Impact of ecological changes on Sydney rock oyster genetics and microbiomes

Within Australia, the Sydney rock oyster (SRO) is cultivated mainly in New South Wales and Southern Queensland. Their cultivation is now threatened by many biotic and abiotic stressors such as QX (Queensland Unknown), winter mortality, temperature and salinity variation due to rainfall. Changing environmental conditions influence the oyster's immune system along with the presence of pathogens and virulence. The microbiome also fluctuates with biotic and abiotic changes, but sometimes the relationship between host, environment and pathogens is not visible. Therefore, I have used SRO as a model to better understand their genetics and microbiomes in this thesis study. The aims of this research were to distinguish cultivated oysters from wild oysters and their inbreeding potential using molecular markers; to assess the transfer of microbiome communities in cultivated and wild oysters and their microbial composition differences; and to determine the level of salinity stressing the growth and survival rates of SRO. Two molecular markers, exon-primed intron-crossing (EPIC) primer pair markers, were developed and used to distinguish cultivated from wild oysters and to measure their inbreeding potential. By using the genome of Saccostrea glomerata as a reference, I therefore designed and examined 3 EPIC primer pairs for SRO. Another experiment was performed on oyster rearing in aquariums to assess if microbiome communities in cultivated and wild oysters can transfer from oyster to oyster and to determine the microbial composition differences in oysters during 3 experimental periods: microbiota of cultured SRO, microbiota of wild SRO, and microbiota of SRO in a mixed period of rearing. Two bioassay experiments were carried out to determine the level of salinity stressing the growth and survival rates of SRO