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    Metagenomic analysis and culture-based methods to examine the prevalence and distribution of antimicrobial resistance on two New Zealand dairy farms : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand
    (Massey University, 2022) Collis, Rose
    Antimicrobial resistance (AMR) is a global threat to human and animal health, with the misuse and overuse of antimicrobials being suggested as the main driver of resistance. In a global context, New Zealand (NZ) is a relatively low user of antimicrobials in animal production. However, antimicrobial usage on NZ dairy farms and its potential for driving the spread of AMR within the dairy farm environment is under-researched. This research addresses the hypothesis that antimicrobial use on NZ dairy farms influences the prevalence of AMR in dairy farm environments, taking into consideration seasonality and contrasting farm management practices. The aims of this study, focused on two NZ dairy farm environments over an 15 month period, were to (i) determine the prevalence and distribution of AmpC- and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli, utilising culture-based methods, and (ii) to determine the abundance and diversity of antimicrobial resistance genes (ARGs), utilising a metagenomic approach, and lastly (iii), to assess the impact of systemic antimicrobial treatment on the bovine faecal microbiome. Overall, the research presented in this thesis has shown a low sample level prevalence of ESBL-producing E. coli from two NZ dairy farms (faeces 0%, 1.7%; farm dairy effluent (FDE) 0%, 6.7% from Dairy 1 and Dairy 4, respectively) but AmpC-producing E. coli were more frequently isolated across both farms (faeces 3.3%, 8.3%; FDE 38.4%, 6.7% from Dairy 1 and Dairy 4, respectively). AmpC- and ESBL-producing E. coli were isolated in spring and summer, during months with varying levels of antimicrobial use. Analysis at the individual animal level showed a decrease in bacterial diversity and richness during systemic antimicrobial treatment and in many cases the microbiome diversity recovered post-treatment when the cow re-entered the milking herd. Compared to overseas data in a similar context, NZ dairy farm environments had a low abundance of ARGs, with the highest abundance detected in soil (0.20 - 0.63 copies of ARG per 16S rRNA gene). However, many of the ARGs identified in soil are not frequently found in human pathogens or acquired genes. FDE had a lower ARG abundance but the ARGs were more diverse (0.03 - 0.37 copies of ARG per 16S rRNA gene). There was no association between the normalised ARG abundance and antimicrobial use or collection date, however the low ARG abundance in the farm samples may have made any associations difficult to detect. AMR is a burden for human, animal and environmental health and requires a holistic "One Health" approach to address. The outcomes from this research improve our understanding of the current levels of AMR on two NZ dairy farms and identifies areas for future research. Prevention is better than a cure and urgent action is required to slow the development and dissemination of AMR and to improve antimicrobial stewardship in humans and animals.
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    Perceived adaptive capacity of New Zealand dairy farmers in the face of policy and economic volatility : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Farm Management at Massey University
    (Massey University, 2022) Shokri, Elham
    Increasing global demand for dairy products provided the New Zealand dairy sector with the opportunity to expand. However, that expansion has come at a cost, with dairy farms becoming more reliant on external feed sources, increased debt financing, and irrigation water. At the same time, they have been exposed to a turbulent global economic environment and the increasing domestic concern over the environmental impact of dairying. Consequently, dairy farmers must balance economic efficiency and environmental sustainability in the face of increasing government regulation particularly around addressing deteriorating water quality. This requires dairy farmers and their farm businesses to be resilient, demonstrating some level of buffer capacity, adaptive capacity, and/or transformability. In a changing environment, adaptive capacity is key because a system’s existing buffer capacity is unlikely to cope with such changes. In addition, it is important to avoid inadvertent transformation. Due to the nature of adaptive capacity, the difficulty lies in attempting to measure it. To address this challenge and regarding the role of the decision-maker around adaptive capacity, a shift has begun to measure perceived adaptive capacity. For this measurement, a conceptual framework is required. A combination of five capitals and a decision-making framework was chosen. This conceptual framework is considered natural, physical, financial, human, and social capital. In addition, the risk or uncertainty confronting the business and the management practices are considered in the determination of dimensions for perceived adaptive capacity. In this research, a sequential mixed method was selected. Four in-depth case studies were conducted via face-to-face interviews, focusing on the dimensions of the defined conceptual framework for perceived adaptive capacity. These interviews helped the researcher understand the New Zealand dairy farming context. In addition, the findings from the qualitative phase, alongside previous studies in New Zealand, informed the survey, disseminated to a larger sample of dairy farmers nationwide. The response rate for the survey was 51% (106 out of 209 emails sent) with usable data for analysis of 31% (65 farmers). Principal Component Analysis and Equal Weighting were utilised to calculate the score for seven dimensions for each farmer. The Analytical Hierarchy Process helped to identify the relative importance of each dimension within the framework for each farmer. Finally, the farmer’s perceptions of these dimensions and the relative importance of dimensions were used to develop an index of perceived adaptive capacity. Introducing a new framework and developing an index for perceived adaptive capacity was novel to the literature. The framework provides a lens through the various dimensions that can be used to design a tool to assess perceived adaptive capacity. Moreover, the developed index for each farmer demonstrates that farmers have unique perceptions that build their index. Therefore, classifying farmers as adaptive or less adaptive cannot be conclusive. Instead, the relative importance of different dimensions illustrates whether the individual farmer perceives a dimension as more important than any other to them. A major step toward understanding and increasing the farmer’s adaptive capacity starts from investigating their perceptions. It includes how they see the uncertainty in the environment, how they perceive their farming systems’ capitals, and how important they see the management practices to cope with ongoing changes. The index of the perceived adaptive capacity, also, assists industry agents or advisors to see the farmer’s self-assessment of their capacity to adapt to ongoing changes. In addition, the farmer’s performance in a chosen timeframe shows the consistency (or lack of) between their perceptions and actions. A gap between perceptions and actions can result in a lack of adaptive capacity and may ultimately lead to an inadvertent transformation for the business.
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    The organisation of dairy farming in the Waikato, New Zealand
    (1931) Stephens, Frank Burcon
    The present study is an attempt to combine a descriptive account of the technical and financial organisation of Waikato Dairy Farms with an analytical discussion of the factors affecting efficient butterfat production. Management is perhaps the greatest need in the Dairying Industry today. While there is evident a "Desire to know" how to overcome the present difficulties, there is still a great deal of attachment to the routine of habit and custom. This fact is frequently lost sight of and the popular descriptions of farming in New Zealand generally err by discussing farming practice in terms of the best farmers. In the present essay an attempt is made to discuss things as they are and to indicate, where possible, the lines on which advance is being made. [From Preface]
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    The implicit nature of advice on the intimate topic of financial management : an exploration of how the financial management advisory system shapes financial management advice in the dairy sector in Aotearoa : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Agriculture & Environment at Massey University, Manawatu, Aotearoa
    (Massey University, 2019) Hilkens, Aniek
    Financial Management (FM) skills have been argued to be essential for the effective management of a farm in response to pressures like climatic and economic volatility. Internationally, agricultural advisors are considered important actors concerned with supporting farmers in different aspects of farm management. Agricultural advisors are recognised for their role in facilitating the application and use of new knowledge by farmers through advice. Despite the recognized importance of financial management, limited research has looked at the role of advisory services in relation to the topic of financial management in the agricultural sector. This doctoral research takes a systemic view in studying FM advisory provisioning in the New Zealand dairy sector. In particular, this study explores three different areas of the FM advisory system in the New Zealand dairy sector and how they shape FM advisory provisioning. The first area studied is how interactions between farmers and FM advisors are shaped. The second area focuses on how interactions between FM advisors around a mutual client are shaped. Lastly, the third area studied is how FM advisors navigate the multiple accountabilities and demands placed on their role. The findings of this research are informed by forty-seven semi-structured interviews with farmers, accountants, bankers, farm management consultants, specialist financial advisors and employees of the industry good organisation DairyNZ. This study follows a social constructivistic approach and was mainly data-driven; by an empirical social phenomenon. This research explores and enriches the literature on agricultural advisory services, by exploring advisory services in relation to farmers’ FM. This study enriches this literature firstly by highlighting the influence of the sensitivity of the topic. The sensitivity of the topic and how this topic relates to farmer’s identity, influences whom farmers seek advice from and the nature of that advice. Moreover, the presence of an authority dimension in the relationship between advisor and farmer is shown in this research to shape the content and form of farmer-advisor interactions. Regarding advisor-advisor interactions, this research also provides deeper insights on what drives and shapes coordination among agricultural advisors. In particular, duty of care for a farmer and authority and advocacy are found to coordinate relationships and interactions between advisors. Lastly, this thesis contributes empirical insights to discussions about the relationship between formal advisory agendas of agricultural advisory activities on the one hand and on the other hand, the reality of agricultural advisory programs. In particular, it provides a detailed illustration of the complex institutional context placing contradictory demands and accountabilities on advisors and how these advisors navigate these in their everyday practices.
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    Household labour allocation on small dairy farms in eastern Java, Indonesia : implications for gender roles : a thesis presented in partial fulfilment of the requirements for the degree of Master of Applied Science in Rural Development at Massey University
    (Massey University, 1999) Utami, Hari Dwi
    The study was carried out in Andonosari village, East Java, Indonesia to investigate the household labour pattern of small-scale dairy farmers. The objectives were to: (a) investigate the pattern of the household labour allocation; (b) examine the earning contribution of dairy fanning to the total of household income; and (c) quantify the role of gender in dairy farming activities. Time use patterns for household labour were computed as the time spent on work (dairy farming and non-dairy farming, including on- and off-farm activities). Interviews were conducted separately with the husband, wife, and family members aged 15-64 years for 50 households. Households were classified into three strata based on the number of dairy cattle farmed: strata 1 (with fewer than 3 animal units (AUs)), n=16; strata 2 (with 3 to 5 AUs, n=18); and strata 3 (with more than 5 AUs, n=16). Descriptive, univariate, bivariate and multivariate analyses were performed using SAS package. Results showed that household labour for income generating activities was allocated more to dairy farming compared to the farm and non-farm work. Females allocated one third of total time to income generating activities, with most of the time devoted to dairy farming activities, while males tended to allocate more time to non-dairy farming activities. The household labour requirement in dairy farming per animal unit decreased as herd size increased, thereby allowing more time for non-dairy activities. Female participation was most evident in feed preparation and feeding, whereas the predominant male activity was forage collection for the dairy cattle. The size of the landholding had no impact on household labour allocation to dairy farming activities. An increase in household income and dependency ratio had a minor impact on household labour requirement in dairy farming. Non-dairy farming activities contributed about two-thirds to household income, the majority from apple farming. The income of household labour per animal unit tended to decrease with an increase in herd size. Variable costs accounted for 74% of the total expenditure in dairy farming, with majority purchases being concentrates. Fixed costs were 26% of total costs, and the major item was depreciation (8%). It is suggested that farmers, including both men and women, should be trained to be more efficient in allocating household labour to dairy farming activities, and in managing the feeding of dairy cattle to achieve high productivity and income. There is substantial scope to increase herd size and increase labour efficiency in dairy farming. Key words : Household labour, gender, dairy farming, non-dairy farming. Title : "Household Labour Allocation on Small dairy Farms in Eastern Java, Indonesia: Implication for Gender Roles." Author : Hari Dwi Utami Degree : Master of Applied Science (Rural Development)
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    Impacts of dairy farming on water quality and biological communities of streams in Tararua District, New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Ecology at Massey University
    (Massey University, 2003) Ridler, Clare L. R
    Water quality in dairy farming areas has increasingly been the focus of attention in New Zealand as more land is converted to dairying and the intensity of operations increases. Regional councils and the dairy industry have encouraged removal of existing treated dairy shed effluent discharges from waterways and the minimisation of diffuse sources of contaminants such as nutrients and bacteria. There has been limited scientific data collected on the impacts of dairy shed effluent discharges on streams, nor on the overall water quality and biotic integrity in small sub-catchments with intensive dairy farming. This study aimed to address these issues, as well as investigating the scale influence (temporal and spatial) on the results. Streams in two sub-catchments of the Manawatu River, Tararua District, New Zealand, were subject to regular monitoring over the summer low-flow period of 2001. Intensive dairy farming is the predominant land use in the catchments. Twenty-two sites were measured on seven occasions for bacteria, nutrients, turbidity, periphyton, temperature, conductivity, dissolved oxygen (DO) and pH. Macroinvertebrate samples were taken at 18 of the sites on one occasion. Twelve of the sites were paired above and below five dairyshed effluent discharges and one urban sewage treatment discharge. The water quality in the small streams did not meet chemical or microbiological guidelines at most sites on most sampling occasions. While point-source discharges influenced some sites, other sites with no obvious contaminant discharges also did not meet guidelines. However, biological monitoring showed periphyton levels were always within guidelines and macroinvertebrate communities indicated only 'moderate' enrichment. The discharges of treated dairyshed effluent into streams and drains had a significant impact on Escherichia coli (E.coli), dissolved reactive phosphorus (DRP), nitrate, ammonia, turbidity and conductivity measures. However, periphyton levels generally decreased below discharges. Macroinvertebrate communities showed some change below discharges to dominance by indicators of poor water quality, but this was not statistically significant. The variation between individual discharges indicates that there is a need to assess the impacts on a case-by-case basis. Temporal trends below a dairy shed effluent discharge showed 24-hour cycles in temperature and DO but not in conductivity. In addition, there was a weak 12-hour cycle in temperature but this was unlikely to be due to pulses of effluent from twice-daily milking Conductivity within the stream was affected by random events (for example pond desludging) influencing effluent discharges, indicating that individual variation in system management can have localised impacts on water quality. However, the proximity of cows at the time of sampling had no detectable effect on water quality measures. Rainfall affected E.coli levels in both streams, however the influence of rain on periphyton levels appeared to be subject to individual stream characteristics. There was considerable spatial variation in water quality throughout the catchments. While some of this variation could be attributed to point-source discharges, much remains unexplained but is likely due to variation in overland runoff from grazed pastures and groundwater inputs. Data from State of the Environment (SoE) monitoring in the Manawatu catchment was also compared with results from this study to determine if the SoE monitoring is accurately reflecting water quality at these smaller scales. Larger waterways of the Manawatu catchment had similar levels of dissolved oxygen as the smaller streams, however there was a wide variation in nutrient levels in the different waterways.
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    A study of winter milk production and a comparison of town milk and seasonal supply dairy farms in the Manawatu : a thesis presented in partial fulfilment of the requirements for the degree of Master of Agricultural Science in Animal Science at Massey University
    (Massey University, 1989) Baldwin, Gray Walter
    The literature review commences with a brief description of the past and present town milk industry and reviews the consequences of recent legislative changes which have already wrought substantial change to the town milk industry. This is followed by a review of factors affecting milk production per cow (feed intake, level of supplementation, cow quality, breed, stage of lactation, calving date) and factors affecting milk production per hectare (stocking rate) on pastoral dairy farms. The likely effects of these factors on the productivity of town milk and seasonal supply farms is also discussed. There were two major objectives to the present study. The first was to measure the productivity of town milk farms over the winter period. The second was to compare the overall annual productivity of town milk farms with that of seasonal supply farms in the same district. To achieve these objectives, a survey of 58 Manawatu dairy farms (both town milk and seasonal supply) was carried out during the 1988 winter. Average daily milk production per cow on town milk farms during winter was 12.6 litres/cow/day and ranged from 8 to 19 litres/cow/day. Mean pasture cover and mean cow condition score decreased slightly over the winter period. Average daily production per cow of milkfat, protein and total solids fluctuated during winter, but showed a universal downward trend. The percentage of fat, protein and total solids in milk all decreased over the winter period. Average daily milk production per cow in winter was positively correlated with a number of other variables measured including cow condition score and pasture cover in May, annual milkfat production per cow and per hectare, and digestibility of supplement eaten. Daily production per cow was negatively correlated with milkfat % and somatic cell count. Farmers who practiced an "all autumn" calving policy to provide winter lactating cows had significantly higher winter milk production than those farmers who continued to milk late spring / summer calved cows through the winter. On an annual basis, town milk farms produced considerably less milkfat per cow and per hectare than seasonal supply farms although stocking rate on the two farm types was similar. As a consequence of a high winter feed demand, town milk farmers made, brought in and fed more hay and silage supplement than seasonal supply farmers. Town milk farmers grew more forage crops, fed more concentrates and made more extensive use of irrigation and nitrogen fertilizer to boost pasture growth at strategic times of the year than seasonal supply farmers. No significant differences in youngstock grazing policy was observed between farm types. Both seasonal supply and town milk farms were assumed to grow similar amounts of feed per hectare, but town milk farms fed more per hectare when brought in supplements were considered. However feed consumption per hectare was estimated to be significantly higher on seasonal supply farms due to their higher milkfat production per hectare. This resulted in seasonal supply farms having a significantly higher annual feed utilisation efficiency (95 %) compared with town milk farms. Hay and silage quality in terms of DM Digestibility, protein % and DM % was measured on all farms. Mean digestibility of DM was 56.1 % and 64.5 % for hay and silage respectively.