Browsing by Browse by FOR 2020 "300307 Environmental studies in animal production"

Rumen microbial profiles have been shown to be accurate predictors of methane emissions in a variety of species, however, it can be very costly and slow to generate a dataset with a sufficient number of individuals measured for methane who also have had rumen samples collected and processed into rumen microbial profiles for these benefits to be applied in industry. We evaluated the potential of combining datasets from New Zealand and Australian sheep to improve our ability to accurately predict methane emissions in Australian sheep. Prediction of Australian sheep methane emissions using rumen microbial profiles and phenotypes from New Zealand was possible, however, it was important to closely match the diets the sheep were fed to have confidence in the predictions. Prediction accuracies of Australian sheep methane emissions were higher when training on data collected on Australian sheep than training on New Zealand sheep; however augmentation of New Zealand data collected on a similar diet enabled more complex models to be run and an improvement in prediction accuracy.

High concentrations of Total Dissolved Solids (TDS) and salts in drinking water, often exacerbated by drought conditions, have been reported to have a detrimental impact on cattle health and performance. This research investigated water quality parameters including TDS and salts (sodium, calcium, magnesium, potassium, aluminium, zinc, iron, manganese, carbonate, bicarbonate, sulphate, nitrate and nitrite). The project summarised the range of TDS and salts in feedlot drinking water across Australia, thus determining potential impacts on cattle health and production. Additionally, feedlots using surface water sources for drinking water had the cyanobacteria species present identified and quantified. Such a study has not previously occurred in Australia.

The study was split into four parts with this report including over 100 historical water samples taken prior to 2018; 68 feedlot managers/owners completed the survey regarding water use delivered in paper and online format; 82 water samples from April to June 2019 from 58 feedlots were analysed for a suite of parameters. Where multiple water sources were used, the source water was analysed, this occurred for 24 samples. Additionally, water samples that included surface water were analysed for cyanobacteria (27 samples). Feedlots participating in the project were equivalent to over 50% of the licenced cattle feedlots.

Of the 68 feedlots completing the paper based and online survey, the majority (64%) source their cattle drinking water from groundwater. On a per-head basis, the use of groundwater as a drinking water source became even more important, covering two thirds of surveyed feedlot cattle. Surface water from dams and rivers were also a common source of water, and less common sources included reverse osmosis treated water from coal seam gas operations, tank roof water, and irrigation water.

The majority of feedlots (75%) were not aware of any issues with their drinking water quality. Of those that indicated that they had concerns about their water quality, seven feedlots identified cyanobacteria (Blue green algae) and Escherichia coli as an issue; four identified turbidity and scale (likely from calcium build up) clogging floats; and four feedlots reported that they now treat water for use in their boiler, but do not treat for cattle, while one feedlot identified high iron as an issue for boiler water.

Among trough water samples analysed for TDS, the majority (86 %) were considered satisfactory for cattle consumption and would not be expected to limit animal performance (≤ 3,000 mg/L). There were, however, cases of poor water quality identified. The highest TDS reported was 11,600 mg/L in groundwater. This water was shandied with surface water and was the maximum in the mixed trough water (5,400 mg/L), which would be expected to limit cattle performance (NASEM, 2016). Chloride was present in the highest concentration of all anions analysed. Nitrate concentrations were highest in the groundwater samples with only one trough sample exceeding the nitrate concentration threshold of 20 mg/L (NASEM, 2016). Sulphate ranged from undetected (<0.3 mg/L sulphur as sulphate) to 575 mg/L, with the highest values in groundwater samples, all samples were below the 1,000 mg/L guideline (ANZEC, 2000). Only 3% of trough samples exceeded the ANZEC (2000) limit of 5 mg aluminium/L. Manganese concentration was highest in surface water samples with 57% to 90% of trough water samples sourced from surface water exceeding the 0.05 mg/L upper-limit guideline (NASEM, 2016). The biological significance of high manganese waters remains to be elucidated, although water concentrations are well below the Maximum tolerable limit reported for dietary Manganese of 1000 mg/kg dry matter (NASEM, 2016). Two surface water samples were in excess of the trigger value for Microcystis aeruginosa (11,500 cells/mL) and were reanalysed and tested for toxins. Only one sample was below a pH 5.1 and one sample above pH of 9.

Several water treatment scenarios were investigated with distributors and installers in Australia with reverse osmosis being the most suitable treatment option. As there are no Australian references for the effect of water quality on the performance of the cattle, Patterson et al. (2004), a publication from the USA, was used for the analysis of benefit and cost of water treatment with reverse osmosis. Treatment with reverse osmosis lead to increased, and more cost-effective, cattle productivity. However, the water used in the article by Patterson et al. (2004) had high sulphate concentrations, so the same responses are unlikely with Australian water. Future research testing water quality in the range of variation experienced by Australian feedlots, in a controlled manner, would allow the industry to determine the most relevant animal production gains and thus the benefits of reverse osmosis.

In conclusion, water quality was determined to be of suitable quality for the majority of feedlots surveyed. Isolated cases of poor water quality were identified. This project is beneficial to the industry as it has yielded a comprehensive understanding of the current sources and quality of feedlot drinking water for a single point in time. Overall, this project will improve feedlot decision-making regarding the conditions when water quality parameters may impact animal health and production in beef cattle feedlots.

The development and validation of management practices to mitigate greenhouse gas (GHG) emissions from livestock require accurate emission measurements. This study assessed the accuracy of a practical inverse dispersion modelling (IDM) technique to quantify methane (CH₄) emitted from a small cattle herd (16 animals) confined to a 63 m × 60 m experimental pen. The IDM technique calculates emissions from the increase in the CH₄ concentration measured downwind of the animals. The measurements were conducted for 7 d. Two types of open-path (OP) gas sensors were used to measure concentration in the IDM calculation: a Fourier transform infrared spectrometer (IDM-FTIR) or a CH₄ laser (IDM-Laser). The actual cattle emission rate was measured with a tracer-ratio technique using nitrous oxide (N₂O) as the tracer gas. We found very good agreement between the two IDM emission estimates (308.1 ± 2.1 – mean ± SE – and 304.4 ± 8.0 g CH4 head⁻¹ d⁻¹ for the IDM-FTIR and IDM-Laser respectively) and the tracer-ratio measurements (301.9 ± 1.5 g CH4 head⁻¹ d⁻¹). This study suggests that a practical IDM measurement approach can provide an accurate method of estimating cattle emissions.

The macroalgae, Asparagopsis spp. naturally synthesizes and accumulates halogenated compounds such as bromoform, which has shown to be an effective enteric methane inhibitor. In sheep, a methane reduction of 80% was observed when A. taxiformis was included at 3% (OM basis) compared with the control (Li et al., 2018). Li et al. (2018) included the Asparagopsis in a modified total-mixed ration of a pelleted basal ration with additional crushed lupins as the carrier. Work in beef cattle (Kinley et al., 2020) reported high abatements (80% at 0.2% OM inclusion in comparison to the control) in a total-mixed ration. The effects of diet composition, namely increasing fibre content and influence on enteric methane abatement has also been reported (Roque et al., 2021), with lower abatement associated with higher dietary fibre. In Australia, most sheep are managed in extensive systems consisting of high-fibre forage diets and are unlikely to be offered a feed additive in a total mixed ration. At present, it is unknown what the recommended dietary inclusion level of A. taxiformis is for grazing systems, where animals are on a high-fibre diet. The aim of this study was to determine the dose-response of bromoform presented in a canola oil (SEAFEED™ SeaForest Pty Ltd) using a supplementary pellet as a carrier for sheep fed a high-fibre diet.

The feasibility and efficacy of inoculating with rumen fluid as a method to control hydroxypyridone (DHP) toxicity in ruminants on high leucaena diets in eastern Indonesia were investigated. Rumen fluid collected from 2 buffalo identified as 'protected', due to low levels of DHP excretion in urine, was orally administered to animals identified as 'unprotected' and concentrations of urinary DHP monitored. Control animals were dosed with water only. Treatments were randomly allocated to 10 recipient animals: 3 goats and 7 cattle. All animals were fed a diet containing freshly cut 100% leucaena during the 18 day study period. Measurement of urinary DHP via colorimetric analysis commenced 8 days prior to animals being drenched with rumen fluid or water and continued for 10 days afterwards. Urinary DHP levels in animals that received the inoculum did not differ from those in the control group 10 days post-inoculation (mean 425 mg DHP/L; P = 0.50). Unexpectedly, DHP levels in all animals (rumen fluid and water) declined with time, although the difference did not reach statistical significance (P = 0.12), and remained above considered safe threshold levels. These results suggest that transfer of rumen fluid to overcome leucaena toxicity in animals in eastern Indonesia may not be effective despite great care having been taken to ensure the viability of the anaerobic organisms during the inoculation process; this methodology is also not a practical solution to replicate on a commercial scale. The findings suggest that inoculation may not be necessary if animals previously naïve to leucaena are able to adapt to DHP toxicity by other means.

Genotype-by-environment interaction is caused by variation in genetic environmental sensitivity (GES), which can be subdivided into macro- and micro-GES. Macro-GES is genetic sensitivity to macro-environments (definable environments often shared by groups of animals), while micro-GES is genetic sensitivity to micro-environments (individual environments). A combined reaction norm and double hierarchical generalised linear model (RN-DHGLM) allows for simultaneous estimation of base genetic, macro- and micro-GES effects. The accuracy of variance components estimated using a RN-DHGLM has been explicitly studied for balanced data and recommendation of a data size with a minimum of 100 sires with at least 100 offspring each have been made. In the current study, the data size (numbers of sires and progeny) and structure requirements of the RN-DHGLM were investigated for two types of unbalanced datasets. Both datasets had a variable number of offspring per sire, but one dataset also had a variable number of offspring within macro-environments. The accuracy and bias of the estimated macro- and micro-GES effects and the estimated breeding values (EBVs) obtained using the RN-DHGLM depended on the data size. Reasonably accurate and unbiased estimates were obtained with data containing 500 sires with 20 offspring or 100 sires with 50 offspring, regardless of the data structure. Variable progeny group sizes, alone or in combination with an unequal number of offspring within macro-environments, had little impact on the dispersion of the EBVs or the bias and accuracy of variance component estimation, but resulted in lower accuracies of the EBVs. Compared to genetic correlations of zero, a genetic correlation of 0.5 between base genetic, macro- and micro-GES components resulted in a slight decrease in the percentage of replicates that converged out of 100 replicates, but had no effect on the dispersion and accuracy of variance component estimation or the dispersion of the EBVs. The results show that it is possible to apply the RN-DHGLM to unbalanced datasets to obtain estimates of variance due to macro- and micro-GES. Furthermore, the levels of accuracy and bias of variance estimates when analysing macroand micro-GES simultaneously are determined by average family size, with limited impact from variability in family size and/or cohort size. This creates opportunities for the use of field data from populations with unbalanced data structures when estimating macro- and micro-GES.

Ruminants are central to the economic and nutritional life of much of sub-Saharan Africa, but cattle are now blamed for having a disproportionately large negative environmental impact through emissions of greenhouse gas (GHG). However, the mechanism underlying excessive emissions occurring only on some farms is imperfectly understood. Reliable estimates of emissions themselves are frequently lacking due to a paucity of reliable data. Employing individual animal records obtained at regular farm visits, this study quantified farm-level emission intensities (EIs) of greenhouse gases of smallholder farms in three counties in Western Kenya. CP was chosen as the functional unit to capture the outputs of both milk and meat. The results showed that milk is responsible for 80-85% of total CP output. Farm EI ranged widely from 20 to >1 000 kg CO₂-eq/kg CP. Median EIs were 60 (Nandi), 71 (Bomet), and 90 (Nyando) kg CO₂-eq/kg. Although median EIs referenced to milk alone (2.3 kg CO₂-eq/kg milk) were almost twice that reported for Europe, up to 50% of farms had EIs comparable to the mean Pan-European EIs. Enteric methane (CH₄) contributed >95% of emissions and manure ~4%, with negligible emissions attributed to inputs to the production system. Collecting data from individual animals on smallholder farms enabled the demonstration of extremely heterogeneous EI status among similar geographical spaces and provides clear indicators on how low EI status may be achieved in these environments. Contrary to common belief, our data show that industrial-style intensification is not required to achieve low EI. Enteric CH₄ production overwhelmingly drives farm emissions in these systems and as this is strongly collinear with nutrition and intake, an effort will be required to achieve an "efficient frontier" between feed intake, productivity, and GHG emissions.

Effects of feeding levels below maintenance requirements of metabolizable energy (MER) and of feed supplementation on fecal nutrient and microbial C concentrations were evaluated. In experiment 1, Rhodes grass hay only was offered to Boran steers at 80%, 60%, and 40% of individual MER, while steers at 100% MER additionally received a concentrated mixture. This reduction in MER decreased N, increased fungal C but did not affect bacterial C concentrations in feces. In experiment 2, Holstein × Boran heifers were offered a poor-quality roughage diet without supplement, with sweet potato vine silage or with a urea-molasses block. These two supplements did not affect the fecal chemical composition or fungal C but increased bacterial C concentrations in feces. Across all data, the fungal C/bacterial C ratio was positively related to N and negatively to neutral detergent fiber concentrations in feces, indicating diet-induced shifts in the fecal microbial community.

Dust collected from the poultry house has been increasingly used as a population-level sample to monitor the presence of pathogens or to evaluate the administration of live vaccines. However, there are no guidelines for the storage of this sample type. This study investigated the stability of infectious laryngotracheitis virus (ILTV), a DNA virus, and infectious bronchitis virus (IBV), an RNA virus, in poultry dust kept under temperature and moisture conditions that mimic on-farm and laboratory storage. Dust samples were collected from chicks spray vaccinated with a live IBV vaccine and inoculated with a field ILTV strain via eye drop. Samples were stored under different moisture conditions (dry = 2% moisture, moist = 22%-71% moisture) and temperatures (-20, 4, 25, and 37 C) for different durations (0, 7, and 14 days, and 1, 2, 3, and 4 mo) in a factorial arrangement, followed by quantitative PCR for detection of virus genome copies (GC). The length of storage, moisture level, and storage temperature affected the viral genome load for ILTV and IBV but did not affect the number of positive samples for each virus. All treatment combinations were ILTV positive for at least 4 mo. In dry dust samples, all storage temperatures or durations had quantifiable ILTV or IBV GC. Moisture addition had a detrimental effect on viral genome load, causing an overall reduction of 0.3 log ₁₀ for ILTV GC (7.29 and 6.97 log ₁₀, P = 0.0001), and 1.3 log ₁₀ for IBV GC (5.95 and 4.66 log ₁₀, P = 0.0001), which are unlikely to have biologic significance. In conclusion, dry dust can be stored at any temperature up to 37 C for at least 4 mo without loss in qPCR detection of ILTV or IBV GC. Collection or storage of moist dust should be avoided, or air drying prior to storage is recommended if only moist dust is available.

The impact of cold stress on feedlot cattle has received limited investigation in temperate climates. However, cold stress has been found to impact cattle welfare and production in temperate climatic conditions, where ambient temperature (T_A), precipitation, relative humidity (RH), wind speed (WS) and solar radiation (SR) all influencing apparent temperature. While there are many indices to quantify cold stress in cattle, there are limited indices that directly relate to cattle and account for all the interactions between climatic variables. This makes cold stress difficult to quantify, with on-cattle measures such as core body temperature and shivering difficult metrics to obtain in feedlot cattle. Moreover, individual cattle will react differently to cold conditions based on their production, age, sex, coat characteristics (colour and type), breed and nutrition. While cold stress can be difficult to measure, the production status, behavioural and physiological effects of cold stress have been identified, but generally under what could be considered as extreme cold stress events. Similarly, while mitigation strategies such as shelter, bedding and windbreaks have been investigated, limited information is available surrounding their usefulness in temperate climates. Further research is needed to fully investigate the effects of cold stress and how to mitigate those effects in feedlot cattle under conditions, such as those found in Australia.

The objective of this study was to evaluate the influence of supplementing lactating dairy cows with Saccharomyces cerevisiae on milk production and composition, cow behavior, and physiological responses during summer. Twenty primiparous cows were used and two treatments were imposed: (1) control (CON); and (2) probiotic supplementation (PRO; S. cerevisiae, providing 1010 colony forming units (CFU) per day). Rumen temperature (TRUM, °C) and pH were obtained via rumen boluses. Rumen temperatures were obtained from all cows (n = 20) at 10-min intervals and ruminal pH were obtained from five cow pairs (n = 10) at 10-min intervals. Ambient temperature (TA; °C), relative humidity (RH; %), wind speed (WS; m/s), and solar radiation (SR; W/m2) were recorded at 10-min intervals. The temperature humidity index (THI) was calculated using TA and RH. Cows were milked twice daily. Milk fat (%), protein (%), lactose (%), and somatic cell count (SCC, ‘000) were evaluated on 16 occasions. Cows were observed three times (0800 h; 1200 h; and 1400 h) daily for panting score (PS); respiration rate (RR); posture (standing/lying); shade utilization; and cow activity (eating/drinking/ruminating). Individual PS were used to calculate a mean panting score (MPS) for CON and PRO treatments for each observation. S. cerevisiae did not influence milk yield (P = 0.87), fat (P = 0.82), protein (P = 0.26) or SCC (P = 0.19), although there was a tendency for PRO cows to have higher lactose (P = 0.06). Probiotics did not influence the proportion of cows utilizing shade (P = 0.42); standing (P = 0.41); ruminating (P = 0.72); or drinking (P = 0.40). All cows exhibited an increase in RR (> 24 bpm) at 1200 h and RR showed a steady increase as THI increased (P < 0.0001), regardless of treatment (P = 0.96). Both CON (35.8%) and PRO (40.2%) exhibited an increase in MPS as THI increased from thermoneutral (THI ≤ 74) to very hot (THI ≥ 84.1; P < 0.001). However, PRO cows had lower (2.19 ± 0.09; P < 0.0001) MPS compared with CON (2.54 ± 0.22) cows when THI was categorized as very hot (THI ≥ 84.1). Rumen pH were not influenced by treatment (P = 0.38), however TRUM of PRO cows were 0.2 °C lower across days (P < 0.0001) and hours (P < 0.0001). These results suggest that supplementing cows with S. cerevisiae may support thermoregulation via decreased TRUM and MPS; however, further studies are required.

Dark cutting beef is defined by Meat Standards Australia (MSA) as carcasses that have an ultimate pH (pH_u) > 5.70 when measured at grading. Dark cutting beef is associated with deteriorated meat quality, thus beef producers are generally penalised by abattoirs to compensate for reduced saleable quality product. Non-compliant Meat Standards Australia beef, based on pH, has been estimated to cost the Australian beef industry approximately A$55 million per year and the estimated cost to beef producers is approximately A$0.50 per kg carcass weight or A$7.09 for every carcass graded in the Meat Standards Australia system.

Dark cutting (DC) is a complex multifactorial problem that is influenced by nutrition and preslaughter factors which induce stress and exercise and increase muscle glycogenolysis. The condition is generally attributed to low muscle glycogen stores at slaughter, which is either a function of insufficient glycogenesis on farm or too much glycogenolysis during the preslaughter period due to exercise or stress.

The 2015 Meat Standards Australia Australian Beef Quality audit showed the incidence of dark cutting in grain fed beef was between 1.5% and 2.5% with a peak incidence of 2.5% in March. Australian feedlot producers have anecdotally suggested there is an increased incidence of dark cutting during the summer months. Cattle under heat stress have higher respiration rates and panting to induce evaporative cooling, and have a reduced feed intake. The lowered nutritional intake combined with increased levels of epinephrine (adrenaline) and catecholamine expression during heat stress decrease glycogenesis and stimulate glycogen mobilisation. However, the influence of environmental conditions and/or the duration of exposure to these hot conditions on the incidence of dark cutting had not been established. The overarching objective of this research was to establish whether there was an association between environmental conditions and the incidence of dark cutting in grain fed cattle. This thesis is comprised of four experimental chapters examining the seasonality of dark cutting, a retrospective analysis of historical MSA grading data, plus an in depth examination of feedlot and processor factors affecting the incidence of DC.

The first experiment investigated if there was any inherent impact of seasonality on the incidence of dark cutting in Australian grain fed beef, using a Meat Standards Australia carcass data set. Carcasses were classified as dark cutting when pH measured at grading was > 5.70 in the rib eye muscle (longissimus thoracis et lumborum) of the chilled carcass at the quartering site approximately 12–24 hours post-mortem. Utilizing data from 2,005,925 Meat Standards Australia carcasses, which were supplied from 12 feedlots and sent to 17 different abattoirs over 5 years were analysed. Carcass data were categorised into five groups based on the location of feedlots across geographical regions. These data were then analysed using a seasonal and trend decomposition using locally estimated scatterplot smoothing (loess time series analysis) to establish if a seasonal trend in dark cutting exists in Australian grain fed carcasses. Results show that the majority of feedlots had seasonality scores below 0.3 suggesting that dark cutting in grain fed beef has either low or no seasonality. Three feedlots had slightly higher seasonality scores (0.3 to 0.4), however these are still considered to be low scores. These results highlight there is limited evidence of a seasonality effect on dark cutting in the carcasses evaluated in this study. However, the presence of seasonality scoring above 0.3 for three participating feedlots, highlighted the need for a deeper understanding of the impacts of climatic conditions and specific weather events at the feedlot on the incidence dark cutting.

The second experiment evaluated the relationship between climatic conditions prior to feedlot departure on the incidence of dark cutting in grain fed beef by combining historical Meat Standards Australia carcass data with Bureau of Meteorology weather data. Data records for 2,795,754 carcasses from 17 commercial feedlots sent to 16 abattoirs over 6 years were evaluated in this study. Weather data recorded at 30 minute intervals were obtained from the weather station closest to each feedlot. Climatic data were amalgamated into daily observations and a series of predictors including ambient temperature, relative humidity, wind speed and direction, rainfall, solar radiation and temperature humidity index were included in the analysis. Lag interactions from 24 hours out to 28 days before leaving the feedlot were generated. The incidence of dark cutting was determined as percentage per cohort with an ultimate pH > 5.7. The data were analysed using three separate models. Model 1 included feedlot, abattoir, hormone growth promotants status and sex as fixed effects. Model 2 incorporated the fixed effects within Model 1 and minimum, maximum and standard deviation of ambient temperature and relative humidity, daily range in ambient temperature, average wind speed and rainfall as covariates. Model 3 incorporated minimum, maximum, range and standard deviation of temperature humidity index, average wind speed and rainfall as covariates in addition to the fixed effects of Model 1. The results showed that higher maximum ambient temperature, relative humidity and temperature humidity index in the 3 to 28 days before consignment were all associated with an increased incidence of dark cutting (P < 0.05), but not in the 48 hours before consignment (P > 0.05). Lower minimum ambient temperature and lower temperature humidity index values were also associated with an increase in the incidence of dark cutting across all lag periods (P < 0.05). Increased variation in the temperature humidity index and ambient temperature in the 48 hours before consignment increased dark cutting (P < 0.05) while increased standard deviation of temperature and temperature humidity index range also increased dark cutting in the 14 and 28 day before feedlot exit (P < 0.05). Smaller minimum ranges in ambient temperature in the 28 days before consignment also reduced dark cutting (P < 0.05). Even though many different climatic conditions impacted the incidence of dark cutting, they only accounted for a further 0.1% to 0.2% of variance in the incidence of dark cutting. In contrast, the feedlot and abattoir animal management factors included in the models accounted for 21% of the variation in dark cutting. This analysis showed the major causes of dark cutting in lot fed cattle were driven by factors within the feedlot and abattoir which needed to be quantified further.

The supply chain experiment analysed the significance of feedlot and abattoir factors including carcass traits, lairage time, weather conditions during lairage and other abattoir factors on the incidence of dark cutting in 142,228 grain fed carcasses. This study analysed data from cattle that were supplied from seven feedlots and processed at three abattoirs over 1 year. The average incidence of dark cutting was 2.8%. Increased wind speed (P < 0.05) and rain (P < 0.001) during lairage at the abattoir was associated with an increased risk of dark cutting, whereas variation in ambient temperature, relative humidity or temperature humidity index in lairage did not influence dark cutting. Heavier carcasses with whiter fat, larger hump heights, more rib fat, higher marble scores and lower ossification had lower incidences of dark cutting (P < 0.001). The abattoir and the grader at the abattoir also had significant effects on the incidence of dark cutting (P < 0.001). Increased time in lairage and reduced time to grading markedly increased the incidence of dark cutting (P < 0.001), which suggests that reducing the time in lairage and increasing the time between slaughter and grading are the two major ways to reduce dark cutting in grain finished carcasses. These factors reduce the opportunity and time for the cattle to experience stressful situations before slaughter and maximise the opportunity for the meat to reach pH_u, reducing the incidence of false positive dark cutting caused by grading too early.

The feedlot component of the supply chain experiment analysed the effect of climate, animal and feedlot factors on the incidence of pH non-compliance in Australian grain fed cattle. Data on the same 142,228 carcasses from seven feedlots processed at three abattoirs over 1 year were analysed. The production factors which were associated with increased pH noncompliance included feedlot, sex, hormone growth promotants, cattle morbidity and longer days on feed. pH non-compliance was also increased by reduced solar radiation, lower wind speeds, increased ambient temperature, more rain, higher average temperature humidity index and more hours spent above heat load index threshold of 86 in the week before consignment. Interestingly transport duration did not impact the incidence of dark cutting.

The causes of dark cutting in grain fed cattle are extremely multifactorial with many small factors having an impact. This thesis identified the main drivers across the supply chain which increased the risk of dark cutting in Australian grain fed cattle. This will help lot feeders identify cattle that are at higher risk of dark cutting and alter their pre-slaughter management to ensure cattle have minimal time in lairage and maximal time post-mortem before grading. Climatic conditions do impact the incidence of dark cutting, however management of cattle before slaughter and of carcasses after slaughter has a larger effect on the incidence of dark cutting.

Population growth and improving living standards are leading to a growing demand for beef. The understorey in the 19 million hectares of oil palm plantation worldwide represent a source of cattle feed, while also sparing additional land conversion for grazing. Research on cattle grazing under oil palm is novel and knowledge is lacking on long-term profitability and sustainability of the system, a major deterrent to cattle–oil palm farming system adoption. Here we review the current literature on cattle grazing in oil palm plantations, to highlight the knowns and unknowns of grazing impacts on the understorey, cattle and oil palm productivity, as well as economic implications. This review's major outcomes are the following: (i) although understorey utilization as feed is a major advantage of cattle–oil palm integrated farming systems, declining understorey productivity under ageing plantation indicates the need for alternative solutions for sustained cattle productivity over the plantation's lifecycle; (ii) oil palm yields were reported to increase under cattle integration but evidence was weak, both oil palm yields and the pathways through which oil palm yields are impacted by cattle grazing should be further explored; (iii) economic analyses showed cattle grazing under oil palm plantations was profitable for large-scale oil palm producers due to cattle sales, and returns were further enhanced by reductions in weeding and fertilizer costs; (iv) sustainable cattle grazing was found to be difficult in smallholder oil palm plantations due to land constraints and the current practice of free-grazing; options for improving grazing sustainability and profitability in these systems should be explored. This systematic review concluded that cattle integration in oil palm plantations has great potential but further research is required to develop locally specific productive and sustainable systems of grazed cattle integration with oil palm plantations.

Wet litter is a recognized issue in commercial poultry production and litter quality has come under great scrutiny with the introduction of farming scheme standards by animal welfare organizations in Australia (RSPCA, 2013). According to RSPCA (2013) meat chicken standards, "litter must be maintained in a dry and friable condition." Litter conditions may affect odour emissions and thus litter properties were studied to correlate with specific odorants.

There is a hypothesis in the anthropological literature (e.g. Milton, 2003) that our complex human brains would not have developed without hominoids having routine access to foods of animal origin. In many countries, therefore, the consumption of animal source foods, and meat in particular, became part of a cultural identity, while in others (e.g. India) vegetarianism has long been part of the cultural/religious identity (approx. 30% of Indians are vegetarian, although the majority of those consume milk products). In the twenty first century, humans can, theoretically, have access to non-animal-derived sources of nutrients required for brain development, so animal products are no longer as important for nutrition as they were for our ancestors. There are also other issues, however, associated with livestock production which impact on the consumption of animal products. Culture in many countries has evolved to give a higher priority to the welfare of farm animals and there are additional ethical issues associated with the negative environmental impacts of livestock production. We read a lot, therefore, about the rise of veganism, with calls for diets free of animal products, yet there is also evidence that the consumption of meat at a country level increases as the income of that country increases (FAO, 2009). The average global per capita meat consumption at over 40 kg, has, therefore, doubled from the consumption in 1960. However, the annual global rate of increase in both meat and milk consumption is projected (OECD/FAO, 2017) to decrease slightly in the decade from 2017-2026, to 1.5% per annum for meat and 1.9% per annum for milk.

Ammonia (NH₃) is a nitrogenous environmental pollutant that is associated with eutrophication and contamination of terrestrial ecosystems and can have detrimental impacts on human and livestock health. Livestock production is a significant contributor to global NH₃ emissions largely as a result of nitrogen losses from the breakdown of manure. Intensively housed livestock situations, such as exporting live animals, lead to increased concentration of manure and development of the manure pad through accumulation of faeces and urine. This increase in higher concentrations of NH₃ may also lead to health and welfare concerns of both humans and animals. Due to the complex interactions of factors contributing to the volatilsation of NH₃ from manure, NH₃ production in livestock operations is difficult to accurately predict with the various methods and modelling approaches currently utilised. Live export is an example of an intensively housed livestock industry where NH₃ production has the potential to impact health and welfare of humans and animals on board. Quantification of NH₃ using current methods is difficult in this industry due to highly variable conditions and limited understanding of how voyage conditions may affect NH₃ production. Methods to quantify NH₃ emissions from manure have some limitations in adoption and understanding of manure pad variables introduced directly by animals, such as disturbance. Use of in vitro methods rather than large scale animal experiments allows understanding of ammonia and testing of dose rates of ameliorates and also aligns with the animal ethics replace, reduce and refine.

The primary objectives of the current thesis were to develop an inexpensive, high throughput method of quantifying NH₃ in solution, and an in vitro method of quantifying NH₃ production from manure that would (1) evaluate the optimal microchamber design to quantify NH₃ production rates from manure; (2) quantify the effect of disturbance of manure on NH₃ production rates; (3) succeed as an alternative method of testing NH₃ production to reduce the need for, or better inform, large-scale animal experiments (4) successfully evaluate the effectiveness of mitigation techniques.

This thesis includes a review of the available literature and three experimental chapters addressing the development and use of the in vitro method and assessment of an available NH₃ mitigation technique. Findings and implications of this thesis include:

Development of a novel high-throughput plate-based analysis with a high degree of accuracy adapting the Berthelot method of quantifying NH₃-N in solution. Boric acid solution was shown to be an effective eluent for gas trap sampling of NH₃;

Successful development of a novel microchamber system. The microchamber design was evaluated and a standard size chosen for the following experiments. It is hypothesised interactions with pad surface areas and depth were dependent on variables facilitating mass transfer such as air flow and headspace. Microchamber results did not meet hypotheses, as (i) increasing microchamber manure surface area did not result in constant rates of NH₃/m² production, and (ii) increasing manure depth resulted in lower rates of NH₃/m² as opposed to a consistent production relative to surface area. The standard size chosen for the experiment on clinoptilolite (zeolite) was a surface area of 90mm diameter (SA₉₀) and manure depth of 30mm (D₃₀), based on less variation in results and ease of use;

Simulated animal movement through four repeated disturbances of cattle manure in micro-chambers every 90 minutes, resulted in increasing rates of NH₃ production (slope coefficients) with each disturbance over 480 min for all treatments. This suggests cattle movement may generate continual fluxes of NH₃ production from the manure over time;

The application of zeolite was successful in reducing NH₃ production from cattle manure. All treatments achieved an immediate and sustained reduction in NH₃ production over 21 hours. The minimum (1%) and maximum (10%) in-pad application rates resulted in a 32% to 70% reduction in NH₃ emissions over 21 hours, respectively.

Application of zeolite suspended in the microchamber headspace reduced the presence of gaseous NH₃ contamination in the air by 37% over 21 hours, similar to 1% zeolite applied in-pad over 21 hours.

Overall, the high-throughput plate-based methodology and microchamber system provided valuable insight into increasing fluxes of NH₃ volatilsation with disturbance and optimal application rates of zeolite to reduce NH₃ production. The aim of the microchamber design was to standardise headspace and air exchange rates in order to quantify the effect of increasing manure surface area and depth. The results demonstrated air flow dynamics are important and challenging factors when comparing these variables, however a standardised microchamber was successfully deployed to compare and determine an optimal application rate of zeolite for NH₃ reduction.

The slope of regression in a reaction norm model, where the performance of a genotype is regressed over an environmental covariable, is often used as a measure of stability of genotype performance. This method could be developed further by partitioning variation in the slope of regression into the two sources of genotype-by-environment interaction (G×E) which cause it: scale-type G×E (heterogeneity of variance) and rank-type G×E (heterogeneity of correlation). Because the two types of G×E have very diferent properties, separating their efect would enable a clearer understanding of stability. The aim of this paper was to demonstrate two methods which seek to achieve this in reaction norm models. Reaction norm models were ft to yield data from a multi-environment trial in Barley (Hordeum vulgare), with the adjusted mean yield from each environment used as the environmental covariable. Stability estimated from factor-analytic models, which can disentangle the two types of G×E and estimate stability based on rank-type G×E, was used for comparison. Adjusting the reaction norm slope to account for scale-type G ×E using a genetic regression more than tripled the correlation with factor-analytic estimates of stability (0.24–0.26 to 0.80–0.85), indicating that it removed variation in the reaction norm slope that originated from scale-type G×E. A standardisation procedure had a more modest increase (055–0.59) but could be useful when curvilinear reaction norms are required. Analyses which use reaction norms to explore the stability of genotypes could gain additional insight into the mechanisms of stability by applying the methods outlined in this study.

This data was collected for the thesis entitled: Prospects of cattle integration in plantation systems: lessons learnt from Indonesian and Australian case studies.

Interview Data: Current Indonesian beef production only meets 45% of local demand. Increasing local beef production through integration of cattle production in pre-existing oil palm plantations is a possible solution to meeting this shortfall. The oil palm understorey provides feed, alleviating the need to convert additional land to agriculture. Smallholders are important contributors to both Indonesian cattle and palm oil production. This case study research seeks to understand key aspects of smallholder cattle management in palm oil production areas, to highlight both opportunities and barriers to cattle integration. Thirty-nine smallholder cattle farmers from four villages in South Kalimantan were individually interviewed.

Files: The questionnaire is attached (word document titled 'Questionnaire_SHInterviews', and the interview outcomes are available in the excel file 'SH_Interviews_Data'. The numbers in the questionnaire correspond to the answers available in the excel file (in the field many of the questions included in the questionnaire ended up not being addressed).

All activities in this research were approved by the University of New England Human Research Ethics Committee (approval HE19-156). A research permit (342/E5/E5.4/SIP/2019) and visa (VITAS No: 2A1311EB0365-T) were obtained for research in Indonesia.

Chapter 6:

Context: Most knowledge on grazing management originates from homogeneous pastures. Information on cattle behaviour in silvopasture systems would allow land managers to get a better understanding on forage utilization and vegetation changes, in order to avoid negative impacts on trees and soils and to formulate improved animal management practices promoting weed control and reducing fire fuel loads.

Aim: This study explores the role of manageable landscape elements (presence of open areas, proximity to tracks and the availability of seeded understorey) in determining cattle distribution, in a mixed-species eucalyptus silvopasture system seeded with a broad-leafed paspalum understorey.

Methods: Cattle were tracked with GPS collars set to record locations at 15-minute intervals. A Brownian Bridge Movement model was run using the GPS locations, used to calculate Ivelv's Electivity Index to determine cattle preference and avoidance of specific areas.

Files: A word file is included which describes how the data was collected. The GPS locations for every collar, for each of the three grazing deployments is attached in separate CSV files.

All animal research activities in this study were approved by the University of New England Animal Ethics Committee (approval AEC20-59).

Chapter 5: Silvopasture is the integration of trees, understorey and cattle co-located on the same land management unit, thereby sharing land and producing two commodities. The growing area under eucalyptus plantations in Australia is an opportunity for cattle grazing but there is a dearth of knowledge on suitable understorey forage species that can provide high quality feed and can be sustained underneath eucalyptus trees.

This study examines persistence, palatability and productivity under different tree species of broad-leafed paspalum in a cattle-eucalyptus farming system, and explores associated effects on cattle productivity. Broad-leafed paspalum presence was mapped eight years after seeding in a 184 ha eucalyptus plantation in Northern New South Wales (Australia). Samples were harvested four times over a nine-month period, pre- and post- cattle grazing. Broadleafed paspalum productivity was recorded next to tree trunks and in-between tree rows, for three eucalyptus tree species (red mahogany, tallowwood, ironbark and a mixed species tree stand). The nutritional content of broad-leafed paspalum was analysed, cattle weight change was studied from summer to autumn and the calving rate was recorded over the study period.

Files: the 'Key_Excel_Files' has all the information to be able to understand the individual excel files and contains information on the methodologies. The following excel files are included: 'BiomassData', on the dry weight of broad-leafed paspalum harvested, 'N_Content', the crude protein content of harvested samples, 'NDF_ADF', with results on NDF and ADF content of harvested samples, and finally the excel file 'Visual Soil Assessment', with the results of the site visual soil assessment.

Cattle grazing in plantations is a possible solution for increasing beef production while reducing the conversion of additional land to agriculture. Integrated cattle-plantation farming systems aim to achieve both environmental services and economic benefits, which is especially relevant to the increasing global demand for both beef and tree products to be produced in a sustainable manner.

Integrating tree, livestock, and forage management requires considerable planning and technical expertise, to maximise facilitation and minimise competition between farming system components. This research focuses on reaching a better understanding of understorey productivity, grazing management, and the implications for sustainable silvopasture practices, by carrying out research activities in three case studies. The first case study examines smallholder cattle management in Indonesian oil palm producing regions through smallholder farmer interviews. The second case study assesses tree and cattle productivity in a large-scale, integrated cattle-oil palm plantation by analysing secondary production data. The third case study measures understorey productivity and cattle distribution in an Australian mixed-stand eucalyptus plantation, through biomass harvests and cattle GPS tracking.

In the smallholder system, cattle management was determined by labour availability and the lack of alternative feed sources, with the majority of smallholders adopting freegrazing for cattle management. In the large-scale Indonesian oil palm plantation, cattle management was the most intensive of the case studies, with a rotational grazing system adopted. This system resulted in beef production, while concurrently improving oil palm yields and reducing weeding costs. The Australian case study showed tree species choice affected understorey productivity and distance from tree-trunks was positively associated with understorey productivity. Cattle preferred areas in proximity to vehicle tracks, with high understorey forage availability (in the open areas if available, otherwise under treed stands).

The Australian case study showed the importance of tree species selection and spacing on understorey productivity. A balance should be found between tree and understorey production, in line with the stakeholder's priorities. Broad-leafed paspalum was persistent and productive understorey species well-suited to the conditions of the Australian case study, but in new situations a risk assessment should be applied because of its invasive nature.

All case studies had positive outcomes in terms of beef production, although the magnitude was not assessed. Equally as important is the income diversification offered by beef production, leading to more resilient farming systems in the face of fluctuating palm oil and timber prices.

The socio-economic context and stakeholder priorities were instrumental in determining the intensity of cattle management. When beef production was the sole priority it was associated with lower investment in cattle management, whereas more intensive cattle management was associated with the dual aims of beef production and reduced weeding costs. Increasing grazing hours resulted in increased oil palm yields in the large-scale Indonesian plantation. Experiments under a wider range of tree and cattle management regimes (e.g. older or younger palms and grazing intensity or frequency) are required to extrapolate these findings. Vehicle tracks, fencing and understorey sowing are tools that can be used by stakeholders to attract cattle to target grazing areas. An avenue for future research is fine-tuning the 'optimal cattle distribution' for the most advantageous productivity and economic outcomes and the greatest co-benefits of weeding cost reduction and reduction of fire fuel loads.

Context. Knowledge of genetic and phenotypic variation and the accuracy of different measurement techniques is needed to successfully reduce livestock methane (CH₄) emissions.
Aims. To estimate repeatabilities, heritabilities and genetic correlations of respiration-chamber (RC) and portable accumulation-chamber (PAC) measurements using two different protocols but the same management and feeding conditions.

Methods. Australian Information Nucleus Flock ewes were measured in seven test-batches. The 510 ewes were removed from pasture and habituated to chaffed alfalfa and cereal hay at 1.5-1.6 times maintenance. Methane was measured in RC for two 22-h periods approximately 14 days apart, and 40 min in PAC, either immediately after removal from individual pens (with feed as described above, PAC0), or 1-h after withdrawing feed (PAC1). There were up to 48 PAC0 tests per day (at 0930 hours, 1100 hours, 1230 hours, 1400 hours in 12 PAC) and 24 PAC1 tests per day (at 1100 hours and 1300 hours). Test methods (RC, PAC0, PAC1) were analysed as different traits in a multi-trait repeated-measures model.

Key results. Before adjustment for liveweight (Lwt) or feed intake (FI), CH₄ was highly repeatable (RC 78%, PAC0 83%, PAC1 82%), with heritabilities of 39-55%, permanent environmental (PE) animal variances 23-43% of phenotypic variances (Vp), high genetic correlations between methods (98-100%), and lower PE correlations (44-58%). A second PAC test on the same day decreased CH₄ by 8-12% compared with the ewe's first test that day. Heritabilities of FI from 0800 hours until the test was complete (FIOD) were 16-17% (PAC) and 25% (RC) before adjusting for Lwt, with high PE variances (PAC 67-73%, RC 41% of Vp). FI in the previous 24 h was highly heritable and much less variable than was FIOD in the RC, suggesting that testing introduced additional variation by disrupting feeding patterns. After adjusting CH₄ for Lwt, FIOD and FI in the previous 24 h and Lwt, some additive genetic variation remained, averaging 17% of Vp. Multivariate models of CH₄ and FI, fitting a single animal term (representing genetic+PE variation) showed high animal correlations between FI and CH₄, namely, 90-95% before, and 86-95% after adjusting for Lwt.

Conclusions. PAC measurements are heritable and highly correlated with RC measurements under similar management conditions. The high genetic and animal correlations of PAC CH₄ and FI imply that CH₄ is a useful proxy for FI of grazing animals.

Spittlebugs are the main pest of tropical pastures and Marandu palisade grass (Urochloa brizantha cv. Marandu) is the most representative cultivated pasture in the tropics. Our objective was to characterize Marandu palisade grass responses subjected to Mahanarva (Hemiptera: Cercopidae) attack and to estimate the losses in terms of beef production from pasture-based systems. A set of five experiments were carried out. Three consecutive years of monitoring showed that Mahanarva spittlebugs increased their abundance after first rains with three to four peaks throughout the wet season. A decrease of 66% on herbage yield was observed in the greenhouse trial, with an average decrease of 61% on pools of calcium, magnesium, phosphorus, sulfur, potassium, crude protein, neutral-detergent fiber and in vitro digestible dry matter of Marandu palisade grass. Results from field experiments corroborated with greenhouse trial showing decreases on herbage yield varying from 31 to 43% depending on level of fertilization and grazing severity of Marandu palisade grass. Finally, an unprecedented 154-ha field experiment indicated that Mahanarva decreases 74% the beef productivity (i.e. kg body weight ha^-1) of Nellore heifers grazing Marandu palisade grass.

Livestock produce 10% of the total CO₂-equivalent greenhouse gases in Australia, predominantly as methane from rumen fermentation. Genetic selection has the potential to reduce emissions and be adopted in Australian grazing systems. Developing a breeding objective for reduced methane emissions requires information about heritability, genetic relationships, when best to measure the trait and knowledge of the annual production of methane. Among- and within-animal variation in methane production, methane yield and associated traits were investigated, so as to determine the optimal time of measurement and the relationship between that measurement and the total production of methane. The present study measured 96 ewes for methane production, liveweight, feed intake, rumen volume and components, and volatile fatty acid (VFA) production and composition. Measurements were recorded at three ages and different physiological states, including growing (12 months), dry and pregnant (21 months) and dry (non-pregnant, non-lactating; 28 months of age). The single biggest determinant of methane production was feed intake, but there were additional effects of age, proportion of propionate to (acetate+butyrate) in rumen VFA, total VFA concentration and CO₂ flux. Rumen volume and pregnancy status also significantly affected methane production. Methane production, CO₂ flux, liveweight, feed intake and rumen volume had high repeatability (>65%), but repeatability of methane yield and VFA traits were low (<20%). There were no interactions between sire and age (or pregnancy status) for methane traits. This suggests that methane could be measured at any time in the production cycle. However, because MY is reduced during pregnancy, it might be best to measure methane traits in dry ewes (neither pregnant nor lactating).