Characterisation of the Sydney Rock Oyster microbiota and its association with QX disease

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The Sydney rock oyster (SRO; 𝘚𝘢𝘤𝘤𝘰𝘴𝘵𝘳𝘦𝘢 𝘨𝘭𝘰𝘮𝘦𝘳𝘢𝘵𝘢) is native to Australia and is the most intensively farmed oyster species in the country. However, diseases such as Queensland unknown (QX) disease have caused substantial losses and impeded productivity. The aetiological agent of QX disease is the parasite 𝘔𝘢𝘳𝘵𝘦𝘪𝘭𝘪𝘢 𝘴𝘺𝘥𝘯𝘦𝘺𝘪 causing disease seasonally, generally in the late summer and early autumn. QX infection initiates at the palps and gills before migrating into the digestive gland where sporulation occurs causing blockage and eventual starvation and death in the oyster. Emerging evidence suggests that QX disease outbreaks are driven by a series of complex environmental and host factors such as salinity and oyster genetics. To mitigate the impacts of QX disease, the New South Wales Department of Primary Industries (NSW DPI) has led a selective breeding program using both mass selection methods and family-based breeding to create lines that are resistant. Some families have shown approximately 85% survival through one cycle of disease however, the mechanisms that drive this resistance are poorly understood. One potential factor influencing QX disease resistance is the microbiota which is investigated in this thesis. In other oyster species, the microbiota is emerging as a key factor in disease dynamics and studies have begun to unravel the environmental factors that influence its structure such as location, season, genetics and disease state. For the SRO, there is a paucity of studies examining the microbiota and the factors that influence the SRO microbiota composition. Therefore, this thesis aimed to explore the influence of geographic location, season (comparing summer and winter) and genetics (selectively bred SROs with a range of resistance to QX disease) on the SRO microbiota (Chapter 2). It also investigated microbiota dynamics prior to and during a QX disease event (Chapter 3) and, compared the SRO microbiota across families for identifying taxa that could be used as indicators for healthy and QX-infected oysters (Chapter 4). Overall, this thesis provides new knowledge of the SRO microbiota and the factors that influence the SRO microbiota assemblage and contributes valuable information on how the SRO microbiota shifts during a QX disease event and identifies putative key taxa that may be important for health and disease states and/or good indicator taxa of these states. A better understanding of the SRO microbiota, its potential involvement in health and disease may enable effective disease prevention in the future.
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