CEE 4160/6260: Environmental Microbiology for Engineers
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Instructor:
Dr. Lisa Colosi Peterson (lmc6b@virginia.edu)
Assistant Professor, Department of Civil & Environmental Engineering
D-219 Thornton Hall; Tel: (434) 924-7961
Office Hours: TBD or by appointment
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Prerequisites:
College chemistry and calculus; CE 2100 or equivalent
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Lecture:
MWF 1:00 – 1:50 pm, THN D221
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Text:
There is no required text for this class; however, the following two books
may be useful resources, especially during the early portion of the class.
These texts are available for 2-hour loan from course reserve materials at
the Brown Science & Engineering Library.
a. MT Madigan, JM Martinko, and J Parker. (2006) Brock Biology of
Microorganisms (8th Edition). Prentice Hall, Inc: Upper Saddle River, NJ.
b. RM Maier, IL Pepper, and CP Gerba. (2009) Environmental Microbiology (2nd
edition). Academic Press: New York.
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Website:
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Objectives: This course serves as a general introduction to the principles of applied and
environmental microbiology for advanced undergraduate and first-year graduate engineering
students. Specifically, we will assess the ways in which human activities impact microbial
systems and vice versa. Special consideration will be given to microbe-mediated cycling of
organic materials (i.e. pollutants) in a variety of natural and engineered systems.
https://collab.itc.virginia.edu
The class will be divided into three parts, each addressing a specific skill set:
I. Basics of Microbiology
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Identify critical cellular components and functionalities that enable microbes to
survive and thrive in various environments.
Evaluate the suitability of specific molecular methods/biotechnological techniques
to characterize a microbial population and design recombinant mutants.
II. Microbial Growth & Metabolism
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Identify the thermodynamic underpinnings of metabolic processes mediated by
microbial organisms.
Assess the favorability of microbial growth on an organic substrate (pollutant)
within a selected environmental medium.
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III. Microbiology of Engineered Environmental Systems
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Predict long-term sequence of microbially-mediated transformation reactions
following release of an organic material into an environmental system.
Evaluate the feasibility of bioremediation strategies to mitigate adverse
ecological/health impacts of organic pollutants in environmental media and
engineer appropriate controls to prevent undesired microbial infestation.
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Academic Integrity: Students are reminded of their pledge to uphold the University Honor
System. Please refer to http://www.virginia.edu/honor/proc/fraud.html for guidelines
covering academic fraud as they may apply to submission of work for this course.
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Grading: Final grades will be calculated as follows (item descriptions are below).
Homework Assignments (7)
Midterm 1
Midterm 2
Microbe of the Day
Critical Mini-Review
Final
4160
35%
15%
20%
10%
0%
20%
6260
30%
15%
15%
10%
15%
15%
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Midterm and final examinations will be closed-book with two sides of notes.
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Homework will be assigned roughly every other week and completed in self-selected groups
of two. Each pair will submit only one assignment; however, individual grades will be
adjusted using weighting factors derived from midterm and end-of-semester peer evaluations.
Teams are encouraged to submit professionally-formatted assignments (hand-written
calculations are acceptable). Assignments submitted after 5 pm on the deadline without
previous permission from the instructor will receive half-credit if submitted within one week.
Assignments submitted after one week past the deadline will not be accepted for credit but
will be evaluated for accuracy (“graded”) should the team desire.
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Students will be required to make one five-minute “Microbe of the Day” (MOTD)
presentation during the semester. These will highlight microorganisms of particular
environmental relevance or interest, and students may select any organism they wish so long
as the presentation includes the following components: a picture or video of the organism, its
physiology/morphology, its relevance to a particular natural/engineered environmental
system, and the ecological characteristics which allow it to thrive. All MOTD presentations
will be considered course material and thus may appear on examinations. For this reason,
and because the remainder of the class will evaluate the quality of each presentation,
presenters are asked to prepare a handout (1-page maximum) summarizing his/her most
salient points for distribution to the entire class. Students requiring special audiovisual
equipment (e.g. laptop, projector, overheads) or photocopies of their handout must make
arrangements with the instructor one week prior to their presentation date.
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Graduate students will be required to draft a critical “mini-review” subject to content and
style guidelines put fort by the American Society for Microbiology (ASM) in their
publication, Applied and Environmental Microbiology (AEM) (www.aem.asm.org). Papers
will summarize pertinent literature in environmental microbiology pertaining to a topic of the
student’s choice. Submissions must be no longer than twelve pages (double-spaced) with a
minimum of 20 references cited in AEM format. Prior to March 1, each student must
schedule a brief appointment with the instructor to discuss topic selection and paper scope.
Finalized manuscripts will be due by 5 pm on Monday, May 2.
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Policies:
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Disabilities. Students requiring special accommodations for a learning disability or
physical handicap must make arrangements with the instructor one week prior to an exam
or in-class presentation.
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Teamwork: Because students will be permitted to pick their own homework partners,
and because collaborative learning is integral to the formation of competent engineers,
teams are encouraged to resolve on their own any problems that may arise over the
course of the semester. Serious conflicts should be brought to the instructor’s attention.
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Scheduling. Students who will be unable to attend class on the day of an exam or
presentation for personal reasons (e.g. religious observances, conferences, interviews,
etc.) must contact the instructor at least one week in advance. Instances in which a
student misses an examination or assignment deadline unexpectedly due to extenuating
circumstances (e.g. personal or family emergency) will be handled on a case-by-case
basis, but students should make every effort to contact the instructor prior to the start of
scheduled class time on the day they will be absent.
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Re-grades. Requests for exam or homework re-grades must be outlined in writing and
delivered to the instructor within one week. Papers will not be accepted for reexamination after this time.
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Feedback. Comments, complaints, and compliments from students regarding the course
(structure, grading scheme, work load, etc.) will be most welcome and greatly
appreciated as means to improve the learning experience during this and future semesters.
The course Collab website will be configured to allow anonymous feedback.
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Anticipated Course Coverage by Date
Date
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Topic1
Reading (M or B)2
Course Introduction: What is Microbiology?
Cell Biochemistry
Cell Biochemistry
Cell Biochemistry
Cell Biochemistry
Microbial Diversity & Phylogeny
Microbial Ecology
Microbial Nutrition
Microbial Growth and Enumeration
Microbial Growth and Enumeration
Microbial Genetics: Introduction
Microbial Genetics: Genetic Engineering
Microbial Genetics: Genetic Engineering
Microbial Genetics: Genetic Engineering
Midterm #1
Microbial Genetics: Molecular Methods
Microbial Genetics: Molecular Methods
Fundamentals of Metabolism: Catabolism
Fundamentals of Metabolism: Catabolism
Fundamentals of Metabolism: Catabolism
Fundamentals of Metabolism: Catabolism (or TBA)
Fall Reading Day
Fundamentals of Metabolism: Anabolism
Fundamentals of Metabolism: Anabolism
Fundamentals of Metabolism: Anabolism
Metabolic Energy Considerations
Metabolic Energy Considerations
Metabolic Energy Considerations
Wastewater Treatment Microbiology
Wastewater Treatment Microbiology
Midterm #2
Wastewater Treatment Microbiology
Wastewater Treatment Microbiology
MOTD Presentations
MOTD Presentations
Drinking Water Microbiology
Drinking Water Microbiology
Groundwater Microbiology
Solid Waste Microbiology
Solid Waste Microbiology
Thanksgiving Recess
Thanksgiving Recess
Surface Water Microbiology
Microbial Fuel Cells and Bio-Based Energy Production
Biogeochemical Cycles and Course Wrap-Up
Final Exam is 9:00 am – 12:00 pm in THN D221.
M: Ch 1
B: Ch 3
M: Ch 2
M: Ch 10; 23.1-23.8
M: Ch 3
M: Ch 9 (skim)
M: Ch 13.1 – 13.4
M: Ch 13.5 – 13.9
B: Ch 4.8-4.16
B: Ch 4.17-4.21
B: Appendix 1
M: Ch 24.1-24.6
M. 24.7-24.11
M: Ch 25
M: Ch 26
M: Ch 4
Handout
Handout
B: 14.11-14.20
Schedule is subject to change.
All items available on the Collab website, under “Resources” < “Assigned Reading”. M is “Maier”, B is “Brock”
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