Blue Biotechnology

Learning Outcomes

The course introduces students to the scientific foundations, engineering approaches, and biotechnological applications of marine and aquatic biological systems in the context of synthetic biology. It focuses on the discovery of genes, enzymes, pathways, natural products, biomaterials, and stress-adapted organisms from aquatic environments, and on their use in research, innovation, and sustainable biotechnology. The course also addresses computational analysis, bioprocessing, environmental applications, and ethical and regulatory dimensions.

Knowledge

• Explain the scope, principles, and main application areas of blue biotechnology and its relationship to synthetic biology
• Describe marine and aquatic biodiversity as a source of genes, enzymes, pathways, natural products, and biomaterials of biotechnological interest
• Explain the role of genomics, metagenomics, transcriptomics, and bioinformatics in the discovery of functional components from aquatic systems
• Discuss synthetic biology approaches used in blue biotechnology, including chassis selection, heterologous expression, genome editing, metabolic engineering, biosensors, and the Design-Build-Test-Learn framework
• Describe key areas of application such as marine natural products, industrial enzymes, algal and cyanobacterial biotechnology, marine biomaterials, environmental biotechnology, and bioprocess engineering
• Explain the main ethical, legal, biosafety, and biodiversity-governance issues relevant to marine genetic resources and engineered aquatic systems

Skills

• Analyse marine and aquatic biological systems in terms of their potential for synthetic biology and biotechnology applications
• Interpret sequence, metagenomic, and bioinformatic data in order to identify genes, pathways, and functions relevant to blue biotechnology
• Evaluate and compare engineering strategies for the production of marine-derived compounds, enzymes, and biomaterials in native or heterologous hosts
• Assess major translational challenges related to cultivation, scale-up, downstream processing, techno-economic feasibility, and sustainability
• Use browser-based bioinformatics platforms and public databases to analyse marine biological data and reconstruct biologically relevant pathways or functions
• Formulate and defend a structured research proposal related to a blue biotechnology application in synthetic biology

Competences

• Integrate biological, engineering, environmental, and regulatory perspectives in the analysis of blue biotechnology systems
• Make informed and responsible judgments regarding the innovation potential, feasibility, and broader impact of synthetic biology approaches in aquatic biotechnology
• Work effectively in interdisciplinary teams for the preparation and defense of research proposals
• Critically evaluate scientific literature and use it to support research design and technological choices
• Communicate scientific ideas, research strategies, and technical arguments clearly to specialist and non-specialist audiences

Module Syllabus

The course examines marine and aquatic biological systems as sources of innovation for synthetic biology and biotechnology.

It introduces students to the biological diversity, molecular resources, engineering strategies, and application areas that define blue biotechnology, with emphasis on how aquatic biological functions can be discovered, analysed, redesigned, and translated into useful technologies. The course is organized into the following modules:

Module 1: Foundations of blue biotechnology

This module introduces the concept, scope, and scientific importance of blue biotechnology. It examines marine and aquatic organisms as sources of genes, enzymes, metabolites, biomaterials, and biological functions of biotechnological value, and explains how blue biotechnology relates to synthetic biology, sustainability, and the blue bioeconomy.

Module 2: Marine and aquatic biodiversity, omics, and bioinformatics

This module focuses on biodiversity as a source of innovation in blue biotechnology. It covers marine and freshwater microorganisms, algae, fungi, invertebrates, microbiomes, and extremophiles, together with the use of genomics, metagenomics, metatranscriptomics, environmental DNA, and bioinformatics for the discovery and analysis of genes, pathways, and functional traits of interest.

Module 3: Synthetic biology approaches in aquatic systems

This module examines how synthetic biology can be applied to aquatic biological systems in order to move from discovery to engineering. It includes the Design-Build-Test-Learn framework, chassis selection, heterologous expression, genome editing, metabolic engineering, pathway optimization, and the use of biosensors and synthetic regulatory systems in blue biotechnology.

Module 4: Marine natural products, enzymes, and functional biomolecules

This module explores the diversity and applications of marine-derived molecules with pharmaceutical, industrial, and biotechnological value. It addresses marine natural products, biosynthetic pathways, biosynthetic gene clusters, industrial enzymes, extremophile-derived biocatalysts, and the role of synthetic biology and protein engineering in improving their production and use.

Module 5: Algal, Cyanobacterial, and aquaculture biotechnology

This module examines microalgae, macroalgae, and cyanobacteria as both biological resources and engineerable production systems. It also covers applications of blue biotechnology in aquaculture and aquatic animal health, including microbiome-based approaches, diagnostics, biosensors, sustainable feed systems, and the use of photosynthetic organisms in production and environmental applications.

Module 6: Marine biomaterials, environmental applications, and sustainability

This module focuses on marine-derived polymers, biomaterials, and environmentally oriented biotechnological applications. It includes alginate, agar, carrageenan, chitosan, collagen-like materials, as well as biosensing, bioremediation, wastewater treatment, resource recovery, and the role of blue biotechnology in sustainability and circular bioeconomy strategies.

Module 7: Bioprocess engineering and scale-Up

This module addresses the translation of biological discovery into practical biotechnology. It covers cultivation of marine microorganisms and algae, reactor design, upstream and downstream processing, product recovery, process optimization, scale-up challenges, and techno-economic considerations relevant to blue biotechnology applications.

Module 8: Ethics, regulation, and responsible innovation

This module examines the ethical, legal, and regulatory issues associated with the use of marine and aquatic biological resources. It includes biodiversity governance, access and benefit-sharing, biosafety, intellectual property, environmental responsibility, and the principles of responsible innovation in the development of blue biotechnology and synthetic biology applications.

The course includes a cumulative group assignment in which students prepare an original research proposal related to a synthetic biology application in blue biotechnology, present and defend it orally, and participate in a structured peer-review process.

Laboratory / Seminar Components

The course includes seminar-based hands-on computational and data-analysis activities designed to support the theoretical modules and provide students with practical experience in the use of public databases, browser-based bioinformatics tools, and biological data interpretation approaches relevant to blue biotechnology and synthetic biology

Marine metagenomic dataset analysis (e.g. MG-RAST, MGnify/EBI Metagenomics): Guided exploration of public marine metagenomic datasets to identify microbial diversity and functional traits relevant to blue biotechnology.

Biosynthetic gene cluster annotation (e.g. antiSMASH): Genome mining exercise using marine microbial genomes to identify and interpret putative natural product biosynthetic pathways.

Sequence annotation and similarity search Analysis of selected marine genes and/or proteins to infer function and biological relevance.

Pathway reconstruction and metabolic mapping exercise (e.g. KEGG, BioCyc): Guided reconstruction of a marine-relevant metabolic pathway to identify engineering targets and biotechnological applications.

Protein structure and function exploration exercise (e.g. UniProt, InterPro, AlphaFold Protein Structure Database): Analysis of marine proteins or enzymes to examine structural features, conserved domains, and possible functional properties relevant to blue biotechnology and synthetic biology.

Suggested Bibliography

• Müller, W. E. G., Schröder, H. C., & Wang, X.. (2017). Blue biotechnology: From gene to bioactive product. Springer
• La Barre, S., & Bates, S. S.. (2018). Blue biotechnology: Production and use of marine molecules. Wiley