Benthic Ecosystems

Course manual 2021/2022

Course content

Below each body of water—from deep oceans to mountain lakes—there are ecosystems consisting of benthic (bottom-dwelling) organisms that form complex food-web structures depending on their physical environment. Factors such as light, temperature, salinity, substrate-type and water-flow are important drivers for the structure of each of these dynamic systems. Interactions between organisms at different trophic levels are unraveled by an interdisciplinary approach of biology, geology and chemistry, biogeochemistry in short. Ultimately, the discipline “Benthic Ecology” aims to understand how these ecosystems function, impact their environment and even predict their dynamics in a changing world.

The course is organized in lectures, excursions and the writing of a research proposal. The lectures are divided into three parts:

Part I: Benthic Ecosystems and their physical environment

Which geological, biological and chemical factors control the structure and shape of benthic ecosystems? We will discuss a wide variety of benthic ecosystems from 12 km below sea-level (mid-ocean ridges and deep-sea coral reefs) to 6 km above sea-level (mountain lakes); from temperate (Wadden Sea and Oosterschelde intertidal flats) to tropical (coral reefs, including mangrove and seagrass ecosystems) and from fast flowing (rivers) to stagnant (lakes and ditches).

Part II: Functioning of Benthic Ecosystems

The main processes and material fluxes in sediments and water column will be described:

• Trophic interactions, i.e. how energy and nutrient sources are coupled between pelagic (free-swimming) and benthic (both sessile and motile) organisms.
• The role of benthic communities on organic matter degradation and element cycling between the water column and sediments/substrates of benthic ecosystems.

Part III: Benthic Ecosystems and human impact

Understanding how ecosystems function, enables you to assess how these ecosystems change by human impact, such as overfishing, mega-trawling, ocean acidification and eutrophication. We will analyze whether we can predict shifts in ecosystem structure and functioning as a consequence of these impacts. We will also discuss the application of ecosystem knowledge to construct artificial ecosystems. For example, to develop sustainable forms of multi-trophic aquaculture for food, energy and medicine production. In Part III of the course students will be actively involved in the discussion through interactive lectures.

Excursions:

During this course students will:

• Visit Burger’s Ocean and Mangrove at Burger’s Zoo in Arnhem on Friday 10 December 2021, where we will see and discuss several examples of benthic ecosystems, including a tropical coral reef and mangrove. This day also includes 2 lectures.
• Participate in the yearly AcroporaNet Symposium, in 2021 held at the University of Amsterdam (Roeterseiland) on Friday 17 December 2021. This symposium gives an overview of current and future scientific challenges for coral reef ecosystems to function under anthropogenic influence and presentations will relate to all learning goals of this course. Students will also get the chance to talk to international scientists that are at the forefront of aquatic ecology.

Writing a research proposal to obtain funding:

Applying for funding is a crucial part of a future career in science. Based on an actual funding application format (the KNAW Fund for Ecology), each student will write a proposal using an ecosystem approach, and therefore will apply knowledge derived from the course lectures and excursions. Groups of 5-6 students (supervised by 1 lecturer) will choose a main topic (for example: tropical coral reef; cyanobacteria; mid-ocean ridges/hydrothermal vents; bioremediation; seagrass and mangroves). Each student then collects, reads literature specific for their own topic within the ecosystem and presents (5 min colloquium) the topic in his/her work-group. A research question and a subsequent experimental approach will be formulated as an individual assignment. The end result will be a proposal of maximum 3 pages, which serves to apply for funding for your own specific project.

Study materials

Other

• All study materials will be placed on the Canvas site

Objectives

• Describe benthic ecosystems and their physical environment;
• Describe the functioning of benthic ecosystems based on the biogeochemistry of the ecosystem;
• Analyze the influence of human impact on benthic ecosystems, including artificial ecosystems, using an ecosystem approach.
• Apply the ecosystem approach by writing a research proposal, including a scientific hypothesis and experimental design, to obtain funding for a scientific research project.

Teaching methods

• Seminar
• Presentation/symposium
• Working independently on e.g. a project or thesis
• Supervision/feedback meeting
• Lectures (32 hours),
• Writing a research proposal (56 hours)
• Self-study (40 hours)
• Laptop seminar

This course is based on:

• Lectures (32 hours),
• Colloquium preparation and presentation (10 hours)
• Writing a research proposal (58 hours)
• Excursions (16 hours)
• Self-study (47 hours)
• Exam question hour (2 hours)
• Written exam (3 hours)

Learning activities

Attendance

Requirements of the programme concerning attendance (OER-B):

1. Attendance during practical components exercises is mandatory.

Additional requirements for this course:

Attendance at lectures is not mandatory, but highly recommended. Attendance during excursions is mandatory (from Teaching and Examination Regulations). 

Assessment

A student has passed the course when each partial examination is graded with a 5.0 or higher and when the weighted final grade is 5.5 of higher.

The students will receive a mark for their research proposals, which will be assessed on colloquium (10%), content and focus (30%), organization (15%), writing style (30%) and proposal format (15%). The assessment rubric will be provided through Blackboard. If requirements for research proposal are not met, student is obliged to improve his/her work until cut-off (minimal 5 and overall grade for course >= 5.5) is reached in consult with supervisor.

The written exam consists of 10 questions of which 50% of the grade will be based on knowledge assessment of ILO’s 1 and 2 (knowledge description) and 50% of the grade will be based on knowledge assessment of ILO 3 (knowledge analysis).

Resit is possible for written exam. For at least twenty working days after the announcement of the results of a written examination, the student can, on request, inspect his/her assessed work, the questions and assignments set, as well as the standards applied for marking. The place and time will be announced via Blackboard (from Teaching and Examination Regulations).

Inspection of assessed work

The manner of inspection will be communicated via the digitial learning environment.

Assignments

Research Proposal

• Each student writes his/her own research proposal, which includes presenting research question and approach in colloquium. Feedback on colloquium is given in small workgroups and by supervisor. Feedback on written proposal is given by supervisor (3 times 20 min time slots per student) 

Written Exam

• Written exams are assessed individually. In week 4, 2 hours of questions on upcoming exams are scheduled. 

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

Timetable

The schedule for this course is published on DataNose.

Additional information

This course is obligatory for students that participate in the fieldwork course Coral Reef Ecology within the Master track Freshwater and Marine Biology.

First-year students of the UvA Master’s Programme will be allowed to register for this course in September. The procedure will be announced in August-September. All other students: Registration for this course via https://www.sis.uva.nlat least 4 weeks before the start of the semester is mandatory.There is a maximum amount of students allowed of 30. Order of acceptance:

1. UvA Master-track Freshwater & Marine Biology.
2. Other UvA Master students with an aquatic biology profile.
3. All other students that can apply for this course.

Contact information

Coordinator

• dr. ir. J.M. de Goeij

Staff

• dr. H.G. van der Geest
• dr. F. Mienis
• dr. V. Schoepf
• dr. M.J.A. Vermeij
• dr. Arie Vonk
• dr. Petra Visser