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BI1322

Soil biology and biogeochemical cycles

Markens biologi och biogeokemiska kretslopp
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

Dear all course participants!

On Monday 17th January the course begins with an introductory lecture at 10.15-12. Due to the (still) ongoing Pandemic we have changed all lectures and seminars during the first course week to on-line zoom activities, and depending on the situation we may continue to do so.

Please find the relevant Zoom link below!

The Laboratory Practicals will be on campus, but adapted for maximum safety. The first in-person Practical will be on Wednesday 19/1 at 9.15-12 in the Böl Labs 1+2 at the entrance level in the BioCenter.

We have also postponed the excursion planned for 21/1, but hope to have it in a few weeks instead.

The course schedule has been updated in the PDF.

Looking forward to see you all on zoom at 10.15 on Monday then!

Karina

Topic: SBBC2022 Intro lecture

https://slu-se.zoom.us/j/69629745380

Meeting ID: 696 2974 5380

Passcode: SBBC2022

Course evaluation

The course evaluation is now closed

BI1322-30159 - 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 2020/2021

Soil biology and biogeochemical cycles (BI1322-30243)

2021-01-18 - 2021-03-23

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 kretslopp

Subjects

Soil Science Biology Biology Soil science

Education cycle

Master’s level

Modules

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 requirements
Master’s level (A1N)

Grading scale

5:Pass with Distinction, 4:Pass with Credit, 3:Pass, U:Fail
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

English

Prior 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 assessment of an independent project (degree project), the examiner may also allow a 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:

Department of Forest Mycology and Plant Pathology

Further information

Biology field: Ecology
Replaces: BI1225, MV0172

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

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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

Course facts

The course is offered as an independent course: Yes Tuition fee: Tuition fee only for non-EU/EEA/Switzerland citizens: 38054 SEK Cycle: Master’s level (A1N)
Subject: Soil Science Biology Biology Soil science
Course code: BI1322 Application code: SLU-30159 Location: Uppsala Distance course: No Language: English Responsible department: Department of Soil and Environment Pace: 100%