DEPARTMENT OF RENEWABLE RESOURCES UNIVERSITY OF ALBERTA
Renewable Resources 442/742 Soil Biogeochemistry
2017 Syllabus
Instructors Dr. Karen Thompson, Postdoctoral Fellow ([email protected]) Preston Sorenson, PhD student ([email protected])
Office: ESB 3-40
Office Hours: by appointment Term Winter 2017
Classes Tuesday and Thursday, 11 am to 12:20 pm, ESB 2-36 Labs Thursday or Friday, 2 to 4:50 pm, ESB 2-44
Credits 3-3-0
Teaching Assistants
Brittany McAdams, MSc student ([email protected]) Office hours: by appointment, Office: 3-40 ESB
Paul Sewell, MSc student ([email protected]) Office hours: by appointment, Office: 3-40 ESB
Course Description
Introduction to the main components of the soil biota; the metabolic and molecular diversity of microbial populations and their role in soil processes; the microbiology and biochemistry of decomposition of organic matter in soil; biogeochemical cycling of N, P, S, Si, base cations and metals; and the application of soil microbiology to selected environmental problems.
Course Pre-Requisites
REN R 210 or SOILS 210, or consent of instructor. Credit may be obtained for only one of REN R 442 or SOILS 430.
Course Format
This course will focus on soil microorganisms and the biogeochemical reactions mediated by them. The course is divided into 2 modules. Module 1 will introduce the kinds of microorganisms found in soils and the use and limitations of methods for studying them. Module 2 will examine fundamental microbial processes relevant to soil environments with emphasis on organic molecules and nutrient biogeochemistry. Basic principles and theory will be augmented with practical examples in the laboratory setting related to real world environmental problems.
Lecture Sections MODULE 1
1. Soil organisms and their environment
2. Principles of classification, metabolism and bioenergetics 3. Methods for studying soil microbial communities
4. Soil biodiversity and community structure MODULE 2
5. Soil organic matter: constituents, decomposition and stabilization
6. Nitrogen biogeochemical cycling: forms, distribution and fluxes, response to disturbance 7. Sulfur, phosphorus, and other elemental transformations
8. Microbial adaptation, spatial distribution and applications A written examination will conclude the first module. Module 2 will be evaluated during the final
examination (cumulative).
Laboratory Description
During the laboratory portion of the course, we will examine various analytical techniques including the following exercises: organic matter determination, microbial biomass measurements, elemental sulfur oxidation, nitrogen mineralization and phosphatase activity in different soils. Students are required to participate and will work in groups of 2 or 3. At the end of each of these four exercises, students will be required to submit a lab report (individual work).
A quiz (take-home assignment) is due at the beginning of each lab. At the end of the term, students will synthesize what they have learned from the lab and writing exercises in a final report. The goal is for students to learn lab techniques as well as to get some exposure to scientific writing.
Course Objectives
- Students will understand underlying principles related to how soil microorganisms interact with their environment and the biogeochemical reactions mediated by them.
- Students will be gain knowledge on the kinds of microorganisms found in soils and the use and limitations of methods for studying them.
- Students will understand fundamental microbial processes relevant to soil environments with emphasis on organic molecules and nutrient biogeochemistry.
Upon successful completion of the course, students will be able to:
- Discuss microbial metabolic strategies
- Have knowledge of the tools available for study of soil microbial communities, including fingerprinting and molecular methods
- Understand soil nutrient cycling, microbial involvement in these cycles and implications for ecosystem processes
- Report lab results coherently and cohesively -
Readings and Use of E-Class:
Lecture slides will be posted on E-class before lectures. However, these slides provide an outline of material and are not a complete resource. Attendance at lecture is required. There is no textbook for this course, however recommended readings to be used in class discussion may be posted on E-class before lecture; students are advised to read these articles in preparation for lecture.
Course Requirements, Marking and Grading:
Quizzes 10 % Class Discussion/Participation 10 % Lab reports (4 assignments @ 5% each) 20 %
Lab final report 10 %
Mid-term examination 20 %
Final examination (April 15th at 9 am) 30 % Total 100 %
Handwritten assignments will NOT be accepted and will be given a mark of zero.
Late assignments will NOT be accepted and will be given a mark of zero unless they are due to incapacitating illness, severe domestic affliction or other compelling reasons.
All requests for special consideration regarding lecture and laboratory portions of the course (registration in sections, etc.), the mid-term and final examinations, must be submitted formally to Karen Thompson or Preston Sorenson.
CELL PHONES: Cell phones are to be turned off or set to silent during lectures and labs, and must be turned off during exams.
STUDENTS WITH DISABILITIES: Students who require accommodation in this course due to a disability are advised to discuss their needs with Specialized Support & Disability Services (2- 800 Students’ Union Building).
ACADEMIC SUPPORT CENTRE: Students who require additional help in developing strategies for better time management, study skills or examination skills should contact the Student Success Centre (http://www.studentsuccess.ualberta.ca/). Students who need help with writing can contact: Centre for Writers: http://www.c4w.arts.ualberta.ca/.
SCHEDULE
MODULE 1
Tuesday, Jan 10 Lecture
Thursday, Jan12 Lecture, NO LAB
Friday, Jan 13 NO LAB Tuesday, Jan 17
Lecture
Thursday, Jan 19 Lecture, LAB 1
Friday, Jan 20 LAB 1
Tuesday, Jan 24 Lecture
Thursday, Jan 26 Lecture, LAB 2
Friday, Jan 27 LAB 2
Tuesday, Jan 31 Lecture
Thursday, Feb 2 Lecture, LAB 3 MINI-REPORT 1 due
Friday, Feb 3 LAB 3
MINI-REPORT 1 due Tuesday, Feb 7
Lecture
Thursday, Feb9 Lecture, LAB 4
Friday, Feb 10 LAB 4
Tuesday, Feb 14 Lecture
Thursday, Feb 16
Mid-term EXAM, NO Lab
Friday, Feb 17 NO Lab
READING WEEK
Tuesday, Feb 21 NO Lecture
Thursday, Feb 23 NO Lecture, NO LAB
Friday, Feb 24 NO LAB
MODULE 2 Tuesday, Feb 28 Lecture
Thursday, March 2 Lecture, LAB 5 MINI-REPORT 2 due
Friday, March 3 LAB 5
MINI-REPORT 2 due Tuesday, March 7
Lecture
Thursday, March 9 Lecture, LAB 6
Friday, March 10 LAB 6
Tuesday, March 14 Lecture
Thursday, March 16 Lecture, LAB 7 MINI-REPORT 3 due
Friday, March 17 LAB 7
MINI-REPORT 3 due Tuesday, March 21
Lecture
Thursday, March23 Lecture, LAB 8 MINI-REPORT 4 due
Friday, March 24 LAB 8
MINI-REPORT 4 due Tuesday, March 28
Lecture
Thursday, March 30 Lecture, NO Lab
Friday, March 31 NO Lab
Tuesday, April 4 Lecture
LAB FINAL REPORT due
Thursday, April 6 Lecture, NO Lab
Friday, April 7
GOOD FRIDAY,NO Lab Tuesday, April 11
Lecture
Thursday, April13 Lecture, NO Lab
Wednesday, April 19 FINAL EXAMINATION
Missed examination or assignment
A student who cannot write a term examination or complete a term assignment due to incapacitating illness, severe domestic affliction or other compelling reasons can apply for extension of time to complete an assignment. A student who cannot write the final examination due to incapacitating illness, severe domestic affliction or other compelling reasons can apply for a deferred final examination. Such an application must be made to the student’s Faculty office within 48 hours of the missed examination and must be supported by a Statutory Declaration or other appropriate documentation (Calendar section 23.5.6). Deferral of term work or exams is a privilege and not a right; there is no guarantee that a deferral will be granted. Misrepresentation of Facts to gain a deferral is a serious breach of the Code of Student Behaviour.
Grade Evaluation
Final distributions of grades are not on the basis of a curve or historic distribution of student grades; rather, letter grades reflect a student’s level of achievement based on class
participation, performance on assignments, quizzes and exams, and natural breaks in the distribution of scores as listed in the grading section below.
Descriptor Letter Grade Grade Point Value
A+ 4.0
Excellent A 4.0
A- 3.7
B+ 3.3
Good B 3.0
B- 2.7
C+ 2.3
Satisfactory C 2.0
C- 1.7
Poor D+ 1.3
Minimal Pass D 1.0
Failure F 0
Plagiarism and Cheating
Students must be familiar with standards regarding academic honesty and uphold policies of the University. Academic dishonesty is a serious offence and can result in suspension or expulsion from the University.
All students at the University of Alberta are subject to the Code of Student Behaviour, as outlined in the 2015/2016 University Calendar. Students should familiarize themselves with the current version of the code and ensure they do not participate in any inappropriate behaviour as defined by it. Key components of the code specific to this course include the following statements.
Plagiarism: no student shall submit the words, ideas, images or data of another person as the student’s own in any academic writing, essay, thesis, project, assignment, presentation or poster in a course or program of study. Cheating: no student shall represent another’s substantial editorial or compositional assistance on an assignment as the student’s own work.
The most recent version of the Code of Student Behaviour can be found on line on the University of Alberta web site.
Student Responsibilities: No electronic devices, except non-programmable calculators, are permitted for quizzes or exams. We recommend a simple scientific calculator (pi, exp, ln &
sin, cos, tan keys). Wireless-capable devices are not permitted. Individual lab assignments are to be an individual effort. No trading of word processing files, images or graphs and no copying of ANY parts of assignments is permitted. The submission of words, ideas, images or data of another person or group as their own will be considered plagiarism.