The pelagic microbial community of Macquarie Harbour, Tasmania : ecology and response to aquaculture
Creators: name: Rocha Pavan Da Silva, Ricardo
Publisher: name: University Of Tasmania
Year: 2023

description: Microorganisms are key components of estuarine systems contributing to vital ecosystem services such as nutrient cycling and biogeochemical processes. Pelagic microbial communities are very sensitive and can respond quickly to both natural and anthropogenic perturbations. For this reason, they can be used as sentinels of environmental change. Macquarie Harbour is a highly stratified and relatively shallow semi-enclosed bay located in western Tasmania covering ~280 km<sup>2</sup>. There are naturally low oxygen concentrations in the bottom waters below the halocline and restricted oceanic water exchange. It has a history of anthropogenic activities and environmental stressors such as aquaculture. Aquaculture is a fast-growing industry worldwide, with concern regarding potential effects to surrounding environment such as nutrient loading and release of wastes from uneaten feed, faeces, and metabolic by-products. Presently, little is known about the effects of aquaculture activities on the microbial communities inhabiting the water column of the Harbour. It is vital to understand the ecology of the pelagic microbial communities and how the communities respond to fish farm activities to ensure sustainable aquaculture operations in the long-term.The thesis aims to provide the first insights of the ecology of the microbial community and the potential use of these microorganisms as bioindicators of environmental changes in Macquarie Harbour. For this purpose, high-throughput sequencing of 16S and 18S rRNA genes was performed to explore the structure, distribution, and composition of the archaeal, bacterial, and eukaryotic communities. The two first studies investigated the pelagic microbial community inhabiting Macquarie Harbour, the adjacent ocean, and the Gordon River. Water samples were collected in 2016 and 2018 along spatial and environmental gradients, horizontally and vertically. The first study determined the environmental factors affecting the archaeal and bacterial communities. Horizontally, both communities and associated physiochemical parameters did not vary across the Harbour’s surface, although there were differences between riverine and oceanic samples. In contrast, major differences were observed in archaeal and bacterial distributions with depth, following a vertical gradient of salinity and oxygen. In the oxic surface waters, prokaryotes related to riverine and brackish waters were relatively more abundant. While the halocline is inhabited by phytoplankton metabolite-linked bacteria and nitrite oxidizers, the bottom waters were relatively enriched by microbes involved with the consumption of organic matter and active in nitrogen and sulphur cycling. The second study built on findings from the first study, characterizing Macquarie Harbour itself as a mixed zone where prokaryotic and eukaryotic communities are influenced by both oceanic and riverine inputs. Results also indicated that the heterotrophic community inhabiting the surface and intermediate waters may play key roles in nutrient cycling. Both studies provided valuable understanding of the ecology and distribution of prokaryotes and eukaryotes inhabiting the water column of Macquarie Harbour.The third and fourth studies had the aim to better understand the responses of the microbial communities to aquaculture activities. In December of 2019, water samples were collected from three different depths at three control stations and along and two finfish aquaculture leases. Bacterioplankton and pelagic protists were again heavily influenced by the physiochemical structure of water column, with a south north gradient potentially causing differences in community composition between both leases. Despite the strong effect of water column stratification, differentially abundant taxa were found close to the leases. Bacteria associated with nutrient loading were differentially enriched at lease sites, with some of these possibly playing roles in sulphur, nitrogen, methane, and carbon cycling. Also, microbes relatively more abundant in the leases are known as potential fish pathogens or inhabit the fish gut. Among the protist community, potential bioindicators were found to be enriched close to fish farms. The taxa included those known to be bloom-forming, parasitic or toxic to fish. The results showed localized aquaculture perturbation in the pelagic microbial community. Microorganisms are likely influenced or introduced by inputs from the farms, such as feed and faeces. The use of both 16S and 18S rRNA gene amplicon sequencing of the pelagic microbial communities is a promising approach to detect changes caused by aquaculture activities.Overall, the thesis has presented the first attempt to characterise the horizontal and vertical picture of the microbial community distribution in a highly stratified embayment with minimal water exchange. This provides important knowledge of the ecology of pelagic microbial communities and the aquaculture effects on the microorganisms inhabiting the Macquarie Harbour. It is expected that this thesis could be used as a reference to raise new hypotheses and develop new methods in further microbial studies in the Harbour and in similar systems elsewhere.