HomeMy WebLinkAboutBIO-224 1
Bergen Community College
Division of Mathematics, Science, and Technology
Department of Biology and Horticulture
Environmental Microbiology (BIO-224)
General Course Syllabus
Spring2016
Course Title: BIO 224 Environmental Microbiology
Course Description: This is a course concerning bacteria and other microorganisms and their role in
the environment. Topics will include an introduction to the main groups of
microorganisms and their physiology, soil microbiology, cycles of elements,
aquatic microbiology, sewage treatment, bioremediation, and applied
microbiology encompassing food microbiology, industrial microbiology, and
biotechnology.
Prerequisites: BIO 101 General Biology I, BIO 203 General Biology II
General Ed Course: No
Course Credit: 4.0
Hours per week: 6.0: 3 hours lecture and 3 hours lab
Course Coordinator: Luis Jimenez
Required Lecture
Textbook:
Environmental Microbiology, 3rd Edition, (Pepper, Gerba, Gentry), Academic
Press. Philadelphia, Pennsylvania, ISBN: 978-0123946263
Supplementary Text:
(Optional)
Brock Biology of Microorganisms, 13th Edition, (Madigan,Martinko, Stahl, Clark),
Benjamin Cummings Publishers, Upper Saddle River, New Jersey, ISBN: 978-
0321649638.
Required Laboratory
Manual:
Environmental Microbiology, A Laboratory Manual, 2nd ed., (Pepper, Gerba, and
Brendecke), Academic Press. Philadelphia, Pennsylvania, ISBN: 978-
0125506564
Supplementary
Manual:
(Optional)
Microbiology Lab Manual, 2nd ed., (Bablanian and Payne), Kendall-Hunt, ISBN:
978-0-7575-5789-7.
Laboratory Materials: Students must wear protective eye wear and should purchase latex gloves and
laboratory coats.
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Student Learning Objectives:
The student will be able to:
1. Students will learn the major principles of environmental microbiology and the relationship of
microbes to environmental processes and other living organisms. Assessment will be based
upon performance on exam questions. Assessment can also be based on research
papers/projects.
2. Students will demonstrate proper scientific procedure to identify various type of environmental
microbes. Students will be evaluated by observation in the laboratory and analysis of unknown
bacteria and projects. Assessment will also be based upon performance on exam question and
laboratory projects.
3. Students will be able to explain the scientific basis for each technique used. Students will be
required to answer exam questions designed to allow them to demonstrate their acquisition and
retention of this knowledge.
4. Students will demonstrate proper scientific laboratory record keeping. Students will be
evaluated by periodic notebook collection.
5. Students will learn to practice critical thinking skills and apply them to both material presented in
lecture and the analysis of data generated in the laboratory. Students will be evaluated by
observation in the laboratory and analysis of experimental results. Assessment will also be
based upon performance on exam questions.
6. Students will use the scientific method of inquiry, through the acquisition of scientific knowledge.
7. Students will use computer systems or other appropriate forms of technology to achieve
educational and personal goals.
Student Assessment Tools:
The above student learning objectives will be generally assessed or evaluated by instructors using a variety of
assessment instruments including lecture exams, laboratory exams, quizzes, laboratory reports, written reports,
presentations, projects, etc. The decisions concerning the type or types and number of instruments that are used in a
specific section of the course will be left to the instructor of that section. This information, when given by the instructo r
should be recorded by the student in the Student Assessment Section of this document.
Course Content
Lecture Topics:
Chapter Title Text: Environmental Microbiology, 3rd Edition,
Week 1
Chapter 1 Introduction to Environmental Microbiology
A. Environmental Microbiology as a Discipline.
B. Microbial Influences on our Daily Lives.
Chapter 2 Microorganisms Found in the Environment
A. Classification of Organisms.
B. Prokaryotes.
C. Eukaryotes.
D. Viruses.
E. Other Biological Entities.
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Week 2
Chapter 3 Bacterial Growth
A. Growth in Pure Cultures in a Flask.
B. Continuous Cultures.
C. Growth in the Environment.
Week 3
Chapter 4 Earth Environments
A. Earth’s Living Skin.
B. Physiochemical Characteristics of the Earth Environment.
C. Soil as a Microbial Environment.
D. Microorganisms in Surface Soils.
E. Distribution of Microorganisms in Soil.
F. Microorganisms in Subsurface Environments.
Week 4
Chapter 5 Aeromicrobiology
A. Aerosols.
B. Nature of Bioaerosols.
C. Aeromicrobiology Pathway.
D. Microbial Survival in the Air.
E. Extramural Aeromicrobiology.
F. Intramural Microbiology.
Week 5
Chapter 6 Aquatic Environments
A. Microbial Habitats in the Aquatic Environment.
B. Microbial Lifestyles in Aquatic Environments.
C. Marine Environments.
D. Freshwater Environments.
E. Other Notable Aquatic Environments.
Week 6
Chapter 7 Extreme Environments
A. Low Temperature Environments.
B. High Temperature Environments.
C. Desiccation and UV Stress.
D. Aphotic Environments Based on Chemolithoautotrophy.
Week 7
Chapter 8 Environmental Sample Collection and Processing
A. Soils and Sediments.
B. Water.
C. Air.
D. Detection of Microorganisms on Fomites.
Chapter 9 Microscopic Techniques
A. Visible Light Microscopy.
B. Fluorescence Microscopy.
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C. Electron Microscopy.
Week 8
Chapter 10 Cultural Methods
A. Extraction and Isolation Techniques.
B. Plating Methods.
C. Culture Media for Bacteria.
D. Culture Methods for Algae and Cyanobacteria.
E. Cell Culture-Based Methods for Viruses.
Chapter 11 Physiological Methods
A. Measuring Microbial Activity in Pure Culture.
B. Choosing the Appropriate Activity Measurement for Environmental Samples.
C. Carbon Respiration.
D. Incorporation of Radiolabeled Tracers into Cellular Macromolecules.
E. Adenylate Energy Charge.
F. Enzyme Assays.
Week 9
Chapter 12 Immunological Methods
A. What is an Antibody?
B. Immunoassays.
C. Immunosensors.
Chapter 13 Nucleic Acid-Based Methods
A. Structure and Complementarity of Nucleic Acids.
B. Obtaining Microbial Nucleic Acids from the Environment.
C. Hybridization-Based Assays.
D. Amplification-Based Assays.
E. DNA Fingerprinting.
F. Recombinant DNA Techniques.
G. Sequence Analysis.
Week 10
Chapter 16 Biogeochemical Cycling
A. Carbon Cycle.
B. Nitrogen Cycle.
C. Sulfur Cycle.
D. Iron Cycle.
Week 11
Chapter 17 Microorganisms and Organic Pollutants
A. The Overall Process of Biodegradation.
B. Contaminant Structure, Toxicity, and Biodegradability.
C. Environmental Factors Affecting Biodegradation.
D. Biodegradation of Organic Pollutants.
E. Bioremediation.
Chapter 18 Microorganisms and Metal Pollutants
A. Metals in the Environment.
B. Metal Solubility, Bioavailability, and Speciation.
C. Metal Effects on the Microbial Cell.
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D. Mechanisms of Microbial Metal Resistance and Detoxification.
E. Microbial Metal Transformations.
F. Microbial Approaches in the Remediation of Metal-Contaminated Environments.
Week 12 and 13
Chapter 19 Microbial Diversity and Interactions in Natural Ecosystems
A. Microbial Diversity in Natural Systems.
B. Microbial Interactions.
C. Microbial Diversity and Natural Products.
Week 14
Chapter 23 Indicator Microorganisms
A. Total Coliforms.
B. Fecal Coliforms and Escherichia coli.
C. Fecal Enterococci.
D. Clostridium perfringes.
E. Bacteroides and Bifidobacterium.
F. Heterotrophic Plate Count.
G. Bacteriophages.
Chapters 25, 28 Municipal Wastewater Treatment, Drinking Water Treatment
A. The Nature of Wastewater.
B. Conventional Wastewater Treatment.
C. Oxidation Pools.
D. Septic Tanks.
E. Wetlands Systems.
F. Sludge Processing.
Week 15 - FINAL EXAM
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Laboratory Schedule:
Week Title Text: Env. Micro., A Laboratory Manual, 2nd Ed.
1 Introduction to the Lab, Aseptic
Techniques,
Cultural Characteristics Of Bacteria,
Environmental Sampling
2 Microscopic Techniques
Prep and Care of Stock Cultures
3
Cultural and Physiological Methods
4 Soil Microbiology
5 Air Microbiology
6
Water Microbiology
7 DNA Extraction
8 Amplification of Bacterial 16S rRNA Genes
9 Amplification of Functional Microbial Genes
10
Gel Electrophoresis
11
Sequencing of Bacterial 16S rRNA and
Functional Genes
12 Composting and Thermophilic Bacteria
13 Bioremediation
14 Lab Project
15 Lab Final and Presentation
Student Assessment:
Lecture Examinations____________________ ______________%
Laboratory Component___________________ ______________%
Student Project/Report___________________ ______________%
Class Participation ______________%
Other ______________%
Total 100%
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If you have a medical condition or develop a medical condition during this semester, which prevents you from
fulfilling the requirements of this course, you must notify your physician. You and your physician must decide
whether or not it is appropriate for you to remain in this course. If the decision is to remain in this course, please
obtain a letter from your physician indicating that your continued participation in this course is appro priate and
present it to the Department Chair.
Faculty Addenda: As per individual faculty member
Lecture Attendance: As per instructor;
Lab Attendance: As per instructor;
Policy Concerning Late Assignments: As per instructor;
Policy Concerning Make-Up Testing: As per instructor;
Safety Information: As per instructor and assigned exercise;
College Policies:
Student Responsibility
Students will be held responsible for reading all pertinent information in college publication s regarding withdrawals, course
drops, college deadlines, and tuition refunds. Students are responsible for compliance with the rules and regulations as
stated in college publications.
Absence of Instructor
Students are expected to wait twenty minutes for a faculty member to come to class. If at the end of twenty minutes, the
faculty member does not come, the students should sign an attendance sheet, which indicates the course, date, and
time. A student should deliver the attendance sheet to the divisional office (A304) if between 9:00 a.m. and 5:00 p.m. or
to the Evening Office (C107) if before 9:00 a.m. or after 5:00 p.m. Students cannot be penalized by faculty for not
waiting longer than twenty minutes.
Academic Dishonesty and Plagiarism
Bergen Community College is committed to academic integrity – the honest, fair and continuing pursuit of knowledge,
free from fraud or deception. Students are responsible for their own work. Faculty and academic support services staff
will take appropriate measures to discourage academic dishonesty. Plagiarism is a form of academic dishonesty and
may be a violation of U.S. Copyright laws. Plagiarism is defined as the act of taking someone else’s words, opinions, or
ideas and claiming them as one’s own.
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Consequences of Violations Academic Integrity
A. Instructor’s Sanctions for a Violation
The faculty member will determine the course of action to be followed. This may include:
• Assigning a failing grade on the assignment;
• Assigning a lower final course grade;
• Failing the student in the course
• Other penalties appropriate to the violation;
In all cases, the instructor shall notify the Vice President of Student Services of the violation and the penalty
imposed. The student has the right to appeal the decision of the instructor to the appropriate department head.
B. Institutional Sanctions for Violations
When a violation of academic integrity has been reported regarding a student, the Vice President of Student
Services may impose disciplinary penalties beyond those imposed by the course instructor, which may include
suspension or dismissal from the College. The student shall have the right to a hearing before the Vice President of
Student Services or a designated judicial affairs committee. Judicial procedures governing violations of academic
integrity are contained in the student handbook.
Class Attendance
All students are expected to attend punctually every scheduled meeting of each course in which they are registered.
Attendance and lateness policies and sanctions a re to be determined by the instructor for each section of each course.
These will be established in writing on the individual course outline. Attendance will be kept by the instructor for
administrative and counseling purposes.
Eating and Drinking
Eating or drinking in classrooms, lecture rooms, laboratories, gymnasium, swimming pool, or passageways is forbidden.
Covered beverages only are permitted in the library. Eating and drinking are permitted in cafeteria and vending areas
only.
Learning Assistance
Henry and Edith Cerullo Learning Assistance Center
The Tutoring Center, English Language Resource Center, Math Walk -In Center and Writing Center are collectively
known as the Henry and Edith Cerullo Learning Assistance Center. The Cerullo Learning Assis tance Center is located
in the Pitkin Education Building, in Room L-125. The telephone number is (201) 447-7489. The Learning Assistance
Center, staffed with peer and professional tutors, offers free individual and group tutoring, supplemental instructio n, and
online tutoring for subjects offered at the College. The Center provides alternative approaches to problem solving and
organizational skills. Tutors help clarify classroom lectures and textbooks and help students prepare for exams. These
services build student self-confidence and reduce fear of failure. The Center is equipped with the latest technology and
software, including tapes, books, review sheets, exercises and software.
Services for Students with Disabilities
Bergen Community College aims to create inclusive learning environments where all students have maximum
opportunities for success. Any student who feels he or she may need an accommodation based on the impact of a
disability should contact the Office of Specialized Services at 201-612-5269 or via email at ossinfo@bergen.edu for
assistance.
Sidney Silverman Library
Main Building, Pitkin Education Center, L-wing, 2nd Floor.
Paramus Library Hours: (201) 447-7131 or visit http://www.bergen.edu/library/calendar/gcal.htm
Paramus Service Desk: (201) 447-7970
Meadowlands Location: 1280 Wall Street, Lyndhurst 2nd Floor
Meadowlands Library Hours: http://www.bergen.edu/library/calendar/gcal.htm
Meadowlands Service Desk: (201) 301-9692
www.bergen.edu/library
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Testing Services
The Bergen Community College Office of Testing Services (OTS) is located in Room S-127. OTS serves the college
community by identifying, developing, procuring, administering, processing, and/or evaluating examinations, which meet
a variety of administrative and instructional needs. To contact the OTS, please call (201) 447 -7202. The Office of
Testing Services administers makeup tests as a service for students who, for compelling and exceptional reasons, have
missed a scheduled classroom examination. Students must receive prior permission from and make arrangements with
their course instructors to take these examinations, under specific conditions, in the Office of Testing Services, Room S -
127.
WebAdvisor
WebAdvisor is a web interface that allows students to access information contained in Datatel’s Colleague, the
administrative database used by Bergen Community College. Students may use WebAdvisor to register for classes, to
pay tuition and fees, to view their class schedules, to check grades, to check on progress toward degree requirements,
etc. WebAdvisor accounts are available for all students enrolled in credit programs. New students are strongly
encouraged to attend an in-person registration or advisement session before using a WebAdvisor account. Eligible
students without WebAdvisor user names and passwords may access their WebAdvisor account by going to
go.bergen.edu and selecting “I’m new to WebAdvisor.” Then, follow the on-screen directions. Check the WebAdvisor
FAQ for answers to common questions, such as how to reset your password. Students must have a valid e -mail
address on file with the College to use WebAdvisor