Metabolomics is a rapidly emerging discipline within functional genomics to better understand biochemical phenotypes across a range of biological systems. The approach has many demonstrated applications in aquatic biology, but has not yet been applied to study early lifestages of marine molluscs. This Thesis evaluates metabolomics as an approach to characterise early lifestage phenotypes of molluscs, and demonstrates unique applications in aquaculture, developmental biology, immunology, and toxicology. GC/MS-based metabolomics was first tested for its capacity to classify good and bad quality mussel larvae (i.e., slow- vs fast-growing organisms). Based on the composition of metabolites, larval classes could clearly be discriminated and the data indicated differences energy metabolism, osmotic regulation, immune function and cell–cell communication.

Mussel larvae which had been subjected to handling stress and different culture conditions were also assessed. A decrease in succinate and an increase in alanine were observed after the water exchange, which indicated alterations in energy production and osmotic balance. However, these variations were subtle and it is unlikely that the water exchange practice had any lasting negative effects on larval physiology and performance. A culture condition classification model was also constructed which revealed that larvae from flowthrough vs static systems differed in terms of energy, protein and lipid metabolism. The data also suggests that growth performance is metabolically buffered through an adaptive physiological mechanism to provide similar developmental characteristics under these conditions.

Oyster larvae were assessed during a viral (OsHV-1 μVar) infection to characterise the host-virus interaction at a metabolic level. Responses included a coordinated disruption of the TCA cycle in accordance with mammalian macrophage stimulation via activation of immunoresponsive gene 1 and production of itaconic acid, induction of a Warburg-like effect, and production of free fatty acids for virion assembly, among others. These results provide new insights into the pathogenic mechanisms of OsHV-1 infection in oyster larvae, which may be applied for selective breeding programmes aiming to enhance viral resistance.

Lastly, metabolomics was applied to investigate mechanisms of toxicity in mussel larvae exposed to copper contamination. At sublethal dose levels, metabolic trajectory analysis indicated that larvae were successfully employing various endogenous mechanisms involving biosynthesis of antioxidants and a restructuring of energy-related metabolism in an attempt to alleviate the toxic effects on cells and developing tissues. This was partly confirmed by a targeted analysis of oxidative stress biomarkers (e.g., enzymes). A lethal copper dose induced severe metabolic dysregulation after 3 hrs exposure which worsened with time, substantially delayed embryonic development, initiated the apoptotic pathway, provided many evidences for the occurrence of oxidative stress (validated via oxidative stress biomarkers), and resulted in cell/organism death shortly after 18 hrs exposure.

In summary, this Thesis provides strong support for the application of metabolomics to assess the health status of marine mollusc embryos and larvae.