Massey Documents by Type

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

Browse

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

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
    Bioprospecting soil metagenomes for potential new antibiotics : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University, Albany, New Zealand
    (Massey University, 2017) Hong, Kelly
    Many soil-dwelling microbes have the natural capacity to produce toxic compounds that inhibit growth of competing bacteria; most traditional antibiotics have been derived from small molecules made by such soil-based microorganisms, of which only a small fraction can be grown in the laboratory. Since techniques that require culturing of these microbes in the lab have been the starting point for studying them in the past, our knowledge of the uncultured majority remains limited. Functional metagenomics is a method that circumvents the need for culturing, and thus has the potential to revel a yet untapped reservoir of antibacterial compounds. Here we present a potential application of functional metagenomics using genes isolated from soil microbes that employs high throughput sequencing to identify microbial genes encoding novel compounds that inhibit bacterial growth.
  • Thumbnail Image
    Item
    Comparative genomics of Butyrivibrio and Pseudobutyrivibrio from the rumen : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Microbiology and Genetics at Massey University, Palmerston North, New Zealand
    (Massey University, 2016) Palevich, Nikola
    Determining the role of rumen microbes in plant polysaccharide breakdown is fundamental to understanding digestion, and maximising productivity, in ruminant animals. Rumen bacterial species belonging to the genera Butyrivibrio and Pseudobutyrivibrio are important degraders of plant hemicellulose, an abundant heterogeneous, branched polymer, involved in crosslinking cellulose microfibrils to lignin. To investigate their genes required for hemicellulose degradation, the genomes of 40 Butyrivibrio and 6 Pseudobutyrivibrio strains isolated from the plant-adherent microbiome of New Zealand bovine ruminants, were sequenced, and their CAZyme-encoding genes compared. Within the Butyrivibrio and Pseudobutyrivibrio pan-genomes, respectively, there were a total of 4,421 and 441 glycoside hydrolases, as well as 1,283 and 122 carbohydrate esterases with predicted activities involved in the degradation of the insoluble plant polysaccharides such as xylan and pectin. To examine species differences, the genes of the previously characterised bacterium B. proteoclasticus B316 were compared in detail with those from the newly sequenced B. hungatei MB2003. B316 was found to encode a much more developed polysaccharide-degrading repertoire and it was thus hypothesised that B316 would out-compete MB2003 when grown in co-culture on the insoluble hemicellulose substrate, xylan. To test this hypothesis, the two strains were grown on xylan and pectin, either alone in mono-cultures, or in direct competition in a co-culture. The results showed that MB2003 had little ability to utilise xylan or pectin alone, but was capable of significant growth when co-cultured with B316. This indicates a commensalistic interaction between these species, in which B316 initiates the primary attack on the insoluble substrate, while MB2003 has a secondary role, competing for the released soluble sugars. This work provides the first systematic phenotypic, comparative genomic and functional analysis of ruminal Butyrivibrio and Pseudobutyrivibrio species, which not only defines their conserved features involved in hemicellulose degradation, but is also beginning to differentiate their unique gene complements and growth characteristics that separate them as discrete species.