EHSC 4310/6310
ENVIRONMENTAL MICROBIOLOGY
Spring 2004
Class time:
T/Th 9:30 Ð 10:45 Lecture
T/Th 11:00 Ð 12:15 Lab
Instructor:
Dr. Erin Lipp 144 EHS Bldg.
583-8138 elipp@uga.edu
Office Hours: T/Th 12:30 Ð 1:30 pm, or by appointment (contact by e-mail)
TA:
Theng Theng Fong 134 EHS Bldg.
tfong@uga.edu (preferred)
Textbook and other materials:
- Lecture: Environmental Microbiology by Maier, Pepper and Gerba
- Lab : Microbes Count by Jungck et al.
- Lab notebook with duplicate (i.e., carbon copy) pages
- Supplemental material will be assigned periodically
- Course information will be posted on WebCT (use your MyUGA login to access). Check often for updates, etc.
Course requirements and grading policy
There will be 4 midterm exams and 1 final exam Ð each worth 20% of your grade (100 pts each). Your lab grade will contribute 20% to your final course grade (100 pts). Final grades will be based on the four highest exam scores (i.e., you will drop the lowest score) and the lab (500 possible points). If you are satisfied with your score after the first 4 exams you do not need to take the final.
Make Up Exams:
There will be no make up exams. A missed exam can be your dropped score.
Attendance:
Lecture: Attendance will be taken periodically and will help to determine grades in borderline situations.
Lab: Attendance is expected for lab sessions. Weekly quizzes will be given. You may drop one quiz score and will be allowed one non-quiz absence.
University Honor Code:
All academic work must meet the standards contained in A Culture of Honesty . Each student is responsible to inform themselves about those standards before performing any academic work.
Environmental Microbiology Lecture §
| Week | Topic | Reading | |
| Jan. 8 (Th) | Course overview | ||
| Jan. 13 & 15 | Foundations of Microbiology & Microbial Environments | Intro/Micro. refresher | Chp. 1, 2 |
| Jan. 20 & 22 | Terrestrial & Air Env. | Chp. 4, 5 | |
| Jan. 27 & 29 | Aquatic Env & Transport | Chp. 6, 7 | |
| Feb. 3 (Tu) | Exam I | ||
| Feb. 5 | Methods in Environmental Microbiology | Sampling and Collection | Chp. 8 |
| Feb. 10 & 12 | Microscopy, Culture, Physiology | Chp. 9, 10, 11 | |
| Feb. 17 & 19 | (Lab Only) | ||
| Feb. 24 | Immunology and Genetics | Chp. 12, 13 | |
| Feb. 26 (Th) | No Class (snow day) | ||
| Mar. 2 (Tu) | Exam II | ||
| Mar. 4 | Microbial Ecology & Applied Microbiology | Biogeochemical cycles: Carbon | Chp. 14 |
| Mar. 9 & 11 | Spring Break | ||
| Mar. 16 | Other biogeochemical cycles | Chp. 15 | |
| Mar. 18 | Microbes in Agriculture | Chp. 18 | |
| Mar. 23 & 25 | Biodegradation | Chp. 16, 17 | |
| Mar. 30 (Tu) | Exam III | ||
| Apr.1 | Pathogens | Pathogens in the Environment | Chp. 19 |
| Apr. 6 & 8 | Pathogens, Indicators & Disinfection | Chp. 19, 20, 23 | |
| Apr. 13 & 15 | Water Treatment* | Chp. 21, 22 | |
| Apr. 20 | Risk Assessment (D. Cole) | Chp. 24 | |
| Apr. 22 (Th) | Review and lab presentations | ||
| Apr. 27 (Tu) | Exam IV | ||
| May 8 (Th) | Final Exam 8 Ð 11 am (time may be changed based on class vote) | ||
§ Syllabus may change, please check WebCT for updates
* Field trip to Athens WWTP (9:30 to 12:15) on 4/15/04. Meet at 9:30 at EHS for van or at 9:45 at the plant on Will Hunter Rd.
Environmental Microbiology Lab
Specific requirements and grading policy
Attendance and participation is expected and will contribute towards your lab grade. You are permitted to miss one quiz day and one non-quiz day. Additional absences will result in a 1 pt reduction for each day. Excessive tardiness will also be counted as an absence.
Groups. You will be working in groups. Collaboration within your group and with other groups is essential.
Weekly Quiz (25% of lab grade). A short quiz will be given at the beginning of the first lab of each week. It will cover material primarily from the previous week as well as lab readings for the current week. The lowest quiz score will be dropped. There will be 8 quizzes total:
Jan. 20
Jan. 27
Feb. 3
Feb. 10
Feb. 17
Mar. 16
Mar. 23
Lab notebooks and Pre-lab write ups (25% of lab grade). You are expected to maintain an organized lab notebook detailing your set up for each lab and hypotheses (pre-lab) and results and interpretations. The goal of any lab notebook is to allow anyone to repeat your work by just using your notes; this standard is expected for your notebooks. The interpretation or discussion will be guided by the questions at the end of each lab reading or as noted in class. You will be expected to turn in your pre-lab write up and lab notes at the beginning of class each Tuesday or before each new lab. Turn in the original sheets from your lab notebook and keep your carbon copies. In some cases you will need to share results with other groups. Within each lab group, notebooks should be maintained individually by each student. Notebook pages and pre-labs will contribute 25 pts total to your final score.
Lab reports (25% of lab grade). Lab reports (5 at 5 pts each) are required for the major topical sections covered. You should synthesize the major elements of the results for all experiments in that section and provide a written discussion (typed, 2-3 pages). You can use questions answered at the end of each lab as a guide for the discussion (but it should go beyond these).Your synthesis will also include results from other groups, when appropriate. Your reports should be written individually .
- Microbial Environments (5 pts) - Mar. 16
soil, air, water - Water Quality Assessment (5 pts) - April 1
indicators, stratification & Pfiesteria - Winogradsky Columns (5 pts) - April 8
weekly observations and interpretations - Biodegradation and remediation (5 pts) - April 15
biodegradation of compounds and implications - Microbial identification methods (5 pts) - April 20
Culture vs. genetic methods (incl. tree of life)
Final projects (25% of lab grade) . Laboratory investigations of topical issues in microbiology. Working in groups you will decide on a topic (must be approved by instructor), propose hypotheses, conduct experiments and report your work in a 15 minute oral presentation. You will have most of the month of April to work independently on your projects. Part of your grade will be based on the assessment of your work by peers within your group (% participation score). Your score will be calculated as follows for undergraduate groups:
Instructor's grade (0-25 pts) ´ Average peer grade (0-100%)
* Graduate student groups will also be required to submit an 8-10 page paper on the project. The paper should follow the style of Applied and Environmental Microbiology (see Instructions for Authors at http://aem.asm.org/misc/ifora.shtml ). The presentation and paper will count equally and grades will be determined as follows:
[Presentation grade (0-12.5 pts) + Paper grade (0-12.5 pts)] ´ Average peer grade (0-100%)
Time Line for Projects :
Jan. 20 Ð Pick groups of 3 to 5 and give names to instructor or TA. Include 2-3 possible topics. Conduct library research to narrow down topics. Discuss with instructor or TA Ð project must be feasible with the time and resources allotted.
Feb. 3 Ð Submit a short proposal (2-3 pages) to the instructor or TA including background information (literature review with proper citations), hypotheses, experimental design and materials needed.
Experiments can be carried out as needed, but the month of April will have few formal labs and time will be available for projects.
April 22 Ð Submit an outline of your project, results and interpretations.
April 27 Ð Oral presentations of final projects and peer review.
Possible Topics for Research
- Survival of microbes on surfaces (e.g., evaluating cutting boards)
- Are household sponges reservoirs for microbes? Are sponges microbiocidal?
- How effective are various herbs and spices as antimicrobials? Compare to disinfectants
- Effectiveness of mouthwashes against bacteria and viruses.
- Can sponges, dish towels and mops spread bacteria/viruses?
- How clean is your laundry?
- Microbes in public places (restrooms?)
- How effective are antimicrobial gels?
- volution and resistance of normal dermal flora under exposure to antibacterial lotions.
- Microbes on money Ð it might *need* laundering!
- When are your hands really clean?
- Survival and persistence of microbes under different environmental conditions.
- Changes in a microbial community under varying nutrient regimes (experiments with Winogradsky columns)
- Comparison of water quality assessment tools
- Microbiology of kimchee
There are many other possibilities; please feel free to use one of these or come up with your own.
Environmental Microbiology Lab*
| Week | Topic | |
| Tuesday | Thursday | |
| Jan. 8 (Th) | No Lab | |
| Jan. 13 & 15 | Lab safety | Winogradsky Columns |
| Jan. 20 & 22 | How big are microbes? pt. 1 | How big? pt. 2 Modeling phage growth ( Microbes Count! ) |
| Jan. 27 & 29 | Microbes in soil. pt. 1 Airborne microbes. pt. 1 |
Microbes in soil. pt. 2 Airborne microbes. lab 2 |
| Feb. 3 & 5 | Microbes in soil. pt. 3 Airborne microbes. pt. 3 |
Waterborne microbes. pt. 1 |
| Feb. 10 & 12 | Waterborne microbes. pt. 2 | Microbial identification by culture. pt. 1 Mold fights back ( Microbes Count !) |
| Feb. 17 & 19 | Microbial identification by culture. pt. 2 Microbial identification by genetics. pt. 1 |
Microbial identification by culture. pt. 3 Microbial identification by genetics. pt. 2 |
| Feb. 24 & 26 | No Lab | Snow day (classes cancelled) |
| Mar. 2 & 4 | Microbial identification by genetics. pt. 3 | Tree of life ( Microbes Count !) |
| Mar. 9 & 11 | Spring Break | |
| Mar. 16 & 18 | Microbial identification by genetics. pt. 4 | Biodegradation. pt. 1 Toxic Pfiesteria ( Microbes Count !) |
| Mar. 23 & 25 | Water quality assessment. pt. 1 Biodegradation. pt. 2 |
Water quality assessment. pt. 2 Biodegradation. pt. 3 |
| Mar. 30 & Apr 1 | Biodegradation. pt. 4 Microbial identification by genetics. pt. 5 |
Biodegradation. pt. 5 |
| Apr. 6 | Catch up day | |
| Apr. 8 - 21 | Work on group projects Ð lab open | |
* A lab manual will be posted on WebCT for each lab, except for those listed as Microbes Count ! (which can be found in that book).