This advanced training course provides an integrated and multidisciplinary framework for environmental monitoring in sustainable aquaculture systems. It combines state-of-the-art chemical analytical techniques (LC-MS/MS, MP-AES, biotoxin analysis), standardized ecotoxicological bioassays, molecular biomarkers, and environmental risk assessment methodologies. 

The course bridges theoretical knowledge and practical laboratory implementation. Participants will gain direct experience with cutting-edge Research Infrastructure (RI) facilities and develop competencies to design, implement and interpret integrated monitoring programs tailored to aquaculture environments.

Learning outcomes

By the end of the course the learner will be able to:

• Explain the fundamental principles of light and optical microscopy.
• Describe the main microscopy techniques, including brightfield and fluorescence microscopy.
• Compare and evaluate the strengths and limitations of key imaging approaches (brightfield, fluorescence,confocal, lightsheet) for different marine samples.
• Prepare and mount a range of marine specimens for microscopy.
• Apply simple tricks and good practices to improve image quality.
• Design a microscopy experiment tailored to a research question in aquaculture or marine biology.
• Operate simple imaging systems and implement key practices for acquiring reproducible image data,independently of the specific microscope available.
• Retrieve and interpret meaningful quantitative data from microscopy images.
• Identify and apply modern open-source tools to address image analysis
   

Cognitive competences:

• Understanding limitations and artefacts in optical microscopy.
• Selecting appropriate workflows for different research applications.
• Integrating microscopy into experimental design in aquaculture and marine biology.
   

Technical skills:

• Operate brightfield, contrast-enhancing, and fluorescence microscopy systems.
• Apply sample preparation techniques suitable for marine specimens.
• Acquire and evaluate microscopy images, recognising the features of high-quality data regardless of themicroscope used.
• Use open-source software tools for basic image processing and analysis.

Course Contents

Part 1 (Online: 7 - 25 September 2026)

• M1: Priority Contaminants: metals, PAHs and pharmaceuticals
• M2: HABs, Phytoplankton and Marine Biotoxins
• M3: Emerging Contaminants and Nanoecotoxicology
• M4: Bioassays, Biomarkers and Analytical Platforms
• M5: Data Integration, Risk assessement and Regulation

Part 2 (Onsite: 6 - 9 October 2026, venue CCMAR, Faro, Portugal)

• M6: Field Sampling and Chemical Analysis (Ria Formosa field trip, sample preparation, MP-AES metals analysis
• M7: Plankton, HABs and Biotoxins (FLOWCAM imaging, microscopy, biotoxin LB-MS/MS)
• M8: Bioassays and Biomarkers (acute and sublethal tests, nano exposures, biomarker assays)
• M9: Integration and Final Project (data analysis, project presentation)

Application

Please fill in the Registration form no later than 2 August 2026 (23:59 CEST).

A limited number of seats for the onsite phase is available. Selection will be based on motivation and successful completion of the online phase.

This course is organized and sponsored by the AQUASERV Project. There is no tuition fee to attend the onsite phase. The organizers will offer coffee breaks/refreshments and (light) lunch during the onsite event.

All other costs must be borne by the participant and/or its parent institution (travel, accomodation, etc).

Target Audience

• PhD students and postdoctoral researchers
• Aquaculture industry professionals
• Research Infrastructure technical staff
• Transnational Access (TNA) users of the AQUASERV project: researchers preparing or participating in a TNA call who want to learn ecotoxicology fundamentals to apply these methods in their planned experiments.
   

Prerequisites

• Background in marine science, environmental science, biology, chemistry, or related fields
• Basic understanding of environmental monitoring principles
• Preference for researchers working on or planning to work in:
  • Marine pollution
  • Chemical oceanography
  • Aquaculture successful completion of the online Part I modules (theory and quizzes) is mandatory for participation in the onsite phase.

This course has been funded with support from the European Commission. The AQUASERV project has received funding from the European Union’s HORIZON Research and Innovation Actions under grant agreement N° 101131121.