CEE 4160/6260: Environmental Microbiology for Engineers

▪Instructor:Dr. Lisa Colosi Peterson ()

Assistant Professor, Department of Civil & Environmental Engineering

D-219 Thornton Hall; Tel: (434) 924-7961

Office Hours: TBD or by appointment

▪Prerequisites:College chemistry and calculus; CE 2100 or equivalent

▪Lecture:MWF 1:00 – 1:50 pm, THND221

▪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.

  1. MT Madigan, JM Martinko, and J Parker. (2006)Brock Biology of Microorganisms(8th Edition). Prentice Hall, Inc: Upper Saddle River, NJ.
  1. RM Maier, IL Pepper, and CP Gerba. (2009)Environmental Microbiology (2nd edition).Academic Press: New York.

▪Website:

▪Objectives: This course serves as a general introduction to the principles of appliedand 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.

The class will be divided into three parts, each addressing a specific skill set:

  1. Basics of Microbiology

▪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.

  1. Microbial Growth & Metabolism

▪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.

  1. Microbiology of Engineered Environmental Systems

▪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.

▪Academic Integrity: Students are reminded of their pledge to uphold the University Honor System. Please refer to for guidelines covering academic fraud as they may apply to submission of work for this course.

▪Grading: Final grades will be calculated as follows (item descriptions are below).

41606260

Homework Assignments (7)35%30%

Midterm 115%15%

Midterm 220%15%

Microbe of the Day10%10%

Critical Mini-Review0%15%

Final20%15%

▪Midterm and final examinations will be closed-book with two sides of notes.

▪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.

▪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/hermost 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.

▪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) ( 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 inAEM 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.

▪Policies:

▪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.

▪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.

▪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.

▪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 re-examination after this time.

▪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.

Date / Topic1 / Reading (M or B)2
I / W / Aug 28 / Course Introduction: What is Microbiology? / M: Ch 1
F / Aug 30 / Cell Biochemistry / B: Ch 3
M / Sep 2 / Cell Biochemistry
W / Sep 4 / Cell Biochemistry
F / Sep 6 / Cell Biochemistry
F / Sep 6 / Microbial Diversity & Phylogeny / M: Ch 2
M / Sep 9 / Microbial Ecology
W / Sep 11 / Microbial Nutrition / M: Ch 10; 23.1-23.8
F / Sep 13 / Microbial Growth and Enumeration / M: Ch 3
M / Sep 16 / Microbial Growth and Enumeration / M: Ch 9 (skim)
W / Sep 18 / Microbial Genetics: Introduction
F / Sep 20 / Microbial Genetics: Genetic Engineering / M: Ch 13.1 – 13.4
M / Sep 23 / Microbial Genetics: Genetic Engineering
W / Sep 25 / Microbial Genetics: Genetic Engineering
F / Sep 27 / Midterm #1
M / Sep 30 / Microbial Genetics: Molecular Methods / M: Ch 13.5 – 13.9
W / Oct 2 / Microbial Genetics: Molecular Methods
II / F / Oct 4 / Fundamentals of Metabolism: Catabolism / B: Ch 4.8-4.16
M / Oct 7 / Fundamentals of Metabolism: Catabolism
W / Oct 9 / Fundamentals of Metabolism: Catabolism
F / Oct 11 / Fundamentals of Metabolism: Catabolism (or TBA)
M / Oct 14 / Fall Reading Day
W / Oct 16 / Fundamentals of Metabolism: Anabolism / B: Ch 4.17-4.21
F / Oct 18 / Fundamentals of Metabolism: Anabolism
M / Oct 21 / Fundamentals of Metabolism: Anabolism
W / Oct 23 / Metabolic Energy Considerations / B: Appendix 1
F / Oct 25 / Metabolic Energy Considerations
M / Oct 28 / Metabolic Energy Considerations
III / W / Oct 30 / Wastewater Treatment Microbiology
F / Nov 1 / Wastewater Treatment Microbiology
M / Nov 4 / Midterm #2
W / Nov 6 / Wastewater Treatment Microbiology / M: Ch 24.1-24.6
F / Nov 8 / Wastewater Treatment Microbiology / M. 24.7-24.11
M / Nov 11 / MOTD Presentations
W / Nov 13 / MOTD Presentations
F / Nov 15 / Drinking Water Microbiology / M: Ch 25
M / Nov 18 / Drinking Water Microbiology / M: Ch 26
W / Nov 20 / Groundwater Microbiology / M: Ch 4
F / Nov 22 / Solid Waste Microbiology / Handout
M / Nov 25 / Solid Waste Microbiology / Handout
W / Nov 27 / Thanksgiving Recess
F / Nov 29 / Thanksgiving Recess
M / Dec 2 / Surface Water Microbiology
W / Dec 4 / Microbial Fuel Cells and Bio-Based Energy Production
F / Dec 6 / Biogeochemical Cycles and Course Wrap-Up / B: 14.11-14.20
F / Dec 13 / Final Exam is 9:00 am – 12:00 pm in THN D221.

1 Schedule is subject to change.

2All items available on the Collab website, under “Resources” < “Assigned Reading”. M is “Maier”, B is “Brock”

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