Academic literature on the topic 'Fields of Research – 300000 Agricultural, Veterinary and Environmental Sciences – 300800 Environmental Science'

1. The aim of this research was to determine appropriate microbial indicator systems for use in monitoring the occurrence and source of faecal contamination in aquatic environments. Particular emphasis has been placed on the identification of indicators which might enable faecal contamination of human origin to be distinguished from that of non-human derivation. Two lines of investigation have been pursued; the use of alternative microbial indicator systems for water quality monitoring, and the development of diagnostic molecular methods for identifying the origin of faecal organisms. 2. Field and treatment plant studies were undertaken to investigate the utility of three indicator systems for monitoring water quality impacts in the coastal area surrounding the discharge from Auckland's North Shore City wastewater treatment plant. F-specific bacteriophage (F-phage) and ratios of F-phage to enterococci and faecal coliforms were examined over a twelve month period in which indicator levels at various stages of the wastewater treatment process were measured. These indicators and levels of Clostridium perfringens spores in sediment were measured in four outfall impact studies. 3. F-phage levels in effluent from the treatment plant (median=2.5 x 102 cfu/l00 ml) were too low to enable their use as source-specific tracers of effluent dispersion. However, higher F-phage levels in raw sewage (median=6.2 x l05 cfu/l00 ml) suggested that phage may be an appropriate indicator of raw sewage contamination in the receiving environment. F-phage was detected in coastal waters remote from the sewage outfall, providing presumptive evidence of sewage contamination entering the sea from sources other than the outfall discharge itself. 4. F-phage/enterococci and F-phage/faecal coliform ratios that were determined for sewage and treated effluent derived from the North Shore plant proved to be highly variable and were therefore unreliable for determining the source faecal contamination. 5. The concentration of Clostridium perfringens spores in sediments did not provide a useful means for tracing the distribution of faecal contaminants in the coastal system because the spore levels were found to be similar throughout the study area. This widespread occurrence of C. perfringens spores prevented identification of defined impact zones for any of the potential sources of faecal contaminants examined. 6. Randomly Amplified Polymorphic DNA (RAPD) analysis was used to investigate whether genetic markers could be identified for Escherichia coli isolates derived from different sources. RAPD profiling was found to be a highly discriminative method able to subtype E. coli strains present in both sewage and in the wastewater stream of a mechanical wood-pulping operation. In the pulp mill effluent, RAPD analysis indicated the presence of a restricted range of E. coli strains compared to the range found in the water intake and sewage effluent discharges. The results obtained provide presumptive evidence for the multiplication of E. coli strains within the wastewater stream. 7. Comparison of RAPD profiles derived from a range of human and environmental E. coli isolates led to the identification of a 1.6-kb marker. present in a subset of human isolates, but found only infrequently in isolates from animal origin. Primers based on sequence information obtained from this region of the genome yielded a direct PCR assay for the 'human' marker. The reliability and utility of the assay was improved when fluorescently-labelled primers and an automated DNA detection system was employed for the analysis of the amplified PCR products. 8. The diagnostic polymorphism was localised to the region immediately downstream of the gene encoding the glycine decarboxylase P-protein (gcvP). Comparison of DNA sequences from this region in 'marker-positive' and 'marker-negative' E. coli isolates revealed an abrupt loss of homology immediately downstream of the transcription termination point of the gcvP gene. The region of non-homology extends for at least 130 base pairs beyond the gcvP transcription terminator. Sequences spanning this region in marker-negative isolates exhibited a high level homology with that determined for E. coli K-12. The origin of the sequence for the same region in marker-positive isolates was unable to be identified. 9. The utility of the marker for environmental monitoring was investigated in a field study of a rural stream receiving bacterial contamination of both human and animal origin. The marker was consistently detected both in isolates derived from sewage effluents and in those found immediately downstream from sewage inputs-despite the presence of a high background of E. coli of animal origin. However the utility of the marker as a sewage-specific tracer was limited by the relatively low numbers of marker-positive d. coli in sewage effluents (approximately 8%). 10. In summary, the work described in this thesis has confirmed the need for multiple indicator systems in water quality monitoring and has identified appropriate areas for further research. The most promising area for future research is in the development of molecular tools which might provide both a better understanding of genetic variation in indicator organisms and enable methods to be developed for the detection of host-specific strains. Location of other polymorphisms likely to be present in the E. coli genome should enable further host-specific markers to be identified which could complement the 'human' marker identified in this study.
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There is an extensive debate on the potential environmental impact of dairy farms and in particular the effect of dairy farms on the nitrogen cycle and the effect that this has on ecosystems. Within New Zealand and in particular in the South Island, the expansion of dairying and the adoption of new dairy systems has led to this becoming an increasingly important issue, locally through its effect on water quality and the environment and nationally and internationally through the production of green house gases. Increases in nitrogen usage at the expense of clover nitrogen fixation, irrigation, stocking rate and the introduction of dairy cows onto light free draining soils previously the preserve of arable or sheep farming has led to concern as to the effect intensive pastoral dairying may have on the nitrogen dynamics of the farm and the environment. This study is designed to assess how changes in grazing management in particular changes in pre-grazing and post-grazing residuals alter the clover/ryegrass balance on the farm and the effect that this has on the farm’s nitrogen dynamics. The effects of qualitative changes in grazing management on pasture composition are well established but little is known of the effect of quantitative changes in pasture management on composition, in particular the effect of grazing residuals. There are a number of detailed models of the physiological processes in the energy and nutrient cycling in plants, animals and the soil. There are a smaller number of whole farm models that through integration and simplification of component models attempt to represent the flux of nutrients though a dairy farm. None of these whole farm models is currently able to model the nitrogen flux through a dairy farm at a sufficient level of resolution to capture differences in pasture composition as these occur spatially, temporally and in response to grazing management. This project sought to better understand the nitrogen dynamics on a dairy farm by constructing and then linking component models – a pasture composition and growth model, a cow model, an excretal return model, a soil model and a water balance model – within a whole farm management schedule. The formal null hypothesis is that the mechanistic, mathematical model constructed for this PhD cannot capture and explain the full range of the changes in soil water content, soil nitrogen status, pasture production and composition and animal production, following the alteration in management of the dairy farm between 2002 and 2004. Individual component models were constructed by the author using the computer software package (Matlab) and validated against data extracted from the literature. The models were then converted into one simulation package using C-sharp as the source code language by Elizabeth Post, Senior Computer Scientist at Lincoln Ventures Ltd, Lincoln, New Zealand and the author. This model was then used to investigate the nitrogen dynamics of a dairy farm: the relationship with pasture composition and whether small changes in pasture residuals make a difference to pasture composition and nitrogen dynamics. Two different simulations were run based on the management practice of Lincoln University Dairy farm (LUDF) over two dairy seasons (2002-03 and 2003-04) and validated against the data recorded on this farm. In 2002-03, 50 cows were over wintered and 580 cows were subsequently milked on 200ha. Post grazing residuals where maintained at 1600-1750KgDM/ha. In 2003-04, 125 cows were overwintered and 635 cows were milked on 200ha with post grazing residuals maintained at 1400KgDm/ha. All models operate on a daily time step. Within the pasture model composition is described by 9 state variables describing different components of the pasture and pasture growth is modelled mechanistically from a calculation of component photosynthesis. A further 9 state variables describe the nitrogen composition of the pasture components. The soil model is a variable two layer, mechanistic representation, parametised for the shallow, stony soils of LUDF. Soil water status is an input for the pasture model while water uptake by the growing plants affects the soil water balance within the soil model. Animal intake and production are modelled mechanistically with model cows described in terms of their age, genetic merit, body weight, breed, pregnancy status, conception date and body condition score. Each cow type produces a different quantity of urinary and faecal excretion which varies with dry matter intake, milk yield and the sodium and potassium status of the pasture. Excretal nitrogen composition is predicted within a separate model which calculates daily nitrogen excretion in faeces, urine and milk. Excretions are deposited randomly over the grazed area and account is taken of overlapping excretions that are created on the same day and overlaps that occur with older excretal patches deposited in previous grazing rounds. Each excretal patch has its own associated pasture, water and soil model reflecting the differences in nitrogen status between patches. Grazing preference is expressed within the model between different classes of excretal patch and between excretal patches and the base pasture and between clover and grass. Supplementary silage is conserved and fed according to the management schedule of LUDF. Cows calve, become pregnant and are dried off within the model according to the relevant records from LUDF. Cows are deemed to arrive on the farm on the day of calving and to leave on the day that drying off is finished (a 5 day procedure within the model), except for those cows that are overwintering which remain on the farm. The soil model has multiple nitrogen/carbon pools and is dynamically linked to all the other models. External nitrogen losses from the system are modelled as volatilisation, leaching and denitrification, with pasture nitrogen uptake from the soil model and fixation by clover from the atmosphere. Both the individual component models and the final assembled composite model were successful in matching the available data in terms of pasture and animal production, pasture composition, soil water balance and nitrogen status and external losses. The model indicates that the low residual, high stocking rate farm returns more excreta to the soil. However, this is countered by a reduction in the amount of dead material returned to the paddock and this reduces the relative size of the pool of nitrogen in the dead organic matter. This produces a relative lack of substrate for the soil microbes which are thus unable to exploit all of the nitrogen in the available pool. Soil ammonium and nitrate pools are also increased from the increase in faecal and urinary return so precipitating an immobilising flux from these larger pools to the smaller pool of nitrogen available to the soil microbes. However, the relative inability of the soil bacteria to fully exploit this means that the production of soil organic live matter and the resulting mineralising flux from the dead organic matter pool through the available pool to the ammonium and nitrate pools is reduced. The larger ammonium and nitrate pools will also be associated with increased external losses from the system as denitrification, leaching and volatilisation are increased. The increase in the clover percentage within the sward in 2003-04 led to greater nitrogen fixation and the model suggests that some of the extra nitrogen is effectively captured by the animals in increased production. However, the reduction in the return of dead matter coupled with an increase in excretal return and the consequent increase in the mineral nitrogen pools within the soil lead to greater losses of nitrogen from the soil.

Maud Island (Te Hoiere - "a long paddle or mighty pull") is a moderately sized island of 309 hectares, located in the Pelorus Sound (41°, 02 'S, 173° 54 'E) Marlborough, at the north-east end of the South Island of New Zealand. It has a long history of human modification and impacts since its colonisation by Maori and early Europeans. The vegetation of Maud Island has been studied in the 1980's and again in the early 1990's. The objectives of this study were to (1) describe how the vascular plant communities vary in species composition across Maud Island, (2) determine which environmental factors are important predictors of the variation in species composition of Maud Island plant communities, and (3) describe the pattern of succession of the plant communities on Maud Island over the last twenty years. In this 2001 study, I comprehensively sampled the vegetation on Maud Island using a Reconnaissance Description Procedure in a total of 158 plots across the island and compared these results to previous descriptions. I also retook photos at permanent photo points to provide a visual comparison of vegetation change. In total, 219 plant species were identified; 177 species occurred within the plots and 42 additional species were observed while walking around the coastline and walking tracks. Six dominant plant species occurred in over 70% of the plots. They were Pteridium esculentum, Pseudopanax arboreus, Hebe stricta var. stricta, Melicytus ramiflorus, Ozothamnus leptophylla and Coprosma robusta. Two-Way Indicator Species Analysis resulted in the description of eight different plant communities on the island. Detrended correspondence analysis showed a high degree of turnover in species composition among these communities. Canonical correspondence analysis showed that slope and moisture were particularly important predictors of variation in plant species composition. The environmental factors that best predicted to variation communities were slope, moisture, and a gradient in historical disturbance. Comparisons of present and past vegetation maps and photos (ground and aerial) showed, in terms of the successional pathways of the vegetation on Maud Island, that over time, the vegetation is reverting from short stature grassland and scrub to predominantly forest scrub and young secondary forest.

Loss of indigenous biodiversity continues in New Zealand. Despite admirable goals in the NZBS 2000 to the contrary, efforts at improved biodiversity conservation have been insufficient to halt loss of significant amounts of indigenous forest and wildlife habitat. Increasing numbers of native species are moving towards critically endangered and extinction. Whatever we are doing in New Zealand, it is not effective enough. The aim of this study is to firstly identify factors contributing to the failure, “to halt the decline of indigenous biodiversity” in New Zealand and to then consider opportunities to overcome these barriers. In considering opportunities, this study then reviews the emerging discipline of landscape ecology as an answer to, at least, some of those factors and the recurring calls from New Zealand ecologists for a more integrated and holistic approach to biodiversity conservation. Recent advances in the planning framework and particularly provisions for biodiversity conservation in England are explored as a model of practical application of landscape ecological principles to land-use planning. From this review, the study proposes a new ‘LEEP’ model for strategic biodiversity conservation that produces a regional-scale spatial conservation map and accompanying policy and implementation guide. Together they provide an integrated and holistic approach to restoring or creating functional landscapes that also recognises and provides for human activities and development. Application of the LEEP model is demonstrated through a case study of the Wellington region. Benefits and potential uses of the map and policy outputs are canvassed. Interviews with leading New Zealand and international ecologists provide an assessment of the current status of landscape ecology and interviewees also act as an expert ‘test panel’ against which the Wellington maps and guides produced from the ‘LEEP’ model are assessed. Finally, suggestions are provided for development of the new model and future research needs towards fuller and more effective implementation of this approach to biodiversity conservation in the New Zealand context.

Amphibians are suffering extinctions and range contractions globally. This is caused by numerous factors and most of them are related to human activities. The overall aim of this thesis was to make a significant contribution to the conservation of the endemic amphibian Leiopelma hochstetteri through research. This was achieved by focusing in two of the main conservation issues for this species, the need for standardised and robust monitoring techniques to detect trends and changes in populations, and the determination of the prevalence of chytridiomycosis, caused by the amphibian chytrid fungus (Batrachochytrium dendrobatidis). Two populations of the Auckland Region were selected for this study, one on the mainland (Waitakere Ranges) and the only known offshore island population of this species (Great Barrier Island). For both study sites different monitoring methods were used to obtain some population parameters. Site occupancy models of MacKenzie et al. (2002) gave reliable site-specific estimations of occupancy and detection probability using covariate information and presence-absence data collected from 50 sites in the Waitakere Ranges and four repeated visits during 2008. Elevation and distance searched were found to have an important effect on occupancy levels, while time taken to search the site was important variable determining detection probabilities. Also, parameters were estimated for three age classes separately. Statistical models were used to infer abundance from occupancy analysis, and results were compared with the distribution of relative abundances obtained from repeated transect counts and an established sight/re-sight criterion. In addition, the use of surrogate measures for relative abundance was explored. Detection probability and the distance to first frog found were found to have a significant correlation with relative abundance. These measures can be used to infer relative abundance in future site occupancy surveys. Two surveys and a pilot site occupancy survey were conducted on Great Barrier Island, and presence of frogs was confirmed atthe northern block, and in a small seepage in the central block. No new locations were found. Waitakere Ranges and Great Barrier Is. populations were tested for the presence of chytridiomycosis, and all frogs sampled tested negative (n = 124) which means that if present chytridiomycosis prevalence is lower than 5% with a 95% confidence interval. This and previous evidence suggests that L. hochstetteri may be resistant or immune to the disease. However, to confirm this additional studies are needed.

A two-year lysimeter study was undertaken to compare the environmental effects (e.g. nitrate leaching and nitrous oxide emissions) of soil applied lactose-depleted dairy factory effluent (LD-DFE) with lactose-rich DFE. The aim of this experiment was to determine the fate of nitrogen from LD-DFE and dairy cow urine applied to a Templeton fine sandy loam soil (Udic Ustrochrept), supporting a herbage cover of ryegrass (Lolium perenne) and white clover (Trifolium repens). Measurements were carried out on the amount of nitrogen lost from the soil via leaching, lost by denitrification, removed by the pasture plants, and immobilized within the soil organic fraction. Further, a comparison between the fate of nitrogen in LD-DFE irrigated onto land under a "cut and carry" system, as opposed to a "grazed" pasture system was undertaken. Lactose-depleted dairy factory effluent was applied at three-weekly intervals during the summer months at rates of 25 and 50 mm, until nitrogen loading targets of 300 and 600 kg N ha⁻¹ yr⁻¹ had been achieved. Measured leaching losses of nitrogen averaged 2 and 7 kg N ha⁻¹ yr⁻¹ for Control 25 and Control 50 treatments; 21, 20 and 58 kg N ha⁻¹ yr⁻¹ for 25 and 50 mm "cut and carry" treatments respectively; and 96 kg N ha⁻¹ yr⁻¹ for the 25 mm "grazed" treatment. The range of nitrate-N leaching loss from LD-DFE plus urine is no different from the lactose-rich DFE nitrate leaching loss. Uptake of nitrogen by the growing pasture averaged 153, 184,340,352,483, and 415 kg N ha⁻¹ yr⁻¹ for Control 25, Control 50, LD-DFE 25 and LD-DFE 50 mm "cut and carry" treatments, and the LD-DFE 25 mm "grazed" treatment, respectively. Denitrification losses were 0.06, 4.4, 1.69, 19.70, and 7.4 kg N ha⁻¹ yr⁻¹ for Control 25, the LD-DFE 25 "cut and carry" treatments, the LD-DFE 25 mm "grazed" treatment, and calculated "paddock losses", respectively. Isotopic nitrogen studies found that 29.4 and 25.8% of applied LD-DFE nitrogen was immobilised in the LD-DFE 25 and LD-DFE 50 "cut and carry" treatments. The results of this experiment confirm the findings of the previous lactose-rich DFE study, in that the effects of grazing stock are of greater environmental concern than the removal of lactose from the effluent waste stream.

Species are one of the fundamental components of biology and the accurate delimitation of species is important in evolutionary, systematic and ecological studies, yet there is still confusion over how species can be recognised. Examining different characters allows multiple lines of evidence for successful and accurate species delimitation and identification. In this thesis, morphological, genetic and behavioural variation is investigated within an endemic species of ground weta, Hemiandrus pallitarsis, in the North Island, New Zealand. Twelve morphological characters were measured, and mitochondrial cytochrome oxidase I DNA sequences were analysed from populations across the distributional range of H. pallitarsis. Both methods provide no evidence of a species complex within H. pallitarsis. Instead, the morphometric results suggest females are significantly larger than males, and ground weta in Palmerston North are significantly smaller than weta further north. Additionally, genetic analyses found substantial population structuring, large genetic distances, and an historical south to north pattern of movement in the North Island. The pattern of vibratory drumming behaviour followed that predicted by morphology and geographic proximity – drumming signals were more similar between geographically close populations and did not match the patterns of genetic isolation. Overall, this thesis was able to show that H. pallitarsis is morphologically, genetically and behaviourally variable across the North Island.

Ecological Footprint Analysis (EFA) is a technique that was first developed by Wackernagel as a Ph.D. thesis in 1994, then further developed in combination with Rees and published (Rees & Wackernagel, 1995). EFA is employed in this study to assess the resource utilisation of international tourists visiting New Zealand. Tourism is one of the fastest growing industries in the world and the ecological sustainability of tourism is becoming more important term for managing tourism. This is becoming increasingly important with tourism identified as particularly as a significant contributor to carbon emissions. This study uses EFA to assess whether international tourists visiting New Zealand behave in a sustainable manner. Tourists are surveyed and classed into high, mid and low budget tourist types to gain a detailed account of their behaviour with particular reference to food, accommodation, transport, services, activities attractions, goods and waste. The EFA helps to identify areas of a tourist’s trip that have the greatest impact on the environment, thereby identifying ways to improve the sustainability of tourism in New Zealand. It was found that tourists generally consume more whilst on holiday than they do at home and more than New Zealand residents. The results show that international tourists’ behaviour is sustainable and New Zealand has the ecological carrying capacity to allow the number of international tourists to increase without incurring any significant ecological costs to the country. It was found that there is a positive relationship between ‘high’ income tourists and their ecological footprint and that independent travellers have a larger ecological footprint than the package travellers; however, package travellers have a larger food and housing ecological footprint than independent travellers. The energy footprint was the largest out of the six land types of a tourist’s ecological footprint. Food is the consumption category that is the largest contributor to a tourist’s ecological footprint.

Ovariohysterectomy and castration are common surgical procedures in small animal practice that can result in clinically significant postoperative pain. One way of controlling postoperative pain is administration of a single analgesic or a combination of different classes of analgesics prior to the onset of noxious stimuli. A constraint to the perioperative use of traditional opioids and non-steroidal anti-inflammatory drugs (NSAIDs) is their undesirable side effects. In this series of experiments, the preventive (pre-emptive) analgesic efficacy of two popular human analgesics, tramadol (an ?atypical? opioid) and parecoxib (a NSAID with selective COX-2 inhibition) was evaluated in dogs. Initially, the efficacy and renal safety of parecoxib, tramadol and a combination of parecoxib, tramadol and pindolol (a -adrenoceptor blocker and 5-HT1A/1B antagonist) were screened in anaesthetised healthy dogs. These analgesics increased the dogs? nociceptive threshold to mechanical stimuli, without causing significant alterations in the dogs? glomerular filtration rate (GFR) estimated by plasma iohexol clearance. Subsequently, the efficacy of tramadol was compared with morphine, in dogs undergoing ovariohysterectomy or castration. The Glasgow composite measure pain scale-short form score (CMPS-SF) and changes in intraoperative electroencephalogram (EEG) responses were used to assess the efficacy of analgesics. Of the three treatment groups (preoperative morphine, 0.5 mg kg-1; preoperative tramadol, 3 mg kg-1; a ?combination? of preoperative low-dose morphine, 0.1 mg kg-1, and postoperative tramadol 3 mg kg-1), dogs given the ?combination? had significantly lower pain scores after ovariohysterectomy. In castrated dogs, preoperative tramadol (3 mg kg-1) and morphine (0.5 mg kg-1) were tested and no significant difference in the CMPS-SF score were observed between them. Changes in EEG variables were not specific between the treatment groups in ovariohysterectomised dogs. Finally, the efficacy of test drugs was evaluated against acute noxious electrical stimulation in anaesthetised dogs, using EEG. Median frequency of the EEG, a reliable indicator of nociception, increased significantly in tramadol and parecoxib groups, compared to morphine, after electrical stimulation. These studies demonstrated that tramadol and parecoxib can produce analgesia in dogs with insignificant side effects. The efficacy of tramadol appears to vary with the type of noxious stimulus. A complete prevention of noxious input by administration of analgesics pre- and post-operatively could have important clinical applications.

This study investigated whether behavioural and cognitive dysfunction caused by mucopolysaccharidosis (MPS) IIIA can be detected early in affected dogs’ lives, and to describe the behaviours of these dogs. No other scientific papers have been published on this topic and the population of dogs examined in this study are the only MPS IIIA affected dog colony available worldwide for study. Three main tests were performed on the population of MPS IIIA affected dogs. Physical behavioural assessment tests were performed at six and eight weeks of age and from twenty weeks of age a cognitive function task was taught and then tested to measure the dogs’ performance. A previously validated questionnaire, the canine behavioural assessment and research questionnaire (C-BARQ), was completed at three, six and twelve months of age. The researchers in these studies were blinded to the MPS IIIA status of the dogs examined. The behaviours shown by the MPS IIIA puppies at six and eight weeks of age were not significantly different from the behaviours of the unaffected puppies. This finding supported the research of other MPS IIIA studies and suggests that clinical behavioural changes do not occur at such a young age. The behaviours shown by the MPS IIIA affected puppies appeared to be normal puppy behaviours similar to those described in previous research on puppies. The C-BARQ measured the behaviours shown by the MPS IIIA affected and unaffected dogs. Most of the MPS IIIA affected dogs’ behaviours were not significantly different from the unaffected dogs’ behaviours, but MPS IIIA affected dogs did retrieve significantly more than unaffected dogs at three months of age, and were less distractible at twelve months of age. It would be worth investigating these findings further to decide whether it suggests a subtle alteration in brain functioning. The cognitive function test showed a significant decrease in the success of the MPS IIIA affected dogs in the final maze test. This is the first study on dogs affected with MPS IIIA to find a decline in cognitive function before the occurrence of cerebellar clinical signs and this new knowledge may lead to future developments measuring therapy response and disease progression. The T-shaped maze testing may be valuable in future research on cognitive function in dogs with other diseases such as epilepsy. Thus this thesis provides valuable information on canine MPS IIIA and provides a foundation for future disease investigations.