The New Zealand Green-lipped mussel (Perna canaliculus) is an important corner stone of aquaculture and a major component of the country’s coastal habitat systems. However, unexpected mortalities in farm and wild settings, especially during summer times (summer mortality) present a major ecological and economical challenge. The complex interactions between host, environment, and pathogens during these mortality events are poorly understood and require innovative diagnostic tools. Multi-omics applications are rapidly emerging as powerful tools to accurately and effectively assess the organism’s stress and health condition, among others. This approach allows multi-faceted insights into complex biological processes and can provide insights into disease processes as well as the identification of molecular biomarkers for early warning systems. This thesis was designed to provide, for the first time, an integrative and multi-omics approach of the metabolic, protein and microbiome responses of Perna canaliculus to a range of stressors, such thermal, pathogenic and nutritional stress.

The bioinformatic integration of metabolomic and proteomic data revealed strong evidence of alterations in energy and immune-related metabolic pathways in mussels suffering from heat induced mortality in a mussel farm. Our resulted revealed indication of oxidative stress in unhealthy mussels as a result of perturbations in glutathione metabolism and protein glutathione S-transferases. In addition, degradation in the cytoskeleton structure and regulation of cilia/flagellum gill tissues of unhealthy mussels may be a contributing factor to undesired changes in gill membrane fluidity, permeability, and lipid composition impairing function. The integrative metabolome and proteome profile data provides new insight into molecular interactions associated with incidences of summer mortality in this species.

The application of microbiomics/microbiome analysis initially involved a baseline characterisation of bacteria and fungi within key wild Perna canaliculus tissues (gills, haemolymph, digestive gland, and stomach) using high-throughput amplicon sequencing of 16S rRNA gene and ITS1 region for bacteria and fungi, respectively. The study revealed that different mussel tissue types displayed distinctive bacterial profiles, which were dominated by phyla which reflected a fluid exchange between the circulatory system and surrounding aqueous environment, as well as a highly diverse digestive system microbiota. Along with a distinct pattern in microbiome structure, multiple significant phylum , including Gammaproteobacteria, Campylobacterota, Firmicutes, Cyanobacteria, and Bactroidota were identified in Perna canaliculus tissues. Among these biomarkers, Gammaproteobacteria, Bacteroidota and Cyanobacteria were shown to change in relative abundance when mussels were subjected to short term starvation periods in the laboratory. Further microbiome analysis of farmed mussels suffering from heat induced summer mortality revealed alterations in Gammaproteobacteria, Bacteroidota and Campilobacterota in the gill tissue and hepatopancreas tissue. Numerous significant bacterial genus signature was also identified in this thesis. The most interesting genus, Endozoicomonas, was found to be the most dominate member of the Phylum Proteobacteria in tissue types, such as gill tissue and haemolymph. Its variation in abundance within mussels exposed to different experimental conditions, suggests that this group may be a good biomarker for mussel condition and fitness. Specifically, changes in the relative abundances of Endozoicomonas bacteria were detected in the gill tissues of unhealthy mussels suffering from summer mortality. Endozoicomonas relative abundance was also altered in response to seasonal changes, potentially linked to temperature and salinity parameters. Based on these results, it is suggested that future studies focus on Endozoicomonas as a potential host health biomarker n P. canaliculus.

In conclusion, this thesis has successfully demonstrated the application of multiple omic approaches for the study of Green-lipped mussels, which contributes novel information regarding the animal’s physiological and metabolic responses to stressors, such as temperature, pathogen and nutrition.