Journal Articles
Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915
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Item A novel gyrovirus is abundant in yellow-eyed penguin (Megadyptes antipodes) chicks with a fatal respiratory disease.(2023-02) Wierenga JR; Morgan KJ; Hunter S; Taylor HS; Argilla LS; Webster T; Dubrulle J; Jorge F; Bostina M; Burga L; Holmes EC; McInnes K; Geoghegan JLYellow-eyed penguins (Megadyptes antipodes), or hoiho in te reo Māori, are predicted to become extinct on mainland Aotearoa New Zealand in the next few decades, with infectious disease a significant contributor to their decline. A recent disease phenomenon termed respiratory distress syndrome (RDS) causing lung pathology has been identified in very young chicks. To date, no causative pathogens for RDS have been identified. In 2020 and 2021, the number of chick deaths from suspected RDS increased four- and five-fold, respectively, causing mass mortality with an estimated mortality rate of >90%. We aimed to identify possible pathogens responsible for RDS disease impacting these critically endangered yellow-eyed penguins. Total RNA was extracted from tissue samples collected during post-mortem of 43 dead chicks and subject to metatranscriptomic sequencing and histological examination. From these data we identified a novel and highly abundant gyrovirus (Anelloviridae) in 80% of tissue samples. This virus was most closely related to Gyrovirus 8 discovered in a diseased seabird, while other members of the genus Gyrovirus include Chicken anaemia virus, which causes severe disease in juvenile chickens. No other exogenous viral transcripts were identified in these tissues. Due to the high relative abundance of viral reads and its high prevalence in diseased animals, it is likely that this novel gyrovirus is associated with RDS in yellow-eyed penguin chicks.Item CHANGES IN THE LEVELS OF THEILERIA ORIENTALIS IKEDA TYPE INFECTION IN HAEMAPHYSALIS LONGICORNIS NYMPHS OVER A SIX-MONTH PERIOD.(1/09/2021) Zhao Y; Lawrence KE; Minor M; Gedye K; Wang B; Pomroy W; Potter MThis study aimed to investigate whether the infection intensity of Theileria orientalis Ikeda type organisms within Haemaphysalis longicornis larvae and nymph stages fluctuated over 6 mo after feeding as larvae on infected calves in the field. Naïve larvae, hatched from eggs, were fed on infected calves for 5 days while contained within cotton socks glued over the calves' ears. Larvae were first sampled immediately post-feeding and then sampled every 3 wk for 23 wk in total, after molting to nymphs. All larvae and nymphs were tested for T. orientalis Ikeda organisms using quantitative PCR. The qPCR results showed that the infection intensity of Haemaphysalis longicornis larvae and nymphs was not constant over the sampling period, and after initially dropping after molting to nymphs, it then rose with fasting to a maximum at 17 and 23 wk post-feeding. The significant rise in T. orientalis Ikeda organisms observed at 23 wk postfeeding may explain why more severe clinical cases of bovine theileriosis in New Zealand are seen in the spring when nymphs are the predominant instar questing.Item BfpI, BfpJ, and BfpK Minor Pilins Are Important for the Function and Biogenesis of Bundle-Forming Pili Expressed by Enteropathogenic Escherichia coli(American Society for Microbiology, 1/03/2016) Nisa S; Martinez de la Peña CF; De Masi L; Mulvey G; Tong J; Donnenberg MS; Armstrong GDItem The population genetic structure of the urchin Centrostephanus rodgersii in New Zealand with links to Australia(1/09/2021) Thomas LJ; Liggins L; Banks SC; Beheregaray LB; Liddy M; McCulloch GA; Waters JM; Carter L; Byrne M; Cumming RA; Lamare MDThe diadematid sea urchin Centrostephanus rodgersii occurs in Australia and New Zealand and has undergone recent southward range extension in Australia as a result of regional warming. Clarifying the population genetic structure of this species across its New Zealand range would allow a better understanding of recent and future mechanisms driving range changes in the species. Here, we use microsatellite DNA data to assess connectivity and genetic structure in 385 individuals from 14 locations across the Australian and New Zealand ranges of the species. We detected substantial genetic differentiation among C. rodgersii populations from Australia and New Zealand. However, the population from Port Stephens (located north of Newcastle), Australia, strongly clustered with New Zealand samples. This suggests that the New Zealand populations recently originated from this area, likely via larval transport in the Tasman Front flow that arises in this region. The weak population genetic structure and relatively low genetic diversity detected in New Zealand (global Fst = 0.0021) relative to Australia (global Fst = 0.0339) is consistent with the former population’s inferred history of recent climate-driven expansion. Population-level inbreeding is low in most populations, but were higher in New Zealand (global Fis = 0.0833) than in Australia (global Fis = 0.0202), suggesting that self-recruitment is playing an increasingly important role in the New Zealand region. Our results suggest that C. rodgersii is likely to spread southwards as ocean temperatures increase; therefore, it is crucial that researchers develop a clearer understanding of how New Zealand ecosystems will be reshaped by this species (and others) under climate change.Item Estimating direct N2O emissions from sheep, beef, and deer grazed pastures in New Zealand hill country: accounting for the effect of land slope on N2O emission factors from urine and dung(Elsevier, 2015-03) Saggar SK; Giltrap DL; Davison R; Gibson R; de Klein CAM; Rollo M; Ettema P; Rys GNearly one-half of New Zealand's ruminant livestock graze on hill country pastures where spatial differences in soil conditions are highly variable and excretal deposition is influenced by pasture production, animal grazing and resting behaviour that impact the nitrous oxide (N2O) emission factor from excreta (EF3). New Zealand currently uses country-specific EF3 values for urine and dung of 0.01 and 0.0025, respectively, to estimate direct N2O emissions from excreta. These values have largely been developed from trials on flat pastoral land. The use of the same EF3 for hill pasture with medium and steep slopes has been recognised as a possible source of overestimation of N2O emissions in New Zealand. The objectives of this study were to develop and describe an approach that takes into account the effects of slope in estimating hill country N2O emissions from the dung and urine of ruminant animals (sheep, beef cattle, and deer) across different slope classes, and then compare these estimates with current New Zealand inventory estimates. We use New Zealand as a case study to determine the direct N2O emissions between 1990 and 2012 from sheep, beef cattle and deer excreta using updated estimates of EF3 for sloping land, the area of land in different slope classes by region and farm type, and a nutrient transfer model to allocate excretal-N to the different slope classes, and compare the changes between these hill pastures-specific and current inventory estimates. Our findings are significant - the proposed new methodology using New Zealand specific EFs calculated from a national series of hill country experiments resulted in 52% lower N2O estimates relative to using current inventory emission factors, for the period between 1990 and 2012 and reduces New Zealand's total national agricultural N2O greenhouse inventory estimates by 16%. The improved methodology is transparent, and complete, and has improved accuracy of emission estimates. On this basis, the improved methodology of estimating N2O emission is recommended for adoption where hill land grasslands are grazed by sheep, beef cattle and deer.Item The epidemiology of AmpC-producing Escherichia coli isolated from dairy cattle faeces on pasture-fed farms.(2021-10) Burgess SA; Cookson AL; Brousse L; Ortolani E; Benschop J; Akhter R; Brightwell G; McDougall SIntroduction. Antibiotic use, particularly amoxicillin-clavulanic acid in dairy farming, has been associated with an increased incidence of AmpC-hyperproducing Escherichia coli.Gap statement. There is limited information on the incidence of AmpC-hyperproducing E. coli from seasonal pasture-fed dairy farms.Aim. We undertook a New Zealand wide cross-sectional study to determine the prevalence of AmpC-producing E. coli carried by dairy cattle.Methodology. Paddock faeces were sampled from twenty-six dairy farms and were processed for the selective growth of both extended-spectrum beta-lactamase (ESBL)- and AmpC-producing E. coli. Whole genome sequence analysis was carried out on 35 AmpC-producing E. coli.Results. No ESBL- or plasmid mediated AmpC-producing E. coli were detected, but seven farms were positive for chromosomal mediated AmpC-hyperproducing E. coli. These seven farms were associated with a higher usage of injectable amoxicillin antibiotics. Whole genome sequence analysis of the AmpC-producing E. coli demonstrated that the same strain (<3 SNPs difference) of E. coli ST5729 was shared between cows on a single farm. Similarly, the same strain (≤15 SNPs difference) of E. coli ST8977 was shared across two farms (separated by approximately 425 km).Conclusion. These results infer that both cow-to-cow and farm-to-farm transmission of AmpC-producing E. coli has occurred.Item Bistability in a metabolic network underpins the De Novo evolution of colony switching in Pseudomonas fluorescens(PUBLIC LIBRARY SCIENCE, 12/03/2015) Gallie J; Libby E; Bertels F; Remigi P; Jendresen CB; Ferguson GC; Desprat N; Buffing MF; Sauer U; Beaumont HJE; Martinussen J; Kilstrup M; Rainey PB© 2015 Gallie et al. Phenotype switching is commonly observed in nature. This prevalence has allowed the elucidation of a number of underlying molecular mechanisms. However, little is known about how phenotypic switches arise and function in their early evolutionary stages. The first opportunity to provide empirical insight was delivered by an experiment in which populations of the bacterium Pseudomonas fluorescens SBW25 evolved, de novo, the ability to switch between two colony phenotypes. Here we unravel the molecular mechanism behind colony switching, revealing how a single nucleotide change in a gene enmeshed in central metabolism (carB) generates such a striking phenotype. We show that colony switching is underpinned by ON/OFF expression of capsules consisting of a colanic acid-like polymer. We use molecular genetics, biochemical analyses, and experimental evolution to establish that capsule switching results from perturbation of the pyrimidine biosynthetic pathway. Of central importance is a bifurcation point at which uracil triphosphate is partitioned towards either nucleotide metabolism or polymer production. This bifurcation marks a cell-fate decision point whereby cells with relatively high pyrimidine levels favour nucleotide metabolism (capsule OFF), while cells with lower pyrimidine levels divert resources towards polymer biosynthesis (capsule ON). This decision point is present and functional in the wild-type strain. Finally, we present a simple mathematical model demonstrating that the molecular components of the decision point are capable of producing switching. Despite its simple mutational cause, the connection between genotype and phenotype is complex and multidimensional, offering a rare glimpse of how noise in regulatory networks can provide opportunity for evolution.Item Geostatistical determination of soil noise and soil phosphorus spatial variability(Elsevier Masson, 28/09/2017) Kaul TMC; Grafton MCEThis research studies the effect of stratifying soil samples to try and find a suitable depth to establish a geospatial relationship for a practical soil sampling grid in New Zealand hill country. Cores were collected from 200 predetermined sites in grids at two trial sites at “Patitapu” hill country farm in theWairarapa, New Zealand. Trial 1 was a 200 m 100 m grid located in a gently undulating paddock. Trial 2 was a 220 m 80 m grid located on a moderately sloped paddock. Each grid had cores taken at intervals of 5 m, 10 m, or 20 m. Core sites were mapped out prior to going into the field; these points were found using a Leica Geo Systems GS15 (real time kinematic GPS) and marked with pigtail pegs and spray-paint on the ground. Cores were taken using a 50 mm-diameter soil core sampler. Cores were cut into three sections according to depth: A—0–30 mm, B—30–75 mm, and C—75–150 mm. Olsen P lab results were obtained for half of the total 1400 samples due to financial constraints. The results indicate that there was a significant decrease in variability from Section A to Section B for both trials. Section B and C for Trial 1 had similar variability, whereas there was another significant drop in variability from Section B to C in Trial 2. Measuring samples below the top 3 cm appeared to effectively reduce noise when sampled from 3 to 15 cm. However, measuring from 7.5 cm to 15 cm on the slope in Trial 2 reduced variability so much that all results were almost identical, which may mean that there is no measurable representation of plant available P. The reduction in noise by removing the top 3 cm of soil samples is significant for improving current soil nutrient testing methods by allowing better geospatial predictions for whole paddock soil nutrient variability mappingItem Novel, potentially zoonotic paramyxoviruses from the African straw-colored fruit bat Eidolon helvum(American Society for Microbiology, 2013) Baker KS; Todd S; Marsh GA; Crameri G; Barr J; Kamins AO; Peel AJ; Yu M; Hayman DTS; Nadjm B; Mtove G; Amos B; Reyburn H; Nyarko E; Suu-Ire R; Murcia PR; Cunningham AA; Wood JLN; Wang L-FBats carry a variety of paramyxoviruses that impact human and domestic animal health when spillover occurs. Recent studies have shown a great diversity of paramyxoviruses in an urban-roosting population of straw-colored fruit bats in Ghana. Here, we investigate this further through virus isolation and describe two novel rubulaviruses: Achimota virus 1 (AchPV1) and Achimota virus 2 (AchPV2). The viruses form a phylogenetic cluster with each other and other bat-derived rubulaviruses, such as Tuhoko viruses, Menangle virus, and Tioman virus. We developed AchPV1- and AchPV2-specific serological assays and found evidence of infection with both viruses in Eidolon helvum across sub-Saharan Africa and on islands in the Gulf of Guinea. Longitudinal sampling of E. helvum indicates virus persistence within fruit bat populations and suggests spread of AchPVs via horizontal transmission. We also detected possible serological evidence of human infection with AchPV2 in Ghana and Tanzania. It is likely that clinically significant zoonotic spillover of chiropteran paramyxoviruses could be missed throughout much of Africa where health surveillance and diagnostics are poor and comorbidities, such as infection with HIV or Plasmodium sp., are common.Item Environmental input-output analysis of the New Zealand dairy industry(Inderscience Enterprises Ltd., 2/01/2012) Flemmer CL; Nepomuceno-Silo, JThis work presents data and analysis quantifying the total (direct and indirect) resource use and outputs (products and pollutants) of the New Zealand dairy industry for the year April 1997 to March 1998. It also identifies those sectors supplying the dairy industry which make significant indirect contributions to its total inputs and outputs. Although this data is 14 years old, it is the only large-scale, detailed data available. Further, more modern data can be compared with this baseline data. Comparison with the other major New Zealand food and fibre sectors shows that the dairy farming sector has the highest total water consumption and the highest total effluent. It also has high total land use, electricity use and production of animal methane. The dairy processing sector is water and fuel intensive and has high total water effluent and greenhouse gas emissions. The high resource use and pollutants have to be weighed against the enormous economic value of the dairy sectors.