- Title
- The use of molecular techniques as indicators of estuary health
- Creator
- Suzzi, Alessandra Louise
- Relation
- University of Newcastle Research Higher Degree Thesis
- Resource Type
- thesis
- Date
- 2023
- Description
- Research Doctorate - Doctor of Philosophy (PhD)
- Description
- Urbanised estuaries are often subject to a range of anthropogenic impacts including contamination by heavy metals, stormwater and sewage, and are also particularly vulnerable to the effects of climate change. There is therefore a recognised need to monitor and manage such impacts within these systems, however this requires the development of effective tools and the use of ecologically relevant indicators. Next-generation sequencing has facilitated rapid, broad-scale assessments of biological communities and overcomes many limitations associated with traditional approaches. As a result, specific members of eukaryote and prokaryote communities have been identified for their potential as indicators of environmental condition or anthropogenic impact. Despite this significant progress, further work is needed to disentangle responses driven by anthropogenic disturbances versus natural ecological processes in order to reliably predict and measure responses to stressors, particularly within vulnerable and dynamic estuarine systems. In particular, microbial communities associated with different habitats are likely to have distinct responses to stressors however how these vary between estuarine free-living and host-associated communities is currently unclear. The overall aim of my thesis was to investigate the utility of molecular tools in the monitoring of estuarine systems, addressing questions related to the responses of estuarine communities to anthropogenic impacts. I also aimed to address knowledge gaps concerning the responses of free-living versus host-associated microbial communities and the influence of spatial factors on these communities. Firstly, I used a combination of 16S rDNA gene amplicon sequencing and quantitative PCR (qPCR) assays targeting microbial taxa and anthropogenic marker genes to investigate samples collected from seawater, sediments and the hindgut microbiome of a common NSW estuarine fish, Pelates sexlineatus (Chapter 2). Samples were collected along a legacy metal contamination gradient in Australia’s largest urbanised estuary, Lake Macquarie. The metal gradient had limited influence on seawater microbial communities, however fish from contaminated sites experienced reduced gut microbiome diversity and increased abundances of metal tolerant taxa. These tolerant bacteria may aid in host adaptation to chronically contaminated environments. Contaminated sediments also harboured increased abundances of the intI-1 gene, a marker for anthropogenic contamination that also appears to be involved in the resistance of adaptation to contaminants, indicating that sediment communities possess the capability to adapt to or resist chronic contamination. In chapter 3, I examined the benthic eukaryote community response to the metal contamination gradient in Lake Macquarie using 18S rDNA amplicon sequencing of sediment samples. Significant positive associations between bioavailable metal concentrations and polychaete worms, and negative associations between metal concentrations and meio- and microfauna including nematodes, platyhelminths, diatoms and dinoflagellates were detected. While difficulties with morphotaxonomic identification of these assemblages limit their use in traditional monitoring programs, these findings indicate that eDNA metabarcoding can reliably identify these taxonomic groups and detect shifts in response to chronic sediment contamination. In chapter 4, I employed a unique experimental estuary system, where thermal effluent from power stations discharge water at temperatures consistent with future predicted increases in the region. This system was used to examine the effect of elevated water temperatures on estuarine microbial communities and potentially pathogenic members of the Vibrionaceae. Amplicon sequencing of the 16S rDNA and hsp60 genes as well as qPCR assays targeting the Vibrionaceae revealed that while these consistently elevated water temperatures did not influence seawater microbial communities, the fish hindgut microbiome displayed evidence of dysbiosis and proliferation of an emerging aquaculture pathogen Photobacterium damselae subsp. damselae. In chapter 5, in order to determine the influence of spatial variation on these key estuarine microbial communities, I used 16S rDNA gene sequencing to investigate microbial communities associated with the seawater, sediments and fish hindgut across six NSW estuaries spanning ~500km. These findings emphasised the importance of both spatial and environmental factors as drivers of seawater community variation both across and within estuarine systems and highlighted biogeographic patterns within these communities. Sediment communities, however, were only weakly driven by spatial factors, with distance-decay relationships becoming stronger at smaller spatial scales (within estuaries), likely highlighting the steep biogeochemical gradients within estuarine sediments and influence of stochastic factors on these communities. Host factors appeared to be the strongest drivers of the P. sexlineatus hindgut microbiome, potentially overwhelming the influence of environmental and spatial factors at these scales. The use of molecular techniques in monitoring is a rapidly advancing field that is becoming increasing accessible to environmental managers, including the development of portable environmental DNA field-based platforms that are capable of sample collection, water filtration, DNA extraction and molecular analysis on site. These platforms allow for rapid in-situ detection and quantification of important taxonomic groups across multiple trophic levels and have great potential for integration in future monitoring and management applications. In summary, the findings of this thesis enhance our understanding of how estuarine communities respond to stressors common in urbanised estuarine systems and highlights their potential applications in monitoring programs. Seawater communities likely provide an indication of rapid changes in water quality given their sensitivities to environmental parameters such as salinity and pH but resilience or adaptation to chronic or press stressors such as legacy metal contamination and elevated water temperatures. Sediment communities may be more suitable as indicators of chronic or long-term contamination given the range of tolerances and sensitivities displayed by benthic eukaryotes, with members of the meio- and microfaunal communities demonstrating high indicator potential, as well as evidence for resistance and adaptation in sediment microbial communities. Finally, while host-related factors appeared to control associated microbial communities more strongly than environmental or spatial factors, the observed shifts in the P. sexlineatus hindgut microbiome under long-term exposure to chronic or press contaminants indicates that there are exposure thresholds or tipping points for these communities. These findings assist our understanding of how host-associated communities may provide an indication of host condition, with the potential to inform management actions for important estuarine host organisms. In addition to furthering our understanding of the responses of these estuarine communities to environmental and spatial factors, the application of molecular tools including 18S and 16S rDNA sequencing, qPCR assays and recently described Vibrio-specific primers in this thesis support their utility in both broad-scale and targeted assessments of estuarine communities and taxa of interest.
- Subject
- estuary monitoring; microbiome; bacterial communities; metabarcoding; 16S sequencing; microbial indicators
- Identifier
- http://hdl.handle.net/1959.13/1479248
- Identifier
- uon:50281
- Rights
- Copyright 2023 Alessandra Louise Suzzi
- Language
- eng
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