Microbiology 3154 Microbial Ecology

Spring 2005

 

1/10/2005-4/28/2005

 

8:30am-9:45am TTh (classroom)

Science Lecture Hall LL129

Th 2:00-4:50 (Lab)

Science Lab Building Rm 344

 

Instructor Information:

Instructor:      Dr. Michele Zwolinski

305M Science Building

626-7795

mzwolinski@weber.edu

Office Hours: Tuesday 1:00-2:00 pm, Wednesday 2:30-3:30, and by appointment

Website:  http://faculty.weber.edu/mzwolinski/

 

Course Description:

This course will explore: 1. The factors determining the growth and distribution of microorganisms in their natural habitats,  2. Microbial diversity,  3. Microbial interactions with other living organisms and their surroundings, and 3. Microbial activities in nature, including biogeochemical cycles. 

Prerequisites:  Micro LS2054

Credit Hours: 4

 

Course Objectives:

  1. Gain an appreciation for and understanding of the ecology of microorganisms and the evolution of microbial diversity.
  2. Compare and contrast the study of microorganisms in culture vs the study of microorganisms in their habitats.
  3. Discuss how and why microbial ecology is an integral part of the science of microbiology, even clinically oriented microbiology.
  4. Practice the skills needed to be efficient self-motivated scholars of microbiology.

 

 

Textbooks and Resources:

Required Textbook:  Microbial Ecology: Fundamentals and applications. 4thed. by Ronald Atlas and Richard Bartha (1998). Benjamin/Cummings.  Available in the bookstore; bring this text to class

 

Other Resources:

Instructor’s Course Website:  http://faculty.weber.edu/mzwolinski/ – will include a list of Microbiology related URLs, course announcements, reading assignment links, learning objectives, and lab activities.  Required readings will also be assigned from other free sources (e.g. articles posted on the website, other internet locations or at the library.  NOTE:  I do not carry extra handouts for people who miss class.  If you miss a handout you are responsible for obtaining it from someone else or from the website. 

 

Recommended Textbook:  A Field Guide to Bacteria, by Dryer, B.D. 2003. Cornell University Press.  This text will be especially useful for labs and has great stories and photographs of microbes in action. 

 


 

Policies and Procedures: 

 

Use of technology:

Computer access should not be and issue for anyone in this course.  If you feel you do not have adequate access to a computer (with internet access and word processing) please see me as soon as possible.  I expect that assignments will be prepared with a word processing program and will use correct spelling and grammar.

 

Academic Honesty:

Cheating and plagiarism will be reported to the administration and will result in a failing grade.   

 

Ignorance is not an acceptable excuse for plagiarism.  If you have questions about how to properly cite material see http://library.weber.edu/ref/guides/howto/citing.cfm#cbe.  When in doubt, ask a librarian! 

 

If you need writing assistance, visit the Writing Center http://departments.weber.edu/writingcenter/

 

Attendance policy: 

This is a fast-paced and interactive class.  Your performance will depend on your attendance and participation.  In addition, since much of the work will be done in groups, your absences will also affect the other members of your group.  If you must be absent for class please inform your group prior to missing the class.  You are responsible for retrieving missed information from your group. 

 

In-class quizzes and assignments can not be made up although you may receive copies posted on the website. 

 

This class meets for two 1 hour and 15 minute classroom sessions and a 2 hour and 50 minute lab each week.  Do not expect this class to get over early, it won’t.  If extra time is available at the end of a lab session, this will be the only time in-class review will be offered. 

 

If circumstances beyond your control require you to be absent for more than three classes in a row you MUST tell me when and if you intent to return.  If not, you can expect a phone call from me and/or I will deduct your grade by 3% each class until you earn an E or a UW. 

 

Information for Students with Disabilities:

Any student requiring accommodations or services due to a disability must contact Services for Students with Disabilities (SSD), room 181 of the Student Service Center (http://weber.edu/ssd/). SSD can also arrange to provide course materials (including this syllabus) in alternative formats if necessary.

 

Students who are called up to active military duty need to contact the veterans’ administration on campus to discuss your options. 

 

Extenuating circumstances:

Unforeseen problems can arise during a semester.  Serious illnesses for yourself or a family member, for example, can be a tremendous distraction to your studies.  If you encounter extenuating circumstances that are affecting your ability to attend class, study, or to otherwise perform your best, you should seek assistance from the Dean of Students (http://departments.weber.edu/studentaffairs/DeanofStudents) or the Student Counseling Center (http://departments.weber.edu/CPSC/html/cc.htm) as soon as possible.  I will always be available to help you find assistance.

 

Cell phones:

Cell phones, radios, and other electronic devices must be turned off during class and lab (this includes text messaging).

 

 

 

Teaching Strategies:

This class will use a technique called Team-based learning.  The details of this strategy will be explained in class.  Briefly, you will be assigned to a small group and work with this group to complete quizzes, in-class activities and labs.  Your grade will reflect your individual work as well as your ability to work with your team.

 

Earning Points

Individual and Group Pre-Unit Quizzes:  4 at 25 points

The course content is organized into several units.  Each unit starts with an introductory reading assignment and a Pre-Quiz.  On the first day of each unit you will take a quiz individually, turn it in for a grade, then take the quiz collaboratively with your group.  You will receive points for both the individual and the group quizzes, however, your final group score will be adjusted based on your peer evaluations (see below).

 

Quizzes are developed to train you to read for understanding, introduce vocabulary, provide background information.

 

In-class activities:  (5 at 10 points each)

Each unit will include in-class group activities that are required.  Some of these assignments will require preparation outside of class.  Five of these will be collected randomly throughout the semester for grading.  They may be evaluated individually or as a group.   

 

Homework:

Each unit will consist of required and recommended readings and some recommended questions or problems.  Theses will not be collected or graded – you may do as many or few as you wish.  However, you should keep these in an organized format as evidence of your effort in the course and your understanding of the material.

Labs: 

Labs are required.  You must keep a lab notebook (you may continue to use a notebook from previous courses).  Requirements for the notebook will be provided in Lab.  Lab books will be collected randomly throughout the semester for evaluation

 

Peer Evaluations:   

Twice during the semester you will be asked to evaluate the other members of your group.  These evaluations will determine the percentage of the points you earn for the group quizzes and activities.  More information will be provided as needed.

 

Exams:  4 at 50 points each = 200 points

One exam per unit.  Exams will evaluate your ability to answer questions about the material covered in each unit.  They will be a combination of multiple choice, short answer, and essay.

All exams will be administered via Chi Tester in the testing center and will be available for two or three days (depending on schedule). 

No make-up exams will be given.

 

Final Exam:  1 at 75 points

In-class, during the final exam slot

Thursday May, 5, 7:00am -9:00am

Final exam is cumulative but will focus primarily on concepts covered in the Lab.

 

Your final grade will be calculated as a percentage of the points earned (= points earned/points total). 

Grade %

Letter Grade

Grade %

Letter Grade

Grade %

Letter Grade

Grade %

Letter Grade

92.5-100

A

82.5-87.5

B

72.5-77.5

C

62.5-67.5

D

90-92.5

A-

80-82.5

B-

70-72.5

C-

60-62.5

D-

87.5-90

B+

77.5-80

C+

67.5-70

D+

<60

F

Course Schedule Classroom:

Week

Day of Week

Dates

Topic1, 2

 

1

T

1/11

Introduction, Course policies

 

 

Th

1/13

Microbiology, History of Microbial Ecology

 

 

 

 

 

 

2

T

1/18

Unit 1:  Evolution and Diversity:  Pre-Quiz

 

 

Th

1/20

Unit 1:  Earth’s Timeline and Evolution

 

 

 

 

 

 

3

T

1/25

Unit 1:  Microbial Evolution and Diversity – Prokaryotes

 

 

Th

1/27

Unit 1:  Microbial Evolution and Diversity – Eukaryotes

 

 

 

 

 

 

4

T

2/1

Unit 1: Applications – Astrobiology

 

 

Th

2/3

Unti 1 TBA

 

Unit 1 Exam

 

 

 

 

5

T

2/8

Unit 2:  Microbial populations Biotic interactions

 

 

Th

2/10

Unit 2:  Inter-species: Biofilms

 

 

 

 

 

 

6

T

2/15

Unit 2:  Plant pathogens

 

 

Th

2/17

Unit 2:  Microbes and animals – mutualistic and symbiotic

 

 

 

 

 

 

7

T

2/22

Unit 2:  Evolution, the immune system and pathogens

 

 

Th

2/24

Unit 2: Applications –Staphylococcus aureus

 

Unit 2 Exam

 

 

 

 

8

T

3/1

Unit 3:  Microbial Communities and Ecosystems – pre quiz

 

 

Th

3/3

Unit 3: Ecological Examples

 

 

 

 

 

 

9

T

3/8

Unit 3: Microbial Growth and environmental conditions

 

 

Th

3/10

Unit 3: Abiotic/ Habitat interactions

 

Unit 3 Exam

 

 

 

 

 

Sat

3/12

ASM Intermountain Branch Meeting At Weber State University

 

 

 

 

 

 

10

T

3/15

Spring Break

 

 

Th

3/17

Spring Break

 

 

 

 

 

 

11

T

3/22

Review REDOX

 

 

Th

3/24

 

 

 

 

 

Review Microbial Metabolism – Heterotrophs & Phototrophs

 

12

T

3/29

Review Microbial Metabolism – Chemolitotrophs

 

 

Th

3/31

Unit 4: Biogeochemical cycling – pre quiz

 

 

 

 

 

 

13

T

4/5

Unit 4:  The Carbon Cycle

 

 

Th

4/7

Unit 4:  The Nitrogen Cycle

 

 

 

 

 

 

14

T

4/12

Unit 4:  The Sulfur Cycle

 

 

Th

4/14

Unit 4: Applications:  Waste Water Treatment

 

Unit 4 Exam

 

 

 

 

15

T

4/19

Topics: TBA

 

 

Th

4/21

Topics: TBA

 

 

 

 

 

 

16

T

4/26

Topics: TBA

 

 

Th

4/28

Topics: TBA

 

 

 

 

 

 

Final Exam

Th

5/5

7:00-9:00 am Final

 

All dates are tentative.

 

 

Lab Schedule

Labs:  Methods for observing microbial diversity

Lab 1: Introduction

Safety   Objectives

            Organization/ Set-up and Clean-up Teams

            Activity:  Soil as a model of a complex microbial habitat

Activity Set up soil and water contact slides

 

Lab 2: Environmental Sampling of Air and Water

            Activity: Environmental Sampling and Dilutions

            Activity: Set up Winogradski columns

 

Lab 3: Observing the plate-count anomaly

            Activity:  soil dilutions and culturing actinomycetes and fungi from soil

            Activity:  DAPI and AO Direct counts (demo/mock); FISH

 

Lab 4:  Designing media to cultivate environmental microbes – Lab projects TBA

 

Labs: Abiotic environmental

Lab 5:  The abiotic environment

            Activity:  Characterizing soil moisture, texture, and pH

 

Lab 6:  Hydrophobic, hydrophilic and charged surfaces

            Activity:   Observing microorganisms on surfaces

 

Lab 5:  Set up nutrient cycling cultures (for Unit 4)

            Nitrogen Cycle

            Carbon Cycle

 

Labs: Biotic Interactions

Lab 8 Microbe-plant interactions:

Activity:  Observing ectomycorhizal and endomycorhizal fungi

Activity:  Observing root nodule symbionts (rhizobium)

 

Lab 9 Microbe-animal interactions

Activity: Parasitic nematodes and bioluminescent bacteria

 

Lab 10 Microbe-microbe interactions

            Activity: Consortia, mutualism, and commensalisms

 

Lab 11: Biofilms

            Activity: Observing Biofilms

 

Labs: Nutrient Cycling

            Activity: Observe Nitrogen cycle and Carbon cycle cultures

            Activity: Observe Winogradski columns and culture photrophs

 

Labs 12-15:  Lab Projects and Choose your own lab (choose a lab from a lab manual and give it a try – pending instructor approval and resource availability).