Biological Oceanography

Course manual 2025/2026

Course content

Biological Oceanography: a systems approach

Oceans cover 70% of the surface of the Earth and their vast total volume makes it the largest continuous habitat. Half of the oxygen production on Earth occurs in the oceans. The oceans have a critical function for the supply of food and raw materials, and marine ecosystems are crucial in the regulation of Earth’s climate and biogeochemical cycles. Our understanding of the ocean and the life it supports is, however, far from complete. Biological oceanography improves our understanding of the principles underlying marine ecosystem organization, and the processes that govern spatial and temporal distribution, dynamics, biodiversity and evolution of auto-, hetero- and mixo-trophic organisms as well as trophic interactions. Only an interdisciplinary and (eco)system-wide approach will enable us to unravel the mysteries and the unknowns of the ocean. Physical, chemical and geological processes in the oceans are fundamental to biological oceanography and vice versa, therefore a few of the initial lectures in this course will be dedicated to the different disciplines. This course will give an in-depth insight in the current knowledge of life in the ocean from viruses to whales and from production to burial. The knowledge will be largely framed within the complex suite of processes that are involved in the transformation and transfer of fixed organic carbon (particulate and dissolved) from the surface to the deep ocean (collectively referred to as the ‘biological pump’). The factors involved in the functioning of the biological pump are linked and diverse for different systems but influence virtually the entire ocean ecosystem.

Study materials

Literature

• Lecture notes (e.g. powerpoint slides)

• (not obligatory) the book: Oceanography and Marine Biology. An Introduction to Marine Science. (D.W. Townsend. Sinauer Associates, ISBN 9780878936021) may serve as introduction to the course.

• Selection of scientific papers (will be provided during the course)- available on Canvas

Practical training material

• Handouts will be provided during practicals, and are available on Canvas

Software

• Ocean Data View (freeware)

Objectives

• Identify main biological oceanographic processes (4) and describe their interdependence
• Specify and differentiate between biological processes involved in the biological pump
• Survey relevant literature about a given research topic within biological oceanography and summarize as a research proposal abstract
• Develop and formulate a follow-up research question / objective on a given topic within biological oceanography and describe how the research should be conducted
• Present a lecture aimed at explaining a research topic to a scientific audience and proposing a continuation research project
• Explain the importance of the biology of the ocean for global change developments
• Critically discuss, oppose and defend scientific issues within the field of biological oceanography

Teaching methods

• Lecture
• Seminar
• Computer lab session/practical training
• Presentation/symposium
• Self-study
• Supervision/feedback meeting
• Fieldwork/excursion
• Working independently on e.g. a project or thesis

The course consists of lectures, discussion forums (flipped classrooms), (computer and lab) practicals, and a student-led symposium. For the latter, students can choose a topic from a list provided at the start of the course (including scientific papers as a starting point) which they will read and summarise (research proposal abstract) including the formulation of a follow-up research question for a new research project within the field. Students will be coached by teachers in this course to help students identify a knowledge gap and suggest new research ideas and communicate these effectively to peers. Students are expected to actively participate in discussions and provide constructive comments on each other's topics.    

Learning activities

Attendance

Additional requirements for this course:

Laboratory and computer practicals are mandatory. 

Assessment

Assignments

"Research proposal abstract"

Students will work in pairs, read and discuss literature about a topic in Biological Oceanography, and will hand in the written assignment per pair. Students will get feedback during at least one coaching session. Assignment is graded (20% of final mark).

"Presentation"

Students will give an oral presentation in pairs; this presentation will provide background information about a research topic in oceanography (10 min) and present a new research proposal (10 min) followed by discussion with peers. Assignment is graded (20% of final mark) per student individually.

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Contact information

Coordinator

• dr. K.T.C.A. Peijnenburg

Coordinator: Dr. Katja Peijnenburg

Prof. Dr. Jef Huisman, Prof. Dr. Corina Brussaard, Prof. Dr. Geert-Jan Brummer, Prof. Dr. André de Roos, Dr. Susanne Wilken, Dr. Fleur Visser, Dr. Cara Nissen