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Course Name:  Geomicrobiology 
Course Prefix: MICRO/GEO
Course Number: 3753
             Submitted by (Name & E-Mail):  Michele Zwolinski, mzwolinski@weber.edu

Current Date:  2/18/2009
College: Science
Department:   Microbiology                              
From Term: Fall  2009 

Substantive

new 

Current Course Subject N/A
Current Course Number

New/Revised Course Information:

Subject:  MICRO            

Course Number: 3753

 Check all that apply:
    This is for courses already approved for gen ed.
    Use a different form for proposing a new gen ed designation.
DV  SI  CA  HU  LS  PS  SS 
EN  AI  QL  TA  TB  TC  TD  TE

Course Title: Geomicrobiology

Abbreviated Course Title: Geomicrobiology

Course Type:  LEL

Credit Hours:  3  or if variable hours:    to

Contact Hours: Lecture 2  Lab 2   Other

Repeat Information:  Limit 0   Max Hrs 0 

Grading Mode:  standard

This course is/will be: a required course in a major program
a required course in a minor program
a required course in a 1- or 2- year program
elective

Prerequisites/Co-requisites:

Chem 1210 or approval of the instructor

Course description (exactly as it will appear in the catalog, including prerequisites):

Geomicrobiology is the study of the interactions between microorganisms and minerals. This course will explore 1. geological change mediated by microorganisms, 2. microbial evolution driven by geologically diverse habitats, and 3. applications of geomicrobiology, including understanding the evolution of life on earth, the study of life in extreme environments, and industrial applications of geomicrobiology. This team-taught course includes classroom discussion, laboratories, and field trips. Prerequisites: CHEM1210 or approval of the instructor

Justification: Earth systems, including the lithosphere, hydrosphere, and biosphere have been influencing each other for 3.8 billion years. Microorganisms dissolve and create minerals. Geology provides habitats for microorganisms and influences microbial evolution. Microorganisms catalyze most of the mineral and nutrient cycling on earth (including C, N, and O), but they must observe the physical, chemical and geological constraints of their environment. Thus, understanding the operation of life on Earth requires the study of both geology and microbiology. Traditionally, however, these have been treated as separate fields of study. New techniques and tools in both geology and microbiology are allowing interdisciplinary research which has developed into a new field of science – Geomicrobiology. Students of microbiology and geology need exposure to this field for a thorough understanding of their own discipline. The proposed course in Geomicrobiology has been taught twice as an experimental course. We are now proposing to make it an elective course cross-listed in Microbiology and Geosciences. Our goal is to increase the communication between geoscientists and microbiologists. This course will also create opportunities for interdisciplinary research by providing more in-depth investigation into the chemistry and biochemistry of microbe-mineral interactions. Currently, fragmented geomicrobiology topics are introduced in Microbial Ecology (Micro3154), Environmental Microbiology (Micro3484), Geochemistry (Geosci3080), and Groundwater (Gecosi4500). A cohesive Geomicrobiology is needed to explore this field fully. A team-taught Geomicrobiology course will be unique to Weber State University. Undergraduate Geomicrobiology courses are rare. Those that are available tend to focus on microbial diversity and are generally targeted to microbiology majors. Graduate level courses are often offered in geology departments. Dr. Zwolinski presented a poster on this course at the American Society for Microbiology Conference for Undergraduate Educators meeting in May 2008. The course generated a great deal of interest. Educators from other institutions were especially envious of our proximity to unique microbial habitats including hot springs and the Great Salt Lake. Our course will seek a balance between microbiology and geology and will emphasize current research in geomicrobiology. This course will be divided into four sections. The first section will be an overview of microbiology, geology, and geochemistry. The second section will investigate the role of microorganisms in mediating biogeochemical cycles. The third section will focus the dissolution and precipitation of minerals by microorganisms. The fourth section will discuss the industrial and scientific applications of geomicrobiology, including, bioremediation and global climate change. This course will have a laboratory component. Labs will be used for learning new techniques, collaborative (and mentored) research projects, and field trips to this area’s many unique geomicrobiological “hot-spots” (e.g. the Great Salt Lake, mineral evaporation ponds, contaminated groundwater sites, hot springs, and caves). The small course size will allow us to expose students to cutting-edge research equipment. Students will design and accomplish experiments using molecular biology and advanced instrumentation like the atomic force microscope and the new scanning electron microscope. The microbiology department traditionally serves students pursuing medical or dental school. However, in the past few years, more students have expressed an interest in attending graduate school following graduation. Geomicrobiology is an expanding field of study. Currently there are more jobs available (academic, industrial, and government) in geomicrobiology than there are graduates. NASA, for instance, now hires more microbiologists than physicists. With this course, our students will, at a minimum, gain an appreciation for geomicrobiology. Ideally, some of our students will be motivated to pursue geomicrobiology as a program of graduate study. This course will provide a well balanced introduction to the field.

INFORMATION PAGE
for substantive proposals only

1. Did this course receive unanimous approval within the Department?

true

If not, what are the major concerns raised by the opponents?

2. If this is a new course proposal, could you achieve the desired results by revising an existing course within your department or by requiring an existing course in another department?

None of the related courses offered in the Microbiology department (Microbial Ecology, Environmental Microbiology, and Industrial Microbiology) offer the depth of geomicrobiology content offered in this course. Further, because these courses present detailed material on other aspects of microbiology it is not possible to add geomicrobiology into these courses.

3. How will the proposed course differ from similar offerings by other departments? Comment on any subject overlap between this course and topics generally taught by other departments, even if no similar courses are currently offered by the other departments. Explain any effects that this proposal will have on program requirements or enrollments in other department. Please forward letters (email communication is sufficient) from all departments that you have identified above stating their support or opposition to the proposed course.

The only possible overlaps would be in the Microbiology and Geoscience departments. However, because it is cross-listed and team taught there are no conflicts. Microbiology is not covered in most geosciences courses, although it may be discussed in reference to the history of the early Earth including fossil evidence of early life. This course is unique because it serves both the microbiology and geosciences students. It has been designed so that geosciences students receive a good introduction to microbiology, and the microbiology students a solid introduction to geology.

4. Is this course required for certification/accreditation of a program?

no

If so, a statement to that effect should appear in the justification and supporting documents should accompany this form.

5. For course proposals, e-mail a syllabus to Faculty Senate which should be sufficiently detailed that the committees can determine that the course is at the appropriate level and matches the description. There should be an indication of the amount and type of outside activity required in the course (projects, research papers, homework, etc.).

 

Microbiology/Geology

Geomicrobiology

Syllabus

 

Course Description

Geomicrobiology is the study of the interactions between microorganisms and minerals.  This course will explore 1. geological change mediated by microorganisms, 2.  microbial evolution driven by geologically diverse habitats, and 3. applications of geomicrobiology, including understanding the evolution of life on earth, the search for life on other planets, the study of life in extreme environments, and industrial applications of geomicrobiology.   This team-taught course will meet regularly for classroom discussion, guest lecturers, guided research laboratories, and field trips.

 

Instructors

            Michele D. Zwolinski, Ph.D., Microbiology, SL 305 M, x7795, mzwolinski@weber.edu

            Marek Matyjasik, Ph.D., Department of Geoscience, SL 204M, x 7726, mmatyjasik@weber.edu  

 

Resources: 

 

Required Text: Konhauser, Kurt (2007) Introduction to Geomicrobiology.  Blackwell Publishing

 

Additional required and recommended readings will be posted on the course web-site http://online.weber.edu.

 

The following texts will be placed on reserve at the WSU Stewart Library for reference.

 

 

 

 

 

 

Other Useful References

Books:

·         E. A. Paul; F. E. Clark. 2000. Soil Microbiology and Biochemistry. Academic Press.

·         R. Atlas and R. Bartha. 1998. Microbial Ecology: Fundamentals and applications. 4thed, Benjamin/Cummings.

·         D. R. Lovley,  Environmental Microbe-Metal Interactions, ASM Press, 2000

 

 

 

Journals:

·         Geomicrobiology

·         Geomicrobiology Journal

·         Applied and Environmental Microbiology

·         Environmental Microbiology

·         Global Biogeochemical Cycles

·         Ground Water

·         Nature

·         Science

·         Microbial Ecology

·         Trends in Microbiology

·         Virtual Journal of Geobiology (a collection of geobiology-related articles from Elsevier journals)

(Any article we can’t access through the library we can order through interlibrary loan)

 

Web Sites and Organizations

A list of useful websites will be available on the course website.   

 

Course Organization

This course meets twice a week for classroom and once a week for lab.  Attendance is required.  Preparation for, and participation in, class and lab is expected.  Field trips will occasionally be made and may require time outside of the scheduled meeting times.  Attempts will be made to schedule trips so the majority of students can participate.  

 

Assessment

                        Labs write-ups (2)                    50 points each

                        Assignments (2)                       50 points each

                        Exams (2)                                75 points each

                        Final Exam                              100 points

Attendance and Participation   25 points

                                   

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


 

Geomicrobiology

Schedule

 

Week

Date

Topic

Chapter

Assignments

1

8/24

 

1

 

 

8/24L

Media Preparation – Plan thermophile experiments

 

 

 

8/26

Review physical properties and growth requirements

1.3 

 

2

8/31

Field trip:  Ogden Hot Springs 1:00 – 3:00; Lab 3:00-3:45

 

 

 

9/2

Metabolism Review

2.1 - 2.3

 

3

9/7

Labor Day No class

 

 

 

9/9

Microbial Diversity, Life in Extreme Environments

1.4-1.5

 

 

9/14

Chemoheterotrophic Pathways with Geomicrobiological Importance

2.4

 

4

9/14 L

Complete Thermophile Experiments

 

 

 

9/16

Chemoheterotrophic Pathways with Geomicrobiological Importance: 

2.4

 

5

9/21

Chemolithotrophic Pathways with Geomicrobiological Importance: 

2.5

 

 

9/21 L

Bioinformatics Lab   

 

Thermophile Lab Report Due

 

9/23

Microbiology of Caves

TBA

 

6

9/28

Microbiology of the Deep Sub-Surface

TBA

 

 

9/28L

Plan Halophile Experiments, Media Preparation

 

 

 

9/30

Microbiology of the Great Salt Lake - Halophiles

TBA

 

7

10/5

Evaporation Ponds/ Great Salt Lake Field Trip (Trip may meet on Friday)

 

 

 

 

 

10/7

Exam 1

 

 

8

10/12

Mineral Structures(Dr. Matyjasik)

TBA

Bioinformatics Assignment Due

 

10/12L

Halophile Labs, Media Prep for Groundwater labs

 

 

 

10/14

Mineral Structures (Dr. Matyjasik)

TBA

 

9

10/19

Groundwater well field trip and experiment set up

 

 

 

10/21

Mineral adsorption

3.1-3.4

 

10

10/26

Contaminant transport through porous media (e.g. soil), industrial applications

3.6-3.7

 

 

10/26L

Groundwater experiment,  Adsorption Lab

 

Extremophile Assignment Due

 

10/28

Biomineralizations - biologically induced Fe, Mn

4.1

 

11

11/2

Biominereralizations – biologically induced carbonates and silica minerals

4.1

 

 

11/2L

Atomic Force Microscopy and Scanning Electron Microscopy – Introduction, plan experiments; Finish Groundwater

 

 

 

11/4

Biologically controlled mineralization

4.2

 

12

11/9

Fossilization of microorganisms

4.3

 

 

11/9L

AFM Group 1/ Chitin Experiments

 

 

 

11/11

Exam 2

 

 

13

11/16

Microbial Weathering – surface reactivity and microbial colonization

5.1

 

 

11/16L

AFM Group 2/ Chitin Experiments

 

Groundwater Lab Report Due

 

11/18

Microbial Weathering – global climate

5.1

 

14

11/23

Microbial Weathering – Pyrite oxidation and Acid mine drainage

5.2

 

 

11/23L

SEM Group 1 /TBA

 

 

 

11/25

Microbial Corrosion

5.3

 

15

11/30

TBA

 

 

 

11/30 L

SEM Group 2/ TBA

 

 

 

12/2

Review

 

 

Final Exam