canopy) affect urine patch area, which could have potential implications for the urine N load per urine patch. A limitation of this study was that sward surface height was measured at the paddock level rather than for each urine event simulated. The first field experiment (Chapters 5 and 6) was split into two chapters to evaluate two objectives. The first objective was to investigate the effect of pre-graze pasture mass and time of pasture allocation, on total soil N levels from urine patches and subsequent N recovery from pasture following a regrowth period. The experimental design was a 2 x 2 x 2 factorial arrangement of treatments replicated twice within two experimental runs. The first factor corresponded to two levels of pasture mass using moderate to high mass (2226 or 2662 kg DM/ha respectively) to create lower herbage crude protein content in the high mass treatment. The second factor corresponded to time of allocation of pasture using morning or afternoon allocation. The third factor corresponded to time of urine deposition using anticipated peak (dawn) vs nadir (mid-morning) urinary N concentration and urine N load. A two-way interaction indicated larger urine patch areas for moderate mass at peak times (P < 0.05). As well as a three-way interaction which showed that moderate mass allocated in the afternoon resulted in larger urine patch areas (P < 0.05). Total soil N content was 6% higher (P < 0.05) for moderate mass but did not differ (P > 0.05) between peak and nadir times. High mass treatments showed better regrowth in both urine and non-urine patches. For non-urine patches, the herbage N yield was 18% lower for the moderate compared to the high mass pastures (P < 0.05). From this, we concluded that managing pasture mass can influence pasture recovery and nitrogen utilisation, with potential implications for reducing N leaching risk from dairy farms. Chapter 6 aimed to investigate the relationship between volume per urination, urine patch area, and compressed pasture height. The objective of this chapter was to understand if pasture management practices can affect urine patch area and subsequent urine N load. Cows were fitted with acoustic urine sensors (AgResearch, New Zealand) on their hind legs. The sensors captured the timing, duration, volume per urination, and frequency of urination. Thermal digital imaging with an automated algorithm (AgResearch) was used to estimate urine patch area. Our findings revealed that compressed pasture height did not affect the urine volume and patch area relationship. The relationship was also weaker compared to the findings in Chapter 4. The results showed the importance of accurate urine volume measurement and the impact that measurement errors with different methodologies could have on the relationship with urine patch area. Further research with accurate measurements of volume per urination and corresponding patch area is needed to develop tools to model urine and urine patch characteristics and N leaching risk accurately before they can inform management strategies. The second field experiment (Chapter 7) was carried out to collect additional data on the urine volume and patch area relationship. This study investigated the impact of pasture treatments and height on this relationship through simulated urination events. Conducted at Lincoln University Research Dairy Farm, the experiment utilised a 2 x 8 factorial design, comparing perennial ryegrass-white clover pasture with Italian ryegrass-plantain-red and white clover pasture across eight volume treatments (1-8 L). The study found no significant difference in urine patch area between pasture treatments. A curvilinear relationship between urine volume and patch area was identified (similar to that in Chapter 4), with a quadratic model (Urine patch area = 0.129 + 0.056v – 0.003v²) explaining 54.8% of the variance. Additionally, sward surface height significantly influenced urine patch area, with taller pastures reducing urine patch area, especially at higher urine volumes. This interaction was modelled (Urine patch area = 0.1259 + 0.09278v – 0.004742v² – 0.002363vh + 0.0001293v²h), explaining 70% of the variance. In summary, effective strategies must combine reduced N inputs with mitigation practices targeting N transfer from high N sources, such as cow urine patches, to improve N use efficiency and reduce leaching risk. This thesis has shown that altering pasture mass or the timing of pasture allocation does not significantly influence urine patch area; instead, it was primarily affected by the time of urine deposition. Additionally, these grazing management practices do not enhance plant N uptake from urine patches. Management practices aimed at reducing urine N load at peak times might be more effective at reducing N leaching risk than grazing management. However, grazing management can increase N transfer during the regrowth phase from small urine events. By managing sward surface height when smaller urine events fall within the linear part of the volume and patch area relationship, the urine patch area can be increased at the time of deposition, improving urine N load distribution and plant N uptake. Ultimately, the urine patch model indicated that reducing daily N intake and increasing daily urine volume throughout the year can reduce N leaching by up to 14.5%.Publication Open Access The abundance, activity, and community composition of comammox Nitrospira and canonical ammonia oxidisers in New Zealand soils : A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University(Lincoln University, 2024) Chisholm, ChrisNitrification, the microbial oxidation of ammonia (NH3) via nitrite (NO2-) to nitrate (NO3-) is an important process in terrestrial ecosystems, as it contributes to the production of two environmentally significant products, nitrous oxide (N2O), and nitrate. Traditionally, nitrification was thought to be a two-step process, where ammonia is first converted to nitrite by ammonia-oxidising bacteria (AOB) before nitrite oxidising bacteria (NOB) complete the oxidation to nitrate. Later, it was discovered that a group of archaea (ammonia oxidising archaea, AOA) could also undertake ammonia oxidation, typically in oligotrophic/extreme conditions such as low ammonia availability and pH. The separation of nitrification into two steps involving different microorganisms has puzzled scientists as a single organism completing both steps of nitrification was theoretically assumed to be more efficient. The presence of complete ammonia oxidisers (comammox) was later confirmed by cultivating them from an aquaculture system and a core from a deep-sea oil well. It was found that comammox belongs to lineage II of the genus Nitrospira, a group of bacteria traditionally thought to be responsible for nitrite oxidation. Comammox Nitrospira and canonical Nitrospira can be distinguished by the presence of the ammonia monooxygenase gene (AMO). Furthermore, comammox Nitrospira can be separated into clade A and clade B based on the phylogeny of this gene. Clade A can also be further divided into sub-clades A.1, A.2.1, A2.2, and A.3. Since its initial discovery, comammox Nitrospira has been found in a variety of terrestrial ecosystems. Typically, studies have shown that clade B are more abundant in forest and paddy soils, whilst clade A.2 may prefer agricultural soils. Clade A.1 is seen to be the dominant cluster in natural and artificial aquatic ecosystems such as freshwater wells and wastewater treatment plants. However, the presence and distribution of comammox Nitrospira, relative to canonical ammonia oxidisers, in different soils and relationships with soil and environmental conditions are not fully understood. The research described in this Thesis was designed to fill this knowledge gap and improve our understanding of comammox Nitrospira and canonical ammonia oxidisers. Experiment 1 determined the abundance and community composition of comammox Nitrospira throughout New Zealand Dairy farms and quantified the abundance and community composition of comammox Nitrospira in New Zealand under various land uses. It was concluded that comammox Nitrospira are ubiquitous throughout New Zealand soils. Comammox Nitrospira amoA abundance shared a strong positive and strong negative correlation with soil moisture and pH, respectively. Interestingly, the sequencing analysis determined that the comammox Nitrospira community solely consisted of clade B. Two experiments were devised to investigate these correlations, with respect to canonical ammonia oxidisers. Experiment 2 explored the effect of soil pH, with N inputs, on comammox Nitrospira abundance and community composition in New Zealand dairy pasture soils. Comammox Nitrospira preferred the natural (6.1-6.2) soil pH with no nitrogen amendment. Comparatively, the AOB community (dominated by Nitrosospira) responded positively to soil pH and nitrogen input. This may be due to the difference in ammonia availability. Estimated ammonia availability in the synthetic urine treatments (equivalent to 700 kg N ha-1, N700) accurately predicted the AOB amoA gene abundance. Interestingly, the AOA communities (which were predominantly made up of Thaumarchaeota group I.1b clade E) seemed to prefer the natural and high pH soils over the low pH. This may be due to the lineage of AOA present. AOA did not respond to the application of nitrogen. Experiment 3 investigated the effect of soil moisture and temperature on comammox Nitrospira abundance, transcriptional activity, and community composition, relative to canonical ammonia oxidisers. AOB was the dominant nitrifier in the synthetic urine treated soil regardless of temperature or moisture. Peak AOB amoA transcript abundance was positively correlated with estimated soil ammonia availability. While the nitrification rate and changes in AOB amoA gene abundance followed a similar relationship. Ammonia oxidising archaea were strongly influenced by soil temperature. At 20 °C, AOA amoA peak transcript abundance averaged over 1 order of magnitude higher than at 8 °C. A member of the AOA community associated with the Nitrosocosmicus subclade was positively correlated with ammonium and estimated soil ammonia concentrations. The presence and relative increase of Nitrosocosmicus AOA in a high nitrogen environment poses an interesting contrast to the current scientific opinion. Contrary to Experiment 1, the abundance of comammox Nitrospira amoA was not positively correlated with soil moisture. This suggests that the association is more complex than previously thought. Further research is required to determine the drivers of comammox Nitrospira abundance in a high moisture environment. Overall, the results of this thesis indicate that in New Zealand, AOB are the dominant ammonia oxidiser in a nitrogen-rich environment, such as a dairy farm soil. While the majority of the AOA community prefer a high temperature, low nitrogen environment. However, Nitrosocosmicus-like AOA may respond positively to nitrogen amendment, which challenges our current understanding of terrestrial AOA. Comammox Nitrospira may prefer a slightly acidic, oligotrophic soil environment and do not respond to temperature change. However, they may be the main ammonia oxidiser in some high moisture environments, potentially due to biotic interactions with plants or microbes.Item Open Access Can additives or controlled release coating improve the nitrogen use efficiency of urea fertiliser?(New Zealand Grassland Association, 2024) Bryant, Racheal; Greig, JL; Mangwe, MA plot trial was undertaken to determine whether tactical use of nitrogen (N) fertiliser, applied with or without coating or additive, improved herbage yield and N use efficiency. A randomised complete block design was used to compare no fertiliser (CON), frequent low rates of urea (FL), infrequent moderate rates of urea (IM), IM with controlled release (IM+CR), IM with Progibb (IM+PG), IM with AgriSea (IM+AS), or IM with N-Boost (IM+NB) on irrigated, grazed perennial ryegrass and white clover dairy pastures in Canterbury. The total annual N applied in all fertilised treatments was 190 kg N/ha. The use of fertiliser increased annual herbage yield (16.9 vs 14.5±0.44 t DM/ha/y; P<0.05). Combining urea with a coating or additive altered the distribution of pasture growth but did not affect net annual production or herbage quality. Due to the lack of response and greater application costs with liquid versus granule products, these results highlight the need to consider expected responses to different fertiliser regimes when adopting practices to achieve economic benefits and N efficiency.Item Open Access Forage lucerne for grazing dairy cows: Effects on milk yield, milk urea and fatty acid composition(CSIRO Publishing, 2024) Mangwe, MC; Bryant, Racheal; Beckett, P; Tey, L; Curtis, J; Burgess, R; Al-Marashdeh, Omar; Eastwood, CallumContext. The value of milk components is increasingly recognised for human health benefits (e.g. omega-3 fatty acids, FA), or indicators of nutrient-use efficiency for both animal and environmental benefits (e.g. milk urea, MU). Aims. The study explored whether inclusion of lucerne (Medicago sativa L.) in a perennial ryegrass and white clover (Lolium perenne L. and Trifolium repens L, PRW)-based diet affects milk production, MU concentration, and milk FA composition of dairy cows during mid-lactation. Methods. Thirty-two cows, balanced for milk production (26.1 ± 3.03 kg/cow), MU (16.6 ± 2.84 mg/dL), and days in milk (94 ± 7 days), were evenly allocated into eight groups of four. Groups were then randomly assigned one of two dietary treatments, namely, PRW only (control), and PRW plus lucerne (lucerne). During an 8-day adaptation, control cows were fed a fresh allocation after each milking at 08:30 hours and 16:00 hours to provide 25 kg/cow.day DM of fresh PRW herbage above a target post-grazing height of 4.5 cm height. Cows on lucerne were allocated 10 kg DM of fresh lucerne at 08:30 hours, and 15 kg DM of fresh PRW at 16:00 hours. Apparent nutrient intakes and milk composition were determined on Days 9 and 10 of the study. Key results. Diet treatment did not significantly alter DM or metabolisable energy intake, milk production, or milk fat and protein percentage. However, compared with control cows, nitrogen and linoleic acid (LA) intake increased, and soluble carbohydrate, neutral detergent fibre, and alpha linoleic acid (ALA) intake decreased for cows fed lucerne. Milk urea increased by 43% for lucerne compared with control cows (22.4 vs 15.7 ± 1.43 mg/dL, P < 0.001). Cows grazing lucerne produced milk with a higher concentration of LA and ALA than did the control cows. Increases in milk LA from grazing lucerne were congruent with improvement in intake of the FA from the diet, whereas increases in ALA occurred despite the corresponding lower dietary intake. Conclusion. Supplementing a pasture diet with lucerne increased MU and FA. Implications. Lucerne has the potential to enhance dietary protein supply during periods of deficiency and increase the supply of functional FA in the milk of grazing dairy cattle.Publication Open Access Nitrogen dynamics of autumn wheat (Triticum Aestivum L.) sown on two dates in Canterbury, New Zealand : A dissertation submitted in partial fulfilment of the requirements for the Degree of Bachelor of Agriculture Science at Lincoln University(Lincoln University, 2024) Moody, GeorgiaWheat (Triticum aestivum L.) is a major global crop. It contributes to ~ 20% of global protein intake and is also grown for animal feed. In 2023, 40500 ha of wheat were harvested in New Zealand. It is important to understand the factors that affect crop production to maximize yield. However, the effects of nitrogen (N) on vegetative and early reproductive growth of wheat in high yielding environments is relatively uncharacterized. This experiment quantified light interception, biomass accumulation and partitioning of ‘Kerrin’ autumn feed wheat grown at 0%, 50%, 100% and 150% of the N dose required for a grain yield of 18t/ha in Canterbury, New Zealand. There were two independent experiments, one sown on 20th March 2024 (SD1), and the other sown on 16th April 2024 (SD2). Light interception and ground cover were recorded weekly and biomass harvests occurred every three weeks or at the key Zadok’s stages of 25, 30 and 32, whichever occurred first. Total biomass production for SD1 differed among treatments in the second to last harvest at Z30 stem elongation. The 0% treatment produced 487 kg DM/ha less than the 50, 100 and 150% treatments. The 0% treatment accumulated biomass the slowest at 3.56 kg DM/°Cd. The 100% and 150% treatments showed the highest rate of accumulation at 4.41 kg DM/°Cd whilst the 50% treatment was similar to both the 0% and 100 and 150% treatments. Leaf area index (LAI) for SD1 differed among treatments at the final three harvests. The 150% treatment had the highest LAI of 4.18 at final harvest. 50% and 100% treatments were intermediary with an LAI of 3.97 whilst the 0% treatment had an LAI of 3.5. LAI accumulated at 5.22E⁻⁰³ LAI/°Cd in the 50, 100 and 150% treatments which was faster than the rate of LAI accumulation of 3.87E⁻⁰³ LAI/°Cd in the 0% treatment. SLA differed among treatments at the second to last harvest. 150 and 50% had the highest SLA at 214 cm²/g which was higher than the 0% and 100% treatments at 196 cm²/g. In SD1, the 50% and 150% treatments intercepted a total of 330 MJ PAR/mV at the final harvest. This was higher than the 304 MJ PAR/m² intercepted by the 0% N treatment. The 100% treatments intercepted 324 MJ PAR/m² which was similar to the other treatments. In SD2, there were no differences among treatments for total biomass at each harvest, leaf, stem and dead material at the final harvest or rate of biomass accumulation. The 150% and 0% treatments had a lower proportion of leaf (68%) and higher proportion of dead material (7%) at the final harvest when compared to the 50% and 100% treatments. There were no differences in final LAI, rate of LAI accumulation, SLA, total light interception, or radiation use efficiency (RUE) among treatments in SD2. Differences in biomass accumulation in SD1 were attributed to greater light interception driven by increases in LAI. In SD2, the demand for N was not present during early crop growth which explained no differences among treatments.Publication Restricted Autumn production and water use of caucasian and white clover pastures with or without ryegrass: A dissertation submitted in partial fulfillment of the requirements for the degree of Bachelor of Agricultural Science with Honours At Lincoln University New Zealand(Lincoln University, 2003) Beverland, Chris J.The autumn production and water use of Caucasian and white clover pastures with or without ryegrass were examined at Lincoln University from late summer to mid winter 2003. Dry matter (DM) production and botanical composition were measured from 18 January to 16 July and water use from 5 March until 22 July. Pasture species were analysed for foliar nutritive content. Irrigated swards produced 101 % more total DM (3290 kgDM/ha) than did unirrigated swards (1640 kgDM/ha) from 18 January to 16 July 2003. Dry matter production was greater in Caucasian clover (Trifolim ambiguum M. Bieb) and ryegrass (Lolium perenne L.) swards in late summer (1740 kgDM/ha) compared to white clover (T. repens L.) and ryegrass (1020 kgDM/ha). Swards of white clover and ryegrass had increased production in the winter period (910 kgDM/ha) over Caucasian clover with ryegrass (530 kgDM/ha). This was due to increased ryegrass growth in the white clover swards. No differences in yield between the pure clover species occurred during the experimental period. Caucasian clover with ryegrass had an increased legume proportion in both dryland (58 % ) and irrigated (70 % ) swards in late summer compared with white clover and ryegrass (33 and 28% ). Clover composition declined in both species to be below 10 % in July. Water content in dryland Caucasian clover swards (276 mm) was significantly less than dryland white clover swards (319 mm) to a soil depth of 1.5 m. Pure Caucasian clover had a greater water extraction depth of 1.55 m compared with 1.35 min pure white clover swards, this indicates a deeper root system of Caucasian clover. Nutritive analysis showed Caucasian clover had low sodium levels (0.04 % ) compared to white clover (0.24 %) and ryegrass (0.29 %). Caucasian clover has been shown to be more competitive and productive with ryegrass in the summer period compared with white clover. Low winter productivity of Caucasian clover results in reduced cool season production and Caucasian clover and ryegrass swards.Publication Restricted Yield of turnips and kale grown under drought conditions in the Canterbury high country: A dissertation submitted in partial fulfilment of the requirements for the degree of Bachelor of Agricultural Science with Honours at Lincoln University(Lincoln University, 2007) Reynolds, Robert DouglasDry matter production of kale (Brassica oleracea) and turnips (Brassica campestris) was studied in the Lees Valley, Canterbury, during one cropping season. The rainfall over the summer period was very low, and so moisture stress had a large influence on dry matter yields. Peak yields were 3.6 and 6.2 t DM/ha for turnips and kale respectively. There was no significant effect of nitrogen or phosphate treatments on yield of turnips; however nitrogen significantly increased the leaf yield of kale at one harvest date by 42.7%. This was a nitrogen response of 72.3 kgDM/ha/kgN. Radiation interception changed over time due to changes in the leaf canopies caused by environmental factors. The drought combined with insect damage caused much leaf senescence at first, resulting in a low radiation interception. The leaf canopies redeveloped after autumn rain and so radiation interception increased, until winter frosts caused a decline in leaf dry matter. At all stages of growth kale intercepted more radiation than turnips. The yield changed over time according to pressures imposed on the crops by drought and frost. Turnip yield decreased by 32% between 28/02/07 and 08/05/07 due to drought. The yield then increased by 32% as it recovered in late autumn, but then decreased by 47% due to frost in winter. Kale yield continued to increase throughout the drought, but decreased by 32% in winter. The turnip population declined over time from 48 plants/m² on 21/03/07 to 28 plants/m² on 25/07 /07, due to drought and frost damage. The leaf to bulb ratio of turnips also declined significantly over time from a high of 1.81 on 21/03/07 to a low of 0.43 on 25/07/07. Drought decreased leaf dry matter and had a minimal effect on bulb weight, while frost reduced leaf dry matter more than it reduced bulb weight. Both drought and frost damage resulted in a decline in leaf to bulb ratio. In a dryland environment that is likely to encounter significant summer drought kale will probably deliver a greater dry matter yield than turnips. Nitrogen should be applied if the soil cannot provide enough N for the yield potential of the site.Publication Restricted Autumn water use and yield performance of caucasian and white clover in east coast pastures: A dissertation submitted in partial fulfilment of the requirements for the degree of Bachelor of Horticultural Science with Honours(Lincoln University, 2004) McBeth, Sarah L.The production and water use of irrigated Caucasian clover and white clover pastures with or without ryegrass was studied at Lincoln University, Canterbury. The experimental period extended from late summer to early spring 2004. Irrigation did not affect the total dry matter yield of pastures from 1 March to 9 September, 2004. However, irrigated swards produced 115% more dry matter than dryland pastures from 1 March to 2 June. Caucasian clover (Trifolium abiguum M. Bieb.) yield during the summer (3060 kg DM/ha) was higher than the yield of white clover (Trifolium repens L.) (2390 kg DM/ha) and ryegrass (Lolium perenne L.) (2910 kg DM/ha). During the winter, white clover and ryegrass pastures produced 40% more dry matter from April to June than Caucasian clover combined with ryegrass. This increased production in white clover swards was due to the ryegrass producing 50% more yield in the white clover pastures than in the Caucasian clover and ryegrass pastures. In January Caucasian clover and ryegrass pastures were 25-43% clover compared to 5-15% in white clover and ryegrass pastures. The clover content declined in both white clover Caucasian clover pastures to less than 10% by June. Dryland white clover pastures contained more bare ground than dryland Caucasian clover pastures (30% and 20% respectively). Water use from March to September was higher in irrigated (205 mm) pastures compared to dryland pastures (110 mm). White clover used 35 mm more water than Caucasian clover over the same period. Caucasian clover extracted water from a greater depth than white clover (1.7 m and 1.5 m respectively). Less water in the soil profile beneath Caucasian clover pastures below 1.0 m suggested that Caucasian clover has the ability to extract more water from greater depths than white clover.Publication Restricted Dry matter production and water use of red clover, chicory and lucerne in irrigated and dryland conditions : A dissertation submitted in partial fulfilment of the requirements for the Degree of Bachelor of Agricultural Science with Honours at Lincoln University(Lincoln University, 1999) Brown, HamishThe climate in Canterbury is dominated by hot, dry North-west weather conditions during the summer. The New Zealand standard ryegrass/white clover pasture is unsuitable for high animal production in these conditions because it suffers from low production and persistence. There is a need for alternative species that can increase the productivity of dryland areas and improve the efficiency of water use. To address these problems an experiment was established at Lincoln University in 1996. Dry matter (DM) production and water use of three high quality deep rooted perennial species, red clover (Trifolium pratense L.), chicory (Cichorium intybus L.) and lucerne (Medicago sativa L.), were measured under dryland and irrigated situations. Results from the third year of the experiment are presented and compared with the previous seasons to determine the potential of these species for use in Canterbury. Measurements were made over seven rotations from the 16 August 1998 - 24 June 1999. Under dryland conditions lucerne had greater annual dry DM production (21 t ha⁻¹ ) than red clover (15 t ha⁻¹) and chicory (13 t ha⁻¹ ). All species used 500 mm of water through the season and extracted water to about 2 m depth, thus lucerne had the highest water use efficiency (WUE). Similar yields were obtained in irrigated treatments, but 670 mm of water was used. Consequently the WUE was lower in irrigated conditions compared with dryland for all species. Differences in DM production came from greater lucerne production in the first spring rotation and the last three autumn rotations. There was no difference in DM production between species during the middle three rotations in late spring and summer. Root diseases in red clover and chicory contributed to their reduced production at the end of the third year. From this it was concluded that lucerne had greater potential than red clover or chicory for use in dryland or irrigated conditions in Canterbury.Publication Restricted Dry matter accumulation of three cultivars of turnip (Brassica campestris L.) sown in Canterbury on five sowing dates: A dissertation submitted in partial fulfilment of the requirements for the degree of Bachelor of Agricultural Science with Honours at Lincoln University(Lincoln University, 1997) Collie, B. N.Dry matter production of three cultivars of Brassica campestris L. (cv Appin, York Globe, and Green Globe) sown on five dates (28 January, 11 February, 26 February, 11 March, 27 March) was studied in the field during one cropping season. Sowing date had a large effect on maximum dry matter production, with yields of 1540 g DM m⁻² to 595 g OM m⁻² being recorded for plots sown on 28 January and 27 March respectively. Maximum yields of 1105, 1185, and 1327 g OM m⁻² were achieved by cultivars of Appin, York Globe, and Green Globe respectively. Dry matter accumulation was linearly related to intercepted PAR for all sowing dates. However, there was some variation in efficiencies of dry matter accumulation, with 11 February sown crops producing 3.29 g OM MJ PAR' intercepted, compared to 2.5, 2.3, and 1.6 g OM MJ PAR' for the 26 February, 11 March, and 27 March sown crops. There was no difference in efficiency of dry matter production between cultivars, at most sewings. However, Green Globe was more efficient at producing dry matter at the last sowing. Highest yielding crops also had the best WMAGR of about 21 gDMm⁻²d⁻¹. Time to canopy closure was faster for crops sown on 11 February, and 26 February than for the later sowing date of 11 March (58 DAS v's 82 DAS). Plots sown on the 27 March never achieved canopy closure. Reduced canopy development was shown to occur due to a reduced rate of leaf appearance and leaf expansion. Appearance rate differed over a 53% range for the four sowing dates tested, with new leaves appearing every 2.9 days (plants sown on 11 February), 3.6 days per leaf (sown 26 February), 4.7 days per leaf (sown 11 March) and 5.6 days per leaf (sown 27 March). Comparisons between sowing dates in thermal time showed no difference (p>0.05), with one leaf appearing every 40°C.d. Final leaf length was greatest in higher order leaves. Leaf 2 expanded to 35% of the total length achieved by leaf 6 from plants sown on 11 February. Varying temperatures caused large differences (p<0.05) in the duration (days) of expansion between sowing date, with plants sown on the 11 February requiring an additional 8 days for complete expansion of leaf 6. When expressed in thermal time above a base temperature (0°C), individual leaves showed no difference (p<0.05) in the duration of linear growth with leaf 2 requiring 323.8 °C.d for expansion verses 346. 7 of leaf 6. No difference was observed in growth rate between sowing dates for the expansion of leaf 2. The results are discussed in relation to the determination of phenological development by temperature and radiation, and their impact on the growth of turnips.Publication Restricted Early growth of chickpea (Cicer arientinum L.) under various environmental conditions: A dissertation submitted in partial fulfilment of the requirements for the degree of Bachelor of Horticultural Science (Honours) at Lincoln University(Lincoln University, 1997) Foley, Lynette MaryThree experiments were conducted to examine the early growth and nodulation responses of Kabuli chickpea to: a) Low 'starter dose' nitrogen (0, 15, and 30 kgN/ha) under increasing water stressed conditions, with different inoculation methods (dipped roots, solution, solid peat) (trial 1); b) Increasing nitrate concentrations (0, 1, 2.5, 5 Mol NO₃- m⁻³) with different inoculation rates (0, 1x, 4x) under non-water-stressed conditions (trial 2); c) Applied nitrogen (0-90 kgN/ha) with increasing inoculation rates (field trial). Water stress had increasingly negative effects on all plant DW components, except for increasing root DW by 27%, 18 DAS. At final harvest (49 DAS), shoot, root, nodule, and DWs were reduced 65, 20, and 73% respectively. Root:shoot was consistently greater in stressed plants (70, 53, and 84%, at 18, 34 and 49 DAS). Interactions between nitrogen and irrigation (affecting plant and root DWs, 18 DAS) implied that reduced early growth due to mild water stress may be partially offset by nitrogen fertiliser through greater root (but not shoot) growth. However, at 34 DAS), water-stressed total plant DW did not respond to nitrogen, whereas total plant DWs of fully irrigated plants increased by =38% at both 15 and 30 kgN/ha. Inoculation method had little effect. Shoot DW's were increased with increasing nitrogen concentration (11 and 16 % at 15 and 30 kgN/ha, 49 DAS; 41, 85 and 148%, at 1, 2.5, and 5 Mol NO₃- m⁻³, 43 DAS). Rootshoot decreased with increasing nitrogen concentration at all harvests, except at 43 DAS.Item Open Access Light regulates secreted metabolite production and antagonistic activity in Trichoderma(Multidisciplinary Digital Publishing Institute (MDPI), 2025-01) Esquivel-Naranjo, Edgardo Ulises; Mancilla-Diaz, Hector; Marquez-Mazlin, Rudi; Alizadeh, Hossein; Kandula, Diwakar; Hampton, John; Mendoza-Mendoza, ArtemioSecondary metabolism is one of the main mechanisms Trichoderma uses to explore and colonize new niches, and 6-pentyl-α-pyrone (6-PP) is an important secondary metabolite in this process. This work focused on standardizing a method to investigate the production of 6-PP. Ethanol and ethyl acetate were both effective solvents for quantifying 6-PP in solution and had limited solubility in potato–dextrose–broth media. The 6-PP extraction using ethyl acetate provided a rapid and efficient process to recover this metabolite. The 6-PP was readily produced during the development of Trichoderma atroviride growing in the dark, but light suppressed its production. The 6-PP was purified, and its spectrum by nuclear magnetic resonance and mass spectroscopy was identical to that of commercial 6-PP. Light also induced or suppressed other unidentified metabolites in several other species of Trichoderma. The antagonistic activity of T. atroviride was influenced by light, as suppression of plant pathogens was greater in the dark. The secreted metabolite production on potato–dextrose–agar was differentially regulated by light, indicating that Trichoderma produced several metabolites with antagonistic activity against plant pathogens. Light has an important influence on the secondary metabolism and antagonistic activity of Trichoderma, and this trait is of key relevance for selecting antagonistic Trichoderma strains for plant protection.Item Open Access An economic model evaluating competitive wheat genotypes for weed suppression and yield in a wheat and canola rotation(Multidisciplinary Digital Publishing Institute (MDPI), 2025-01) Nordblom, Thomas L; Gurusinghe, Saliya; Hendriks, Pieter-Willem; Rebetzke, Greg J; Weston, Leslie ARecurrent selection for early vigour traits in wheat (Triticum aestivum L.) has provided an opportunity to generate competitive biotypes to suppress agronomically important weeds. Quantifying the potential benefits of competitive genotypes, including yield improvement and reduced frequency of herbicide application when incorporated into a long-term rotation, is vital to increase grower adoption. In this simple economic model, we evaluated a weed-suppressive early vigour genotype utilising on-farm experimental results and simulation analysis to predict gross margins for a seven-year wheat-canola rotation in southeastern Australia. The model applied a local weather sequence and predicted wheat production potential, costs and benefits over time. An early vigour wheat genotype was compared to commercial wheat cultivars for weed control, yield and actual production cost. With respect to weed control, three scenarios were evaluated in the model: standard herbicide use with a commercial cultivar (A), herbicide use reduced moderately by inclusion of an early vigour wheat genotype and elimination of the postharvest grass herbicide (B) or inclusion of an early vigour wheat genotype and withdrawal of both postharvest grass and broadleaf herbicides (C). Cost savings for the use of a competitive wheat genotype ranged from 12 AUD/ha in scenario B to 40 AUD/ha in scenario C, for a total saving of 52 AUD/ha. The model generated annual background gross margins, which varied from 300 AUD/ha to 1400 AUD/ha based on historical weather conditions, production costs and crop prices over the 30-year period from 1992 to 2021. The benefits of lower costs for each of the three scenarios are presented with rolling seven-year average wheat–canola rotation gross margins over the 30-year period. The limitations of this model for evaluation of weed suppression and cost benefits are discussed, as well as relative opportunities for adoption of early vigour traits in wheat.Item Open Access Impact of year and genotype on benzoxazinoids and their microbial metabolites in the rhizosphere of early-vigour wheat genotypes in Southern Australia(Multidisciplinary Digital Publishing Institute (MDPI), 2025-01) Weston, Paul A; Parvin, Shahnaj; Hendriks, Pieter-Willem; Gurusinghe, Saliya; Rebetzke, Greg J; Weston, Leslie AWheat (Triticum aestivum) is grown on more arable acreage than any other food crop and has been well documented to produce allelochemicals. Wheat allelochemicals include numerous benzoxazinoids and their microbially transformed metabolites that actively suppress growth of weed seedlings. Production and subsequent release of these metabolites by commercial wheat cultivars, however, has not yet been targeted by focussed breeding programmes seeking to develop more competitive crops. Recently, the Commonwealth Scientific and Industrial Organisation (CSIRO), through an extensive recurrent selection programme investment, released numerous early-vigour wheat genotypes for commercial use, but the physiological basis for their improved vigour is under investigation. In the current study, we evaluated several early-vigour genotypes alongside common commercial and heritage wheat cultivars to assess the impact of improved early vigour on the production and release of targeted benzoxazinoids by field-grown wheat roots over a two-year period. Using UPLC coupled with triple quadrupole mass spectrometry (LC-MS QQQ), we quantified common wheat benzoxazinoids and their microbially produced metabolites (aminophenoxazinones) in soil collected from the rhizosphere and rhizoplane of wheat plants over two growing seasons in the Riverina region of New South Wales, Australia. The benzoxazolinone MBOA and several aminophenoxazinones were readily detected in soil samples, but actual soil concentrations differed greatly between years and among genotypes. In contrast to 2019, the concentration of aminophenoxazinones in wheat rhizosphere soil was significantly elevated in 2020, a year receiving adequate rainfall for optimal wheat growth. Aminophenoxazinones were detected in the rhizosphere of early-vigour genotypes and also parental lines exhibiting weed suppression, suggesting that improved early vigour and subsequent weed competitiveness may be related to increased root exudation and production of microbial metabolites in addition to changes in canopy architecture or other root-related early-vigour traits. As previously reported, MBOA was detected frequently in both the rhizoplane and rhizosphere of wheat. Depending on the year and genotype, we also observed enhanced biotransformation of these metabolites to several microbially transformed aminophenoxazinones in the rhizosphere of many of the evaluated genotypes. We are now investigating the role of early-vigour traits, including early canopy closure and biomass accumulation upon improved competitive ability of wheat, which will eventually result in more cost-effective weed management.