Biogeochemical Cycles in System Earth

6 EC

Semester 2, period 5

5264BCIS6Y

Owner Master Earth Sciences
Coordinator A. Carles Brangarí
Part of Master Earth Sciences, track Environmental Management, Master Earth Sciences, track Earth System Science, year 1

Course manual 2025/2026

Course content

The biogeochemical cycles of major elements like C, N and P in soil, water and atmosphere are key to the functioning of the ecosystems on our planet. Human pressure has resulted in large scale perturbation of such elemental cycles, which underlies several grand societal challenges humanity is facing. Examples are the current climate and nitrogen crises. In addition, the introduction of human-made compounds such as pharmaceuticals and PFAS into the environment has created novel biogeochemical cycles that form a grand challenge of their own.

This course focusses on the fluxes of elements and anthropogenic substances in Earth’s ecosystems within the context of urgent contemporary environmental challenges. For this, we will combine fundamental theoretical knowledge, mainly focused on insights gained through on-going research at UvA, with their direct application to help address these challenges. Specifically, we will focus on the following topics:

Topic 1: Soil carbon dynamics
Topic 2: Carbon cycling and climate change
Topic 3: Nitrogen cycle and crisis
Topic 4: Nature conservation
Topic 5: Contamination and emerging Pollutants
Topic 6: Microbial roles in the biogeochemical cycles

Study materials

Literature

  • Literature will be specified on the Canvas page of this course and will consist of scientific articles as well as other material presented during the lectures.

Objectives

  • Understand the biogeochemical processes controlling the cycle of major elements like Understand the biogeochemical cycling of C, N, P and pollutants in terrestrial ecosystems within the context of human perturbation thereof.
  • Apply your understanding of biogeochemical cycles in terrestrial ecosystems to develop a case study related to one of the environmental challenges linked to perturbation of biogeochemical cycles in a team.
  • Present the outcomes of your case study orally and in the form of a poster, and subsequently critically discuss them.
  • Discuss approaches to study biogeochemical cycles in terrestrial ecosystems and feedback reactions with peers and external experts

Teaching methods

  • Lecture
  • Presentation/symposium
  • Self-study
  • Working independently on e.g. a project or thesis
  • Supervision/feedback meeting

Theoretical knowledge will be conveyed via lectures given by scientists of the UvA Institute for Biodiversity and Ecosystem Dynamics (IBED) who work on the various topics covered. Combined with the scientific literature covered and exercises/practicals, this will provide students with a solid basis of the functioning of important biogeochemical cycles within the context of relevant societal challenges. 

The existing and newly gained knowledge gained will be applied by the students in an overarching case study on a relevant topic, under supervision of scientists of IBED and its sister institute HIMS. For this, students will work in small groups and schedule individual supervision/feedback meetings with the scientist guiding their case study. The deliverables for the case study are a written report and a poster presentation, where all groups of students present the outcomes of their case study analysis.

Learning activities

Activity

Hours

 

Hoorcollege

38

 

Presentatie

4

 

Tentamen

3

 

Werkcollege

2

 

Self study/working on case study

121

 

Total

168

(6 EC x 28 uur)

Attendance

  • Some course components require compulsory attendance. If compulsory attendance applies, this will be indicated in the Course Catalogue which can be consulted via the UvA-website. The rationale for and implementation of this compulsory attendance may vary per course and, if applicable, is included in the Course Manual.
  • Additional requirements for this course:

    Attendance during the practical components is mandatory. This includes the introductory lecture, as it is when the case studies are assigned, and the final symposium, where the poster presentations are held and graded. 

    Active participation in the groupwork related to the case study analysis is required. In cases where a student does not actively contribute to this groupwork, the coordinator reserves the right to give individual grades reflecting the (lack of) participation, and/or remove the student from the case study.

    Assessment

    Item and weight Details

    Final grade

    0.7 (70%)

    Tentamen

    0.2 (20%)

    Case study report

    0.1 (10%)

    Case study presentation

    The written exam tests the theoretical knowledge conveyed during the plenary lectures as well as contained in the mandatory literature that will be provided via Canvas.  The written exam takes place on April 23 (see calendar in DataNose).

    The case study report is prepared following the instructions provided on Canvas and assessed via the rubrics presented there. The assessment will be done by the scientists guiding the specific case study. The due date for the case study report is April 24 at 11:59 PM CET.

    The poster presentations also link to the case study. In the assessment, both the quality of the posters themselves and their presentation are both considered. Details on the assessment are provided via Canvas. The poster presentations are scheduled on April 20. The posters must be submitted via Canvas before April 19 at 12:00 (noon) CET.

    All individual assessments (written exam, case study report and poster presentation) can be retaken. The resit of the written exam is scheduled by July 2. This is also the deadline for a resit of the case study report. A resit of the poster presentation will be scheduled upon request.

    Please note that a failing grade for the case study report and/or failure for meeting the submission deadline for the case study report will result in an incomplete grade and the necessity for a resit. The maximum grade in the case of a resit of the report will be a 6.0 to prevent the student in question from profiting from the extra available time and additional feedback to complete the work.

    Inspection of assessed work

    The exam can be inspected upon request. This will be organized and communicated via Canvas. Feedback on the poster presentation as well as the case study report will be provided in writing. Additional feedback from the supervisor can be organized upon request.

    Assignments

    The written exam is an individual assignment and assessment.

    The case study analysis, report and poster preparation and presentation are performed in groups. In cases where a student does not actively contribute to this group work, the coordinator reserves the right to give individual grades reflecting the (lack of) participation, and/or remove the student from the case study.

    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

    Weeknummer Onderwerpen Studiestof
    1
    • Introductory lecture and assignment case studies
    • Lectures on Soil carbon dynamics and Climate change
    • First meeting case study supervisor (to be scheduled by the students themselves)
    • Working on case study
    • Lecture slides 
    • Scientific literature
    2
    • Lectures on Nitrogen cycling & crisis and Nature conservation
    • Working on case study
    • Lecture slides 
    • Scientific literature
    3
    • Lectures on Contamination & emerging pollutants, and Microbial roles in the biogeochemical cycling
    • Working on case study and poster
    • Lecture slides 
    • Scientific literature
    4
    • Poster presentations (April 20)
    • Written exam (April 23)
    • Group report (due April 24 at 11:59 PM CET)
    • Scientific literature

    Additional information

    For additional details and information, please consult the dedicated Canvas page for this course.

    Contact information

    Coordinator

    • A. Carles Brangarí

    Staff

    • A. Carles Brangarí
    • dr. P. Dalcin Martins
    • dr. B. Jansen
    • dr. A.M. Kooijman
    • dr. W.E. Morriën
    • dr. A. Praetorius