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    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.
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    The potential for submerged macrophyte recovery from the seed bank of the shallow coastal Whakakī Lake, Aotearoa : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Ecology at Massey University, Manawatū, New Zealand
    (Massey University, 2022) Mackay, Ariana
    Shallow lakes provide a range of ecosystem services, including habitat for waterfowl, fish, aquatic plants, and invertebrates, and have significant recreational, aesthetic, and cultural value. Eutrophication is one of the leading causes of shallow lake ecosystem degradation globally. Excess input of nutrients, especially phosphorus and nitrogen, can cause a regime shift where the ecosystem switches from a macrophyte-dominated system to one driven by primary production from phytoplankton. The naturally occurring communities dominated by aquatic macrophytes as primary producers undergo a drastic change, flipping to an algae-dominated state that can result in the degradation or disappearance of natural plant and animal communities. Whakakī Lake is a shallow coastal lake in northern Hawke’s Bay. This lake is in a highly degraded, hypertrophic state that no longer supports a community of submerged macrophytes. Previous work on the macrophyte community of Whakakī Lake in 1992 and 2007 provides an idea of the original condition of the macrophyte communities and the gradual decline in abundance and diversity that preceded the current conditions. Sediment coring at four sites along a transect was conducted in Whakakī Lake to quantify and characterise the seed and oospore bank of submerged macrophytes. A diverse and abundant seed bank was identified with 12 species of macrophytes and charophytes found throughout the lake. The highest abundance of seeds and oospores was located on the northern edges of the lake shore, near the Tuhara Stream inlet. Germination trials using the seeds and oospores collected from the seed bank were run over three months under controlled conditions to assess the viability of the Whakakī Lake seed bank. Species geminated under three salinity treatments: zero, low and moderate salinity levels. Light availability was altered to assess the impact of reduced light (photosynthetically available radiation) on species germination. The lack of germination success of seeds under severely reduced light levels and complete darkness demonstrated how high turbidity and lack of light is hindering seed germination within Whakakī Lake. With improvements to water quality, specifically the reduction of external and internal nutrient loads and increased water clarity, it is possible a submerged macrophyte community could re-establish within Whakakī Lake based on seeds and oospores available within the seed bank.
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    Risk assessment and mitigations of the potential impacts of trout predation on New Zealand’s indigenous fish species : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Ecology at Massey University, Manawatū, New Zealand
    (Massey University, 2022) Coughlan, Ami
    Trout were introduced into New Zealand freshwater ecosystems ~150 years ago as a prized sports fish, despite unknown potential impacts of this introduction. New Zealand’s native fish are experiencing widespread decline, with trout implicated as one potential key stressor. The concurrent introduction of trout with large-scale land use change have made attributing decline to specific stressors difficult. However, understanding the effect of specific stressors is necessary for management of healthy populations of both the native fauna and valued introduced species. This thesis unpacks the predatory impacts of trout on native fish by (1) using the literature to develop a risk assessment matrix to identify fish species at high risk of detrimental impact from trout predation, and (2) experimentally examine whether trout presence alters the habitat preferences of a small non-migratory galaxiid. Risk assessments provide an avenue for wildlife managers to prioritise conservation and remediation efforts towards reducing the impacts of trout predation on the most at-risk native fish. The risk assessment matrix created in this thesis has triaged species most at-risk of detrimental population impact from trout predation. Perhaps unsurprisingly, the risk assessment identified non-diadromous galaxiids and mudfish as the most vulnerable groups to trout predation. Nationally, approximately 10% of river reaches occupied by trout also overlap with locations of at least one native fish species at high risk of trout impact. These reaches should be a focus for future investigation and mitigation efforts, such as physical habitat restoration, water quality improvements, restoration of hydrological regimes, and active population control. Dwarf galaxiids (a non-migratory native fish) were identified as highly vulnerable to trout predation. I investigated potential impacts of trout on the habitat preference of dwarf galaxiids in replicated mesocosms. The experiments examined two contrasting habitats, comparing sand and cobble substrate, and vegetation and no vegetation. Potential changes in refuge seeking behaviours were examined in the physical presence of trout, the presence of trout odour, and the absence of trout. In the gravel substrate experiment, galaxiids were noted in refuge more frequently when exposed to trout odour, no other significant differences were observed. This indicates that dwarf galaxiids are unlikely to alter their refuge seeking behaviour in the presence of trout, which may leave them exposed to trout predation, and further indicates the importance of instream and riparian refuge for dwarf galaxiids.
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    Ecology of ponds : anthropogenic and environmental effects on biodiversity : a thesis presented in partial fulfilment of the requirement for the degree of Doctor of Philosophy in Conservation Biology at Massey University, Auckland, New Zealand
    (Massey University, 2022) Kuranchie, Abigail
    Ponds are a vital component of the freshwater ecosystem but have been understudied worldwide. The paucity of research is especially disturbing due to increasing pressure on freshwater ecosystems. Pond ecosystems are vulnerable due to anthropogenic activities and changing environmental conditions. Ponds are the most ubiquitous freshwater ecosystems found in the Auckland Region of New Zealand. Despite their abundance (occurring in all landscapes) and significant ecological role, there is a lack of knowledge on the ecology of pond ecosystems in New Zealand. Further, literature on the impact of land use/ land cover (LULC) and human population density on pond water quality and biodiversity is lacking globally. I studied aspects of ponds (natural and man-made) ecology in the Auckland region by assessing both abiotic and biotic factors in the summer and winter seasons. Specifically, my study focused on six aspects of the ecology of pond ecosystems: i) the relationship between water quality and LULC at multiple spatial scales across the seasons, ii) the temporal community composition of macroinvertebrates and the relationship between the communities and the abiotic factors, iii) the influence of anthropogenic activities (measured as human population density and as pond types or function) on the macroinvertebrate communities, iv) the phytoplankton communities in ponds across the seasons, v) the limiting nutrient(s) in periphyton biomass in ponds using an in-situ experiment, and finally, vi) a single case study tracking a newly formed pond in a restoration area and development of its macroinvertebrate community over one year. I sampled 50 ponds in the Auckland region across two seasons (summer and winter) to assess pond water quality (evaluated using seven physicochemical variables: pH, percentage dissolved oxygen '% DO', conductivity, temperature, total dissolved solids 'TDS', salinity, nitrate, phosphate and ammoniacal nitrogen). My aim was to understand the relationship between water quality and the landscape features (physical variables and LULC types: ‘forest, grass, and impervious surface’) at multiple spatial scales (10m, 100m, 500m and pond catchment) from the pond. I found a significant seasonal difference in the water quality of ponds. All the water quality variables measured apart from ammoniacal nitrogen were higher in summer, suggesting that the water was of lower quality at that time. Also, the effect of LULC on the physicochemical water quality parameters varied spatially and seasonally. LULC at the catchment and 500m scale influenced the water quality in winter, while the LULC at 100m affected the water quality in summer. The results highlight the critical and complex role of environmental factors and LULC in determining the water quality in ponds. I assessed the macroinvertebrate community compositions and water quality in 12 ponds across two seasons for two years. I found an average of 15 macroinvertebrate taxa in focal ponds. Insects were the most diverse group found, although Crustacea were most abundant. The community composition of the macroinvertebrates varied among ponds and varied across seasons and years. Macroinvertebrates were more abundant, and the community was more diverse in summer. The % DO in the ponds was negatively correlated to the macroinvertebrate abundance. My results suggest that macroinvertebrates and water quality in ponds are temporally variable. I assessed the influence of anthropogenic activities on the macroinvertebrate communities of 11 ponds. Four categories of human population density were used (rural, small urban, large urban, and major urban; in order of increasing human population) to group ponds for analysis. By applying taxonomic and trait-based (functional feeding groups) approaches, I found that high human population density was negatively associated with the macroinvertebrate communities, especially in summer. Ponds in rural areas had the highest diversity of macroinvertebrates and the highest composition of functional foraging group relative to the other areas assessed. This finding suggests that ponds in rural areas had the lowest anthropogenic impact. Ornamental ponds were rich in macroinvertebrates, primarily due to a comparatively more heterogenous pond habitat. I sampled and analysed the phytoplankton community composition of 12 ponds in summer and winter. Overall, the communities were dominated by taxa in the phylum Chlorophyta (green algae) and class Bacillariophyceae (Diatoms). Although I did find seasonal differences in the phytoplankton communities, these were influenced by temperature and conductivity. In addition, ponds within areas of denser human populations had the most motile diatoms in summer, suggesting high siltation. Despite being moderately polluted, these results show that all ponds generally had healthy phytoplankton communities. Furthermore, by using an in-situ nutrient diffusion experiment, I found that nitrogen is likely to be the limiting nutrient for periphyton growth in ponds. Finally, I sampled and monitored a newly created and a nearby established pond for a year to obtain insights into the progression of a pond from creation into a functional ecosystem using macroinvertebrates as indicators. I found that Crustaceans were the first to colonise the new pond. The macroinvertebrate community in the new pond was more taxonomically distinct than the established pond at the end of the first year of its creation. Shannon Weiner's diversity index was similar between the ponds, and environmental factors influenced the macroinvertebrate abundance. My results indicate that new ponds can create new habitats and boost local freshwater biodiversity. By combining water quality analyses, and detailed biodiversity assessment, my thesis demonstrates that pond ecosystems support a high diversity of macroinvertebrates and phytoplankton. Environmental variables, LULC, and human population density influence the biodiversity in ponds, and the extent, relationship, and impact of these are complex and vary seasonally. My study provides new baseline information and valuable insights for future research on pond ecosystems in New Zealand.
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    The effect of landuse and geology on macroinverterbate communities in East Coast streams, Gisborne, New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Ecology at Massey University, New Zealand
    (Massey University, 2020) Roil, Harriet
    Chapter 1. Land use and geology both potentially influence streams and rivers by altering hydrology, water chemistry, light levels, sedimentation, channel form, food sources and habitat structure for the macroinvertebrate community assemblages. This study investigated the effect of geology and land use on stream macroinvertebrate communities in the East Coast region of the North Island, New Zealand. Macroinvertebrate communities were monitored every year between 2016-2018 at 79 sites during the austral summer in; exotic forest, indigenous forest and pasture streams that either had a hard or soft geology. Both land use and geology independently influenced biotic indices (MCI and %EPT abundance) and macroinvertebrate communities, but there seemed to be limited interactive effects. Exotic forest and pastoral land use were dominated by Molluscs and Ephemeroptera. Pastoral land use supported the highest number of macroinvertebrate individuals and indigenous forest had the highest densities of sensitive species. Sixty five percent of sites had deposited sediment levels greater than 20% cover. Sedimentation reduced the abundance of sensitive taxa, decreased biotic indices and was elevated in exotic forest, pastoral land use and soft geology. Calcium and conductivity levels were the parameters most strongly linked with macroinvertebrate community structure, with higher conductivity levels in exotic forest, pastoral land uses and soft geology. These results demonstrate the complex relationship between geology and land use. This is important for future regional decisions as the combination of land use in a certain geology type could have extrapolated negative effects on macroinvertebrate assemblages indirectly through changes in habitat and water chemistry. Chapter 2. The influence of forest harvest on macroinvertebrate communities in soft geology was investigated at fourteen stream sites in the upper Waipaoa River catchment, Gisborne, New Zealand. Stream reaches were surveyed under summer base flow conditions in March 2019 at sites that varied in time following forest harvest from recently harvested (0 years) to mature exotic forest (27 years). Macroinvertebrate communities were most influenced by turbidity, mean particle size, sediment size and bank erosion up to ten years following harvest. Macroinvertebrate communities following forest harvest were dominated by species sensitive to degraded stream conditions including Coleoptera and Diptera, with Diptera being one of the dominant taxa at all sites throughout the forest rotation. Fine sediment particle size did not change over the harvest cycle with all sites having silt present, and benthic sediment density decreasing as the forest established. The density of sensitive EPT taxa increased from ten years following forest harvest and communities became dominated by Hydrobiosis, Deleatidium, Austroclima and Coloburiscus. The QMCI increased with time since harvest with sites having high values after ten years. Recovery of macroinvertebrate communities was dependent on riparian shade, vegetation, hydraulic heterogeneity and habitat quality, with the recovery time being at least ten years following harvest. The results highlight the importance of retaining or establishing continuous riparian buffers along streams within harvested areas of forest to reduce negative impacts on freshwater communities.