DEPARTMENT OF RENEWABLE RESOURCES UNIVERSITY OF ALBERTA
Renewable Resources 442/742/501 Soil Biogeochemistry
WINTER 2018 SYLLABUS
Instructor Sylvie Quideau
Professor, Soil Biogeochemistry Office: ESB 3-40B
Telephone: 780-492-5397
Email Address: [email protected] Office Hours: by appointment
Term Winter 2018
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
Sarah Thacker, Msc student ([email protected]) Liam Heffernan, PhD student ([email protected]) Course Description
Soil as an habitat for microorganisms; soil bioenergetics; the structural and functional diversity of soil microbial populations; soil fauna; the microbiology and biochemistry of organic matter decomposition; biogeochemical cycling of N, P, S, Se, 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 Objectives
This course will focus on soil microorganisms and the biogeochemical reactions mediated by them. The course is divided into 3 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. Module 3 will present how soil microorganisms interact with soil fauna and plants, and selected environmental and land management applications.
Basic principles and theory as portrayed during class 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. Soil microbial biomass, numbers, and activity
4. Microbial cell structure and structural diversity MODULE 2
5. Microbial functional diversity
6. Soil organic matter: constituents, decomposition and stabilization
7. Nitrogen biogeochemical cycling: forms, distribution and fluxes, response to disturbance
8. Sulfur and phosphorus transformations MODULE 3
9. Soil fauna
10. Plant-soil biota relationships
11. Microbial adaptation and spatial distribution 12. Applications to land reclamation and management A written examination will conclude the first two modules.
Module 3 will be evaluated during the final examination (cumulative examination).
Laboratory Description
During the laboratory portion of the course, we will examine various analytical techniques including the following four exercises: organic matter determination, microbial biomass measurements, phosphatase activity, and microbial respiration. Students are required to participate and will work in groups of 2 or 3 during the laboratory exercises.
Quizzes to be submitted at the beginning of labs, lab reports, and homeworks are individual assignments.
E-Class, Moodle, Course Website
The course syllabus, the powerpoint presentations used during the class period, notes for the laboratory portion of the course, assignments including homeworks, quizzes, and lab reports, and representative past exams will be placed on E-class. You should have a link to this class when you logon at https://eclass.srv.ualberta.ca/portal/.
Professionalism and Classroom Rules of Engagement
Students are expected to treat their instructor, guest speakers and fellow students with respect. That means coming to class on time and not leaving before the class has been formally dismissed, and not participating in disruptive behavior in class. Laptops or tablets may be used if they are for taking notes, not Facebook, Instagram or Twitter!
Cell phones are to be turned off or set to silent during lectures and labs, and must be turned off during exams.
Audio or video recording, digital or otherwise, of lectures, labs, seminars or any other teaching environment by students is allowed only with the prior written consent of the instructor or as a part of an approved accommodation plan. Student or instructor content, digital or otherwise, created and/or used within the context of the course is to be used solely for personal study, and is not to be used or distributed for any other purpose without prior written consent from the content author(s).
Marking and Grading
Students will be assigned a final letter grade based on their final mark. University policy for grades and student evaluations are outlined on the following website:
https://policiesonline.ualberta.ca/PoliciesProcedures/Pages/DispPol.aspx?PID=101
I will use the following as a guide to assign letter grades:
Descriptor Letter Grad Grade Point Value Final Mark (percent)
Excellent A+, A, A- 4.0, 4.0, 3.7 90-100
Good B+, B, B- 3.3, 3.0, 2.7 75-89
Satisfactory C+, C, C- 2.3, 2.0, 1.7 66-74
Poor D+ 1.3 56-65
Minimal Pass D 1.0 51-55
Failure F, F4* 0 50 or less
*F4 denotes eligibility of student to apply for reexamination of a course 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.
Plagiarism and Cheating
The University of Alberta is committed to the highest standards of academic integrity and honesty. Students are expected to be familiar with these standards regarding academic honesty and to uphold the policies of the University in this respect. Students are particularly urged to familiarize themselves with the provisions of the Code of Student Behaviour (online at www.governance.ualberta.ca) and avoid any behaviour that could potentially result in suspicions of cheating, plagiarism, misrepresentation of facts and/or participation in an offence. Academic dishonesty is a serious offence and can result in suspension or expulsion from the University.
Key components of the code specific to this course include the following statements.
All students are subject to the Code of Student Behaviour, as outlined at:
http://www.governance.ualberta.ca/en/CodesofConductandResidenceCommunityStandards/C odeofStudentBehaviour.aspx. Please familiarize yourself with it and ensure that you do not participate in any inappropriate behavior as defined by the Code.
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.
Students should speak with the course instructor about any questions or concerns about the code. Students should be particularly aware of the code as it pertains to internet and library research, use of previous class notes, reclamation plans of former students and interviews or discussions with others.
“Policy about course outlines can be found in Course Requirements, Evaluation Procedures and Grading of the University Calendar.”
Mark Distribution- RENR 442 (UNDERGRADUATE LEVEL)
Quizzes (5 quizzes at 2% each)§ 10%
Lab reports (6 reports at 1 % each)# 6%
Homework 1** 10%
Homework 2** 15%
Midterm 1*¶ 15 %
Midterm 2*¶ 15 %
Final examination¶ 29 %
Total 100 %
*: If you have a legitimate reason to miss a midterm exam, the assessment on that midterm exam will be allocated to the final exam.
§: due at the beginning of the lab period or the Quiz will be given a mark of zero.
#: due at the end of the lab period or the Report will be given a mark of zero.
**: 25% per day will be deducted from a late report. Assignment is considered late after 4:30 pm on the due date.
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.
Handwritten assignments will NOT be accepted and will be given a mark of zero.
¶ Only approved non-programmable calculators permitted should you wish to bring a calculator to the mid-term or final exams. Wireless-capable devices are not permitted.
Mark Distribution- RENR 501/742 (GRADUATE LEVEL)
Quizzes and lab participation 20 %
Homeworks 20 %
Module examinations (Midterms) 20 %
Final examination 20 %
In-class presentation 20 %
Total 100 %
Soil Biogeochemistry 2018-‐ Tentative lecture schedule-‐
MODULE 1
TOPIC
Tuesday Jan 9 Introduction
Thursday Jan 11 Soil as an habitat for microorganisms
Tuesday Jan 16 Microbial classification and bioenergetics (Part 1) Thursday Jan 18 Bioenergetics (Part 2)
Intro to lab
Tuesday Jan 23 Biomass, numbers and activity
Thursday Jan 25 Structural diversity (cell components) Tuesday Jan 30 Structural diversity (communities) Thursday Feb 1 Wrap-‐up and review
Tuesday Feb 6 Module 1 test (in class)
MODULE 2
TOPIC
Thursday Feb 8 Functional diversity
Tuesday Feb 13 Soil carbon-‐ overview of measurement techniques Thursday Feb 15 Organic matter-‐ decomposition and stabilization
Tuesday Feb 27 Biogeochemical cycling of carbon and organic pollutants Thursday Mar 1 Nitrogen biogeochemistry
Tuesday Mar 6 S, Se and P biogeochemistry Thursday Mar 8 Wrap-‐up and review
Tuesday Mar 13 Module 2 test (in class)
MODULE 3
TOPIC
Thursday Mar 15 Biogeochemical cycling of metals
Tuesday Mar 20 Soil fauna, biodiversity and role in ecosystems Thursday Mar 22 Plant-‐ soil biota interactions
Tuesday Mar 27 Mycorrhizal fungi and carbon
Thursday Mar 29 Ecology and management of soil biota Tuesday Apr 3 Wrap-‐up and Lab discussion
Thursday Apr 5 Student presentations Tuesday Apr 10 Student presentations
Thursday Apr 12 FINAL EXAM (CUMULATIVE, in class)
Soil Biogeochemistry-‐ Lab schedule-‐ WINTER 2018
TOPIC DUE
Jan 11/12 No lab
Jan 18/19 The soil environment: pH and soil organic matter (Part 1)
Preparation for lab incubation experiment (water addition)
Quiz 1 Lab report 1
Jan 25/26 Soil organic matter (Part 2) Preparation for lab incubation experiment (start)
Quiz 2 Lab report 2
Feb 1/2 Soil microbial biomass Lab incubation (sampling 1)
Quiz 3 Lab report 3 Feb 8/9 Lab incubation (sampling 2)
Work on Homework 1
Feb 15
Homework 1 due
Feb 15/16 Lab incubation (sampling 3)
March 1/2 Lab incubation (sampling 4) Phosphatase activity
Quiz 4 Lab report 4 March 8/9 Lab incubation (sampling 5)
Sulfur lab (Part 2)
Quiz 5 Lab report 5 March
15/16
Lab incubation (Finish) Lab report 6 March
22/23
Work on Homework 2
March 27
