Massey Documents by Type

Permanent URI for this communityhttps://mro.massey.ac.nz/handle/10179/294

Browse

Has files: YesSubject: search.filters.subject.Microbial ecology

Search Results

Now showing 1 - 3 of 3
  • Thumbnail Image
    Item
    Genomics and eDNA provide a holistic understanding of microbial communities and zoonoses in Aotearoa's waters : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Ecology at Massey University, Palmerston North, New Zealand
    (Massey University, 2024-03-18) Davis, Meredith Taylor
    In Aotearoa, water quality and freshwater ecosystem health is declining. Much of that decline has been blamed on livestock farming and is quantified by using invertebrate communities or Escherichia coli levels. However, the wider microbial community, particularly archaea and eukaryotes, have been overlooked in the current ecosystem health measures. Some of the more well-known impacts of microorganisms on waterways are sporadically measured (e.g., algae blooms, drinking water contamination by faeces, and shellfish toxins) but the drivers of their community structure, both individually and as a whole, in Aotearoa is poorly understood. This thesis is a start at rectifying this knowledge gap. The studies in this thesis were approached with a One Health perspective and provide a quantitative, holistic analysis of microbial communities by investigating three significant challenges facing Aotearoa’s freshwater ecosystems. Those challenges - the spread of waterborne disease, eutrophication, and microbial biogeochemical cycling - were investigated using microbiological cultures and environmental DNA, analysed with metagenomic and other molecular methods. I was able to determine that targeted testing for genetic loci associated with antimicrobial resistance and Shiga toxin-producing E. coli virulence was a useful in monitoring three Canterbury waterways for human health. Furthermore, enteropathogenic human and bovine strains of E. coli appeared unresponsive to in-stream nitrate-nitrogen concentrations of 0, 1, and 3 mg/L and native in-stream biota in microcosms. However, environmentally sourced E.coli imported as part of the in-stream biota survived longer in NO3-N concentrations of 1 and 3 mg /L than at 0 mg/L. Microorganism groups (e.g., archaea, bacteria, and microbial eukaryotes) responded to different environmental, spatio-temporal, and physico-chemical drivers depending on taxonomic level. As a group, lotic pressures and dispersal outweighed other drivers in community structuring. Archaeal communities were highly correlated with Austral season and the most abundant functional groups reflected a likely response to common agricultural pollutants found the Waiotahe catchment and in many rural rivers across Aotearoa (e.g., nitrogen pollution and livestock waste/effluents). The drivers commonly associated with bacterial survival (e.g., conductivity and temperature) were less important than dispersal and lotic pressures, particularly at lower taxonomic levels. Cultured E. coli concentrations from sediment and/or the water column were poorly indicators of Campylobacter, Enterobacter, and Enterococcus relative abundances. Additionally, neither Enterobacter nor Enterococcus relative abundances were correlated with E. coli/E. cloacae group concentrations or Campylobacter relative abundances. These findings have important implications for water quality monitoring and recreational human health risk assessments in Aotearoa. Currently, microbiological water testing is limited to bathing season (i.e., late spring to early autumn) and to culturing either Enterococcus in saline/brackish water or E. coli in freshwater. Effective water quality monitoring must include both water and benthic substrates to accurately portray the entire riverscape. Genetic loci associated with zoonotic human pathogens are present in some of Aotearoa’s waterways and they are likely a result of catchment land use, livestock farming, and effluent contamination. Additionally, genetic loci can be detected with collection methods similar to those employed for current water quality monitoring using Escherichia coli and some molecular methods are more specific (i.e., not proxies). Metagenomic methods allowed for the discernment of microbial communities and core biomes from genetic information extracted from environmental samples. Microbial communities were affected by many different in-stream conditions; however, dispersal and the pressures associated with lotic systems proved to be more important than adjacent land use, precipitation levels, or season. In contrast, archaeal communities were better explained by season. It is clear that water monitoring in Aotearoa needs an overhaul and to incorporate new technology in a thoughtful and ecologically informed manner. A review of the current methods and new technologies should be undertaken by a multi-disciplinary group of experts in the fields of microbiology, epidemiology, and freshwater and microbial ecology. Community buy in and the inclusion of Māori values and indigenous rights should be at the forefront of any proposed changes to freshwater restoration and conservation.
  • Thumbnail Image
    Item
    Biomass yield dependence on inhibitory substrate concentration : a thesis presented as a requirement for the degree of Master of Technology in Biotechnology at Massey University
    (Massey University, 1992) Setter, Peter Brian
    Variations of growth yield coefficient with substrate concentration of a mixed microbial population was studied. Substrates used for growth were 2,4-dichlorophenoxyacetic acid (2,4-D) and para-chloro-ortho-cresol (PCOC). The synthetic medium used was designed so that substrate was the limiting-nutrient. The microbial culture was obtained from an activated sludge system treating effluent containing 2,4-D and PCOC. This was acclimated to the particular substrate metabolised in the investigations. Growth was conducted in batch and chemostat configurations. Experimental data obtained indicated variations in growth yield did occur and were dependent on substrate concentration. Growth yield and specific growth rate biokinetics were directly calculated from the data obtained. Analysis of specific growth rate help in understanding culture-substrate systems. Specific growth rate increased to a maximum then decreased with increasing substrate concentration in batch configuration. Decrease in growth rate began above 500 mg/I for 2,4-D and above 60 mg/I for PCOC. This is an indication of substrate inhibition. The design of the chemostat maintained a constant specific growth rate. Growth yield decreased with increasing substrate concentration with growth on either 2,4-D and PCOC in batch and chemostat configurations. A review of the literature indicated maintenance coefficient is a key parameter in explaining variations in observed growth yield. Data analysis for determination of the biokinetic constants of maintenance coefficient, me, and half-saturation constant, K , was performed. Analysis techniques for these constants are traditionally derived from Monod kinetics. Monod kinetics adequately explains growth on innocuous substrates. However analysis of specific growth rate had indicated the substrates used were inhibitory. Determination of maintenance coefficient and half-saturation constant by Monod derived techniques was unsatisfactory. The effect of maintenance coefficient on growth yield was considered. The literature indicated maintenance coefficient is constant for growth on innocuous substrates. The substrates used in the investigations have phenolic structures. Phenolic compounds are recognised to be destructive to cell membranes. It was proposed that maintenance coefficient increased with increasing inhibitory substrate concentration as a result of increasing cell damage. An explanation for the decreasing growth yield with substrate concentration is adequately given by considering the variable maintenance coefficient. Substrate used for maintenance is substrate that is not available for growth. The relationship between growth yield and substrate concentration is essentially linear. Linear regression of yield on substrate was performed for growth on 2,4-D and PCOC in batch configuration and PCOC in chemostat configuration. Fitting of the linear functional form was considered appropriate. Analysis of the linear models for the three biosystems indicated yield variations with substrate concentration are significant. The models for the three biosystems have been given: For growth on 2,4-D in batch configuration Y(s) = 0.334 - (2.8xl04 )s For growth on PCOC in batch configuration Y(s) = 1.03 - (5.6xl0-3)s For growth on PCOC in chemostat configuration Y(s) = 0.799 - (6.0xl0.3)s Growth yield models may be incorporated into an overall growth model when similar biosystem configuration and substrates are studied. It is considered that this will give a growth model with greater accuracy in design and operation of biological treatment plants.
  • Thumbnail Image
    Item
    The microbial ecology of Campylobacter jejuni in New Zealand within a spatial-temporal framework : a thesis presented in partial fulfilment of requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Manawatu, New Zealand
    (Massey University, 2015) Binney, Barbara Mary
    Campylobacter jejuni (C. jejuni) is an important cause of gastroenteritis internationally; it is a complex bacterium carried by multiple hosts, showing phenotypic and genotypic variation. This thesis systematically examines the molecular ecology and evolution of C. jejuni in New Zealand from the levels of population movement, phenotype, genome and metabolism. First, the demographic history of cattle, sheep and poultry importations into New Zealand (1860- 1979) was quantified. Australia was the most common reported source of cattle sheep and poultry, with large numbers of cattle and sheep being imported in the 1860s, and large numbers of poultry imported from the 1960s onwards. This suggests the population structure of cattle and sheep and the microbial organisms they carried may exhibit a founder effect. The second level investigated the phenotypes of related sequence types (ST) with generalist and specialist lifestyles and compared them at 42°C and 22°C on the basis of carbon source utilisation in Biolog phenotypic microarrays. The isolates utilised a total of 29 carbon sources in a pattern that clustered them together on the basis of ST at 42°C more than lifestyle and host. At 22°C they utilised a limited palette of carbon sources (9) related to the tricarboxylic acid cycle (TCA). The third level, used genomic comparisons to identify a putative new species C. sp. nov. 4 spp. in the Australian purple swamphen (Porphyrio porphyrio melanotus). Overall, the pattern of relationship between isolates associated with the pukeko (Porphyrio porphyrio melanotus), takahe (Porphyrio hochstetteri) and the Australian swamphen isolates suggested a recent common ancestor and then divergence after separation. Despite high levels of recombination in C.jejuni, the genomes grouped by clonal complex and ST, this suggests there are factors restricting regular recombination between more distant C. jejuni STs. The draft genomes for the wild-bird and agricultural-related isolates clustered by lineages in a host(s). The fourth level involved the comparison of C. jejuni metabolic pathways (subsystems) to identify host association. Type VI secretion system, Coenzyme A biosynthesis and Campylobacter spp. iron metabolism were identified as important pathways in distinguishing between wild-bird and livestock associated isolates.