Zooplankton plays a crucial role in coastal water ecosystems by linking energy transfer from primary producers to higher trophic level organisms and facilitating the biogeochemical cycle through their metabolism and vertical migration. However, our understanding of the zooplankton physiological response to nutrient variability in their living environment, particularly at the gene expression level, remains limited. This knowledge gap hinders our understanding of their physiological processes, which are essential for the biogeochemical cycle. To investigate the impact of coastal environmental nutrient heterogeneity on zooplankton community physiology, we conducted zooplankton samplings during the summer season in the western, southern, and eastern Coastal Hong Kong Waters. Meta transcriptomics analysis was employed to unravel the community composition and gene expression profiles of the sampled zooplankton. Our study revealed distinct patterns of differential gene expression associated with nitrogen and amino acid metabolism functions within the sampled zooplankton communities across the different sampling regions. Furthermore, we found several KEGG pathway members of gene modules which are classified as metabolism functions that highly correlated with nutrient concentrations. Importantly, these gene expression patterns corresponded to the observed heterogeneity in dissolved inorganic nitrogen and phosphorous concentration within coastal waters environment. To further validate our findings, we conducted reanalysis on the zooplankton model organism, Daphnia magna, transcriptome data under laboratory nitrogen and phosphorous imbalanced treatment which the result supported the gene ontology functions identified in the zooplankton community meta transcriptome. Our results contribute to a better understanding of zooplankton's physiological processes, especially highlighting the importance of incorporating gene expression analysis in studying zooplankton's role in the biogeochemical cycle.
