NPLK14021U Soil and Water Pollution - Concepts and Theory

Volume 2019/2020

MSc Programme in Environmental Science
MSc Programme in Nature Management


Review of the biogeochemistry of soils and natural waters critical for pollutant fate and effects. Environmental microbiology: microbial community theory, terrestrial and aquatic microbial lifestyles emphasizing microbial degrader populations. Reviews of concepts used for characterization of abiotic and microbial status of soils and natural waters.

Overview of priority pollutants including heavy metals, radionuclides, pesticides, pharmaceuticals, hormones,  natural toxins, solvents, detergents, antibiotic-resistant genes, and microbial pathogens in soil and aqueous environments, with emphasis on their sources, physical-chemical, and microbiological properties. The main part of the course focus on application of chemical and microbial principles to study and quantify pollutant mobility, bioavailability and fate. This includes solubility, speciation of metal ions, and pollutant binding and partitioning to soil and sediments (mineral surfaces, humic matter), and living media (bioconcentration, biomagnification). Pollutant degradation and transformation is treated both seen from a chemical and microbial perspective. Chemical degradation includes hydrolysis, photochemical degradation, and oxidation/reduction processes. As we are working with soils and sediments, the role of particle surfaces for pollutant transformations is important and given a clear focus. For microbial degradation of organic pollutants we look at microbial/enzymatic degradation and mineralization pathways, metabolite formation, and transformation kinetics. Biodegradation and toxicity, microbe-metal interactions, metal toxicity and resistance as well as xenogenetic pollutants and antibiotic resistance will be introduced. 

Introduction of small computer models for QSAR estimation of organic pollutant properties (EpiWin), and for computing speciation and binding (MINTEQ) (requires windows platform). Theory is exemplified with cases and supported by real-life examples.

The course includes a short introduction to soil and water remediation (cleaning), usually with an excursion for demonstration of examples of cleanup. 

Outlook: Emerging pollutants, genes and microorganisms

Learning Outcome

The objectives of the course are to comprehend and to study how: i) soils and natural waters are affected by pollution, ii) soils function as “filters” for natural attenuation of pollutants, iii) pollutants bind and transform, and iv) how we quantify the chemical and microbial processes.

After completion you should be able to:


  • Classify and provide overview of main pollutants in terrestrial ecosystems, and to present knowledge on the relationships between land use, soil and water quality
  • Describe how microbes interact with soils and how this affect pollutant degradation
  • Describe key properties and processes of pollutants critical for sorption, abiotic and microbial degradation, bioavailability and biomagnification in terrestrial systems
  • Classify and summarize the molecular mechanisms controlling pollutant degradation, transformation and bonding in soils and water
  • Acquire knowledge on the methods available for predicting the fate of chemical substances in soil and aquatic environments
  • Describe analytical procedures and monitoring strategies for pollutants in terrestrial systems



  • Retrieve and critical examine environmental chemical data
  • Apply and demonstrate the use of general principles from chemistry and microbiology for quantification and evaluation of pollutant fate and balances
  • Estimate chemical and physical properties of pollutants and pollutant fate in terrestrial ecosystems
  • Suggest methods and approaches used for assessing microbe-pollutant interactions
  • Critically report on pollutant fate and remediation in terrestrial and aquatic environments



  • Combine data and information from different sources in calculus, prediction and evaluation of pollutant mass balances, fate and effects in soils and aquatic systems
  • Judge the relative importance of various sorption and transformation processes on the overall distribution and fate of chemical substances in soil and aquatic environments
  • Diagnose the processes critical for the fate of any pollutant, and critical select tools for analysis and evaluation
  • Discuss and assess the complexity of how land use affect soil and water quality
  • Collaborate with fellow students on problem solving and reporting critical pollutant assessments
  • Point to new directions and aspects of emerging pollutants

The full curriculum can be found at Absalon. Examples of literature used for course: 

Hansen, H.C.B. (ed)(2015) Soil Pollution: Biogeochemistry and Modelling - including theoretical exercises. Lecture notes. 

Schwarzenbach, R.P. et al. (2005) Environmental Organic Chemistry, 2nd Ed., Wiley, different chapters (A new 3rd edition will appear end of 2016 and we will probably use that)

Maier, R.M. et al. (2014) Environmental Microbiology, 3rd Ed., Ch. 1-3 (brush-up reading), 4, 6, 15-20 and 31. Also to be used (other chapters) on follow-up course in Block 2.

Handout notes and journal papers.

Software for speciation analysis (Visual MINTEQ)

Software for QSAR estimation of pollutant properties (EpiWin)

Excursion material

The course builds on basic chemical principles corresponding to the level of 1st year university chemistry. Physical chemistry is applied for solving problems in environmental chemistry and hence basic understanding of thermodynamics and kinetics is an advantage. Similarly, the course builds on basic principles in biology and microbiology. The course assumes a basic understanding of structure, composition and properties of soils and natural waters. We recommend the following background:
- Basic university course in general chemistry
- Course on soil or geochemistry, e.g. "Soil, Water and Plants"
- Basic university course in Microbiology
For students who are weak within one or more of the basic disciplines we offer short brush-up lectures incl. reading/training: thus usually happens during last week of August

Academic qualifications equivalent to a BSc degree is recommended.
Lectures, theoretical exercises incl. use of computer computations, and small project work. One half-day excursion comprising examples of soil and water pollution, remediation, and monitoring. Lectures to provide overview and highlight main topics. Emphasis on computational exercises to train the chemical and microbial principles and models taught. Computer exercises comprise QSAR computation of pollutant properties, and equilibrium speciation. Project work focus on training the tools studied and application of these to particular soil and water contaminants. The projects draw on the general insight in chemical, and microbial processes presented in the course. Each project is solved by groups (3 – 5) of students and it is presented as a written report. Each group of students also present a colloquium based on a paradigm setting paper.
This the course for those students who:
- are interested in applying chemistry and microbiology to pollutant fate in soils, sediments and natural waters
- need an overview of contaminants in soils and water, their souces and the threats
- seeks understanding of contaminant chemical and microbial reactions and impacts in terrestrial systems
- would like hands on and experience with computational approaches
- seeks to learn state-of-the art tools that can quantify pollutant formulation, bonding, and degradation, and who would like to use this insight for remediation
- like to work in a class of international students
  • Category
  • Hours
  • Colloquia
  • 20
  • Exam
  • 4
  • Excursions
  • 4
  • Lectures
  • 28
  • Preparation
  • 78
  • Project work
  • 25
  • Theory exercises
  • 47
  • Total
  • 206
Continuous feedback during the course of the semester
7,5 ECTS
Type of assessment
Written examination, 4 h under invigilation
Written assignment
Exam comprise student-driven colloquium (20 %), project report (20 %) and a written exam (60 %). The colloquium and the project report is usually produced as part of a group of students.
Exam registration requirements

Participated in a student-driven colloquium and  hand-in of project report.

All aids allowed
Marking scale
7-point grading scale
Censorship form
No external censorship
One internal examinator

If 10 or fewer registered for the reexamination the examination form will be oral.

An individual assingment is handed in 2 weeks before re-exam if the requirements are not met.

Criteria for exam assesment

See learning outcome