Soil biology and biogeochemical cycles
A large part of the global elemental cycles takes place in the soil. Here, energy, carbon and nutrients circulate between plants, dead organic matter, minerals, water and air. These fluxes are mediated by soil organisms, such as bacteria, fungi, animals and plant roots. These organisms and their activities are of crucial importance in agriculture and forestry, as well as for water quality and biodiversity. Ultimately, biological processes in soils have a major feed-back on the global climate. In this course we will learn about global biogeochemical cycles, and about soil organisms and their roles in these processes. We will not only provide theoretical concepts via course literature and lectures, but will provide hands-on experience in laboratory exercises, field excursions, interactive discussions and in projects on self-chosen topics. Furthermore, we will use our obtained knowledge to discuss how human practises may affect potential feedbacks between soils and biogeochemical cycles with an emphasis on land use, environmental problems and global change.
Information from the course leader
2020-12-01
Preliminary course schedule now online
Hi all, Welcome to our course 'Soil biology and biogeochemical cycles'. We have now uploaded the preliminary schedule. As you can see most of the course will be online but we have planned some activities on campus. It is still very unsure if and how we can proceed with these activities due to the ever changing corona situation. Please understand and be prepared that there may be some drastic last minute changes to this schedule (including obligatory moments). Best wishes, Karina Clemmensen and Eva Krab, course-leaders.
2020-12-14
The schedule has now been updated!
The the first practical on gas fluxes has been moved from Monday the 25th of January to Wednesday morning the 27th of January.
2021-01-04
The schedule has been updated again!
Due to the stricter recommendations of Folkshälsomyndigheten around the corona situation in Sweden, we have limited the number of physical meetings at SLU during our course replacing some of them by digital meetings. Please check the updated schedule to see what has changed. Please note that last moment changes may still occur.
Within the coming days students that have registred for the course in Ladok, will receive an invitation to the course Canvas site via email (to the address you used to register in Ladok). We will provide you with all course information and (zoom) links to the online meetings via this Canvas site. If you have not received this invitation some days before the start of the course please contact eveline.krab@slu.se
2021-01-15
Schedule updated and zoom links to lectures in Canvas
Coming Monday, our course will start at 10.30 in Zoom. Those who are listed in Ladok to join the course will by now have received an invitation to Canvas to their slu email (or alernatively have been contacted by us). On Canvas you can find the Zoom links to the lectures. If you are following the course, but have no access to Canvas yet please contact eveline.krab@slu.se
Please also check the updated schedule
2021-01-28
The course schedule is now updated
You will find the updated schedule by clicking the 'schedule' button.
Course evaluation
The course evaluation is now closed
BI1322-30243 - Course evaluation report
Once the evaluation is closed, the course coordinator and student representative have 1 month to draft their comments. The comments will be published in the evaluation report.
Additional course evaluations for BI1322
Academic year 2024/2025
Soil biology and biogeochemical cycles (BI1322-30239)
2025-01-20 - 2025-03-24
Academic year 2023/2024
Soil biology and biogeochemical cycles (BI1322-30391)
2024-01-15 - 2024-03-19
Academic year 2022/2023
Soil biology and biogeochemical cycles (BI1322-30072)
2023-01-16 - 2023-03-21
Academic year 2021/2022
Soil biology and biogeochemical cycles (BI1322-30159)
2022-01-17 - 2022-03-23
Academic year 2019/2020
Soil biology and biogeochemical cycles (BI1322-30124)
2020-01-20 - 2020-03-24
Academic year 2018/2019
Soil biology and biogeochemical cycles (BI1322-30106)
2019-01-21 - 2019-03-25
Syllabus and other information
Syllabus
BI1322 Soil biology and biogeochemical cycles, 15.0 Credits
Markens biologi och biogeokemiska kretsloppSubjects
Soil Science BiologyEducation cycle
Master’s levelModules
| Title | Credits | Code |
|---|---|---|
| Lectures, literature and seminars | 7.5 | 0102 |
| Laboratory exercises | 3.0 | 0103 |
| Project | 4.5 | 0104 |
Advanced study in the main field
Second cycle, has only first-cycle course/s as entry requirementsMaster’s level (A1N)
Grading scale
The grade requirements within the course grading system are set out in specific criteria. These criteria must be available by the course start at the latest.
Language
EnglishPrior knowledge
Knowledge equivalent to:• 150 ECTS first-cycle courses, including
• 60 ECTS in a scientific subject such as Biology, Agricultural Science, Soil Science, Earth Sciences, Environmental Science or Technology,
• 15 ECTS Chemistry,
• 15 ECTS Soil Science, Earth Sciences or Biology
and
• a level of English equivalent to upper-seconday-school English (Engelska 6).
Objectives
The overall aim of this course is to acquire an advanced understanding of soil biology and biogeochemical cycles, to enable active discussion on the role of soil biota in ecosystems and production systems, and their interplay with global environmental change.
On completion of the course, the student will be able to:
• describe major groups of soil organisms, their interactions and responses to environmental conditions,
• describe biogeochemical processes and their interplay with organisms across scales,
• apply different methods for qualitative and quantitative analyses of soil organisms, biochemistry and major elemental cycles,
• analyze, evaluate and communicate soil biological and biogeochemical data,
• discuss impacts of human practices and potential feedbacks between soils and biogeochemical cycles, with emphasis on land use and global change.
Content
The below topics will be covered by course literature, lectures, assignments, literature discussions, field excursions, laboratory practical and project work.
• global biogeochemical cycles: carbon, nitrogen, sulfur and phosphorus cycling and underlying processes,
• methods for assessment of biogeochemical cycling: isotopes, organic matter quality and elemental fluxes,
• soil organisms and their involvement in processes: metabolism, decomposition, nutrient cycling, weathering and soil structuring,
• ecology: theory, strategies, community dynamics, interactions, and trophic cascading,
• the carbon cycle: organic matter quality, turnover and stability,
• the nitrogen cycle: transformations and soil fertility,
• basic laboratory techniques in soil biology and biogeochemistry,
• human impacts: forestry, agriculture, sustainable intensification, organic farming, ecotoxicology, global change, ecosystem services and conservation,
• the scientific process: experimental design, data analyses, peer review and presentation.
Grading form
The grade requirements within the course grading system are set out in specific criteria. These criteria must be available by the course start at the latest.Formats and requirements for examination
Participation is obligatory for all course elements except lectures. The following is required for a pass mark on the course:
• passed written final examination of theoretical course content based on lectures and literature,
• approved participation in laboratory exercises, literature discussions, and excursions,
• approved participation in project work including oral and written presentation.
- If a student has failed an examination, the examiner has the right to issue supplementary assignments. This applies if it is possible and there are grounds to do so.
- The examiner can provide an adapted assessment to students entitled to study support for students with disabilities following a decision by the university. Examiners may also issue an adapted examination or provide an alternative way for the students to take the exam.
- If this syllabus is withdrawn, SLU may introduce transitional provisions for examining students admitted based on this syllabus and who have not yet passed the course.
- For the examination of a degree project (independent project), the examiner may also allow the student to add supplemental information after the deadline for submission. Read more in the Education Planning and Administration Handbook.
Other information
The right to participate in teaching and/or supervision only applies for the course instance the student was admitted to and registered on.
If there are special reasons, students are entitled to participate in components with compulsory attendance when the course is given again. Read more in the Education Planning and Administration Handbook.
Responsible department
Department of Soil and Environment
Cooperating departments:
Further information
Grading criteria
Learning outcome 1
3: Describe major groups of soil organisms, their interactions and responses to environmental conditions
4: Explain how particular changes in environmental conditions may affect soil organisms and their interactions
5: Demonstrate capacity to critically challenge the course content, to compare contrasting views and to actively integrate course content with earlier personal experience
Learning outcome 2
3: Describe biogeochemical processes and their interplay with organisms across scales
4: Explain how particular changes in organism activities may affect biogeochemical processes across scales
5: Demonstrate capacity to critically challenge the course content, to compare contrasting views and to actively integrate course content with earlier personal experience
Learning outcome 3
3: Apply different methods for qualitative and quantitative analyses of soil organisms, biochemistry and major elemental cycles
4: Compare and discuss outcomes of different qualitative and quantitative analyses of soil organisms, biochemistry and major elemental cycles and how they relate to each other
Learning outcome 4
3: Analyze, evaluate and communicate soil biological and biogeochemical data
4: Demonstrate the ability to communicate and summarize various soil biological and biogeochemical data in a coherent manner.
Learning outcome 5
3: Discuss impacts of human practices and potential feedbacks between soils and biogeochemical cycles, with emphasis on land use and global change
4: Synthesize relevant hypotheses based on current societal/environmental issues concerning soil biology and biogeochemical cycles
5: Argue which new approaches could be used to solve societal/environmental issues concerning soil biology and biogeochemical cycles, and identify current knowledge gaps
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Teaching activities related to each intended learning outcome
- 7.5 ECTS - Approved written final examination of theoretical course content based on lectures and literature (ILO 1,2,5)
- 3.0 ECTS - Approved participation in laboratory exercises, literature discussions, and excursions (ILO 3, 4)
- 4.5 ECTS - Approved participation in project work including oral and written presentation (ILO 4, 5)
Participation is obligatory for all course elements indicated with a * in the schedule
Litterature list
- Chapter 9 - The Metabolic Physiology of Soil Microorganisms Författare: Alain F. Plante, Maddie M. Stone and William B. McGill ISBN: 978-0-12-415955-6 [Chapter 9 - The Metabolic Physiology of Soil Microorganisms] (https://www.sciencedirect.com/book/9780124159556/soil-microbiology-ecology-and-biochemistry) Kommentar: In: Soil Biology, Ecology and Biochemistry, 4th Edition
- Chapter 10 - The Ecology of the Soil Biota and their Function Författare: Sherri J. Morris and Christopher B. Blackwood ISBN: 978-0-12-415955-6 [Chapter 10 - The Ecology of the Soil Biota and their Function] (https://www.sciencedirect.com/book/9780124159556/soil-microbiology-ecology-and-biochemistry) Kommentar: In: Soil Microbiology, Ecology and Biochemistry, 4th Edition
- Chapter 11 - Plant-Soil Biota Interactions Författare: R. Balestrini, E. Lumini, R. Borriello and V. Bianciotto ISBN: 978-0-12-415955-6 [Chapter 11 - Plant-Soil Biota Interactions] (https://www.sciencedirect.com/book/9780124159556/soil-microbiology-ecology-and-biochemistry) Kommentar: In: Soil Microbiology, Ecology and Biochemistry, 4th Edition
- Chapter 12 - Carbon Cycling: The Dynamics and Formation of Organic Matter Författare: William Horwath ISBN: 978-0-12-415955-6 [Chapter 12 - Carbon Cycling: The Dynamics and Formation of Organic Matter] (https://www.sciencedirect.com/book/9780124159556/soil-microbiology-ecology-and-biochemistry) Kommentar: In: Soil Microbiology, Ecology and Biochemistry, 4th Edition
- Chapter 13 - Methods for Studying Soil Organic Matter: Nature, Dynamics, Spatial Accessibility, and Interactions with Minerals Författare: Claire Chenu, Cornelia Rumpel and Johannes Lehmann ISBN: 978-0-12-415955-6 [Chapter 13 - Methods for Studying Soil Organic Matter: Nature, Dynamics, Spatial Accessibility, and Interactions with Minerals] (https://www.sciencedirect.com/book/9780124159556/soil-microbiology-ecology-and-biochemistry) Kommentar: In: Soil Microbiology, Ecology and Biochemistry, 4th Edition
- Chapter 14 - Nitrogen Transformations Författare: G.P. Robertson and P.M. Groffman ISBN: 978-0-12-415955-6 [Chapter 14 - Nitrogen Transformations] (https://www.sciencedirect.com/book/9780124159556/soil-microbiology-ecology-and-biochemistry) Kommentar: In: Soil Microbiology, Ecology and Biochemistry, 4th Edition
- Chapter 15 - Biological N Inputs Författare: Peter J. Bottomley and David D. Myrold ISBN: 978-0-12-415955-6 [Chapter 15 - Biological N Inputs] (https://www.sciencedirect.com/book/9780124159556/soil-microbiology-ecology-and-biochemistry) Kommentar: In: Soil Microbiology, Ecology and Biochemistry, 4th Edition
- Chapter 12 - The Global Cycles of Nitrogen and Phosphorus Författare: William H. Schlesinger and Emily S. Bernhardt ISBN: 978-0-12-385874-0 [Chapter 12 - The Global Cycles of Nitrogen and Phosphorus] (https://www.sciencedirect.com/book/9780123858740/biogeochemistry) Kommentar: In: Biogeochemistry, 3rd Edition
- Chapter 13 - The Global Cycles of Sulfur and Mercury Författare: W.H. Schlesinger and Emily S. Bernhardt ISBN: 978-0-12-385874-0 [Chapter 13 - The Global Cycles of Sulfur and Mercury] (https://www.sciencedirect.com/book/9780123858740/biogeochemistry) Kommentar: In: Biogeochemistry, 3rd Edition
- Chapter 2 - The Soil Habitat Författare: R.P. Voroney and R.J. Heck ISBN: 978-0-12-415955-6 [Chapter 2 - The Soil Habitat] (https://www.sciencedirect.com/book/9780124159556/soil-microbiology-ecology-and-biochemistry) Kommentar: In: Soil Microbiology, Ecology and Biochemistry, 4th Edition
- Chapter 11 - The Global Carbon Cycle Författare: William H. Schlesinger and Emily S. Bernhardt ISBN: 978-0-12-385874-0 [Chapter 11 - The Global Carbon Cycle] (https://www.sciencedirect.com/book/9780123858740/biogeochemistry) Kommentar: In: Biogeochemistry, 3rd Edition
- Chapter 2 - Biotic Interactions in Soil as Drivers of Ecosystem Properties Författare: Richard Bardgett and David Wardle ISBN: 978-0-19-954688-6 Kommentar: In: ‘Aboveground-Belowground Linkages: Biotic Interactions, Ecosystem Processes, and Global Change.
Copies will be provided during course Oxford Series in Ecology and Evolution.
Available via Canvas-website
- Chapter 3 – The Bacteria and Archea Författare: Ken Killham and Jim I. Prosser ISBN: 978-0-12-415955-6 [Chapter 3 – The Bacteria and Archea] (https://www.sciencedirect.com/book/9780124159556/soil-microbiology-ecology-and-biochemistry) Kommentar: In: Soil Microbiology, Ecology and Biochemistry, 4th Edition
- Chapter 4 – The Soil Fungi: Occurrence Phylogeny and Ecology Författare: D. Lee Taylor and Robert L. Sinsabaugh ISBN: 978-0-12-415955-6 [Chapter 4 – The Soil Fungi: Occurrence Phylogeny and Ecology] (https://www.sciencedirect.com/book/9780124159556/soil-microbiology-ecology-and-biochemistry) Kommentar: In: Soil Microbiology, Ecology and Biochemistry, 4th Edition
- Chapter 5 - Soil Fauna: Occurrence, Biodiversity, and Roles in Ecosystem Function Författare: David C. Coleman and Diana H. Wall ISBN: 978-0-12-415955-6 [Chapter 5 - Soil Fauna: Occurrence, Biodiversity, and Roles in Ecosystem Function] (https://www.sciencedirect.com/book/9780124159556/soil-microbiology-ecology-and-biochemistry) Kommentar: In: Soil Microbiology, Ecology and Biochemistry, 4th Edition
- Chapter 6 - Molecular Approaches to Studying the Soil Biota Författare: Janice E. Thies ISBN: 978-0-12-415955-6 [Chapter 6 - Molecular Approaches to Studying the Soil Biota] (https://www.sciencedirect.com/book/9780124159556/soil-microbiology-ecology-and-biochemistry) Kommentar: In: Soil Microbiology, Ecology and Biochemistry, 4th Edition
- Chapter 7 - Physiological and Biochemical Methods for Studying Soil Biota and Their Functions Författare: Ellen Kandeler ISBN: 978-0-12-415955-6 [Chapter 7 - Physiological and Biochemical Methods for Studying Soil Biota and Their Functions] (https://www.sciencedirect.com/book/9780124159556/soil-microbiology-ecology-and-biochemistry) Kommentar: In: Soil Microbiology, Ecology and Biochemistry, 4th Edition