Shellfish aquaculture has become an increasingly vital component of global food production, providing a sustainable and nutritious source of protein. As the demand for seafood continues to rise, the shellfish farming industry has experienced significant technological advancements and innovations in recent years. This Special Issue of Aquaculture Research aims to highlight the latest developments in shellfish aquaculture, with a particular focus on improvements in farming practices and advancements in disease diagnostics.

The shellfish aquaculture industry faces a variety of challenges, including environmental pressures, disease outbreaks, and the need for more efficient and sustainable production methods. Environmental factors, such as water quality, temperature fluctuations, and the impacts of climate change, can significantly affect the health and productivity of shellfish farms. Additionally, the prevalence of diseases, such as viral, bacterial, and parasitic infections, can lead to substantial economic losses and threaten the long-term sustainability of the industry. Addressing these challenges requires innovative approaches to farming practices, as well as the development of advanced diagnostic tools to detect and manage disease outbreaks effectively.

This Special Issue of Aquaculture Research displays innovative advancements addressing current challenges in shellfish aquaculture. Featured articles cover novel farming techniques like integrated multi-trophic and recirculating aquaculture systems; advanced molecular tools including next-generation sequencing, metagenomics, and single-cell diagnostics for disease detection and pathogen characterization; innovative biosecurity measures; and exploitation of host-pathogen interactions and immune responses for improved health management. The issue explores DNA methylation studies, environmental impacts on shellfish diseases, and development of biosensors and lab-on-a-chip platforms for in-situ diagnostics. It covers the utilization of digital PCR for pathogen quantification and the validation of advanced molecular diagnostic tools. By highlighting these innovations, the Special Issue aims to provide a comprehensive overview of latest developments, inspiring further research to enhance the sustainability and growth of this vital industry.

Potential topics include but are not limited to the following:

• Novel husbandry methods for enhanced shellfish growth, health, and productivity
• Novel farming techniques, such as integrated multi-trophic aquaculture and recirculating aquaculture systems, and their impact on shellfish immunity and growth
• Comparative immunology in shellfish species: implications for disease resistance and selective breeding
• Nutritional interventions and their effects on shellfish immune responses and growth performance
• Application of next-generation sequencing and metagenomics for pathogen discovery and microbiome analysis in shellfish
• Development of multiplexed PCR, isothermal amplification assays, and single-cell diagnostics for rapid and sensitive shellfish disease diagnosis
• Utilization of digital PCR and droplet digital PCR for quantification of shellfish pathogens and immune markers
• DNA methylation studies to understand epigenetic factors in shellfish health, disease resistance, and immune function
• Exploitation of host-pathogen interactions, immune responses, and 'omics' profiles as disease biomarkers and indicators of shellfish health
• Innovative biosensors and lab-on-a-chip platforms for in-situ molecular diagnostics and immune function assessment in shellfish
• Validation and field implementation of advanced molecular diagnostic tools for shellfish health management
• The application of innovative biosecurity measures to prevent and control disease outbreaks
• Environmental impacts on shellfish diseases, immune responses, and adaptation strategies