Microbiology for Environmental Engineers (3 Units)

CE503

Microbiology for Environmental Engineers (3 units)

Fall 2013

Course Description: Basic microbiology of water, air, and soil. Application of microbiology

to the practice of environmental pollution control

Instructor: Professor Mike Pirbazari (Dr. P)

Office: KAP260; Phone: (213)740-0592, Fax:(213)744-1426

E-mail:

Office Hours: To be announced

Class Time & Location:

Tuesday 6:30 to 9:10pm; KAP 141

Grading Criteria:

Midterm 15%

Final Exam 30%

2 Quizzes 10% (5% each)

Homework 15%

Term Project 20%

Class Participation 10%

-----------

100%

Schedules for Exams and Quizzes:

1st Quiz September 17, 2013

1st Midterm October 15, 2013

2nd Quiz November 12, 2013

Final Dec. 17, 2013; 7:00 to 9:00pm

Textbook:

Maier, R. M., Pepper, I. L., and Gerba, C. P. “Environmental Microbiology”, Second

Edition, Academic Press, Elsevier Inc. 2009.

Class Notes:

Pirbazari, M; "Class Notes for CE 503, Environmental Microbiology" with

Supplementary Reading Materials; adapted by Prof. M. Pirbazari, 2013.

References:

Alcamo, I. Edward; Microbiology, Wiley Publishing, Inc. 1996

Rittmann. B. E., and McCarthy, P.L., Environmental Biotechnology: principles and

applications, McGraw Hill Publishers, 2001

Students with Disabilities

Any student requesting academic accommodation based on disability is required to register with Disability Services and Programs Office (DSPO) each semester. A letter of verification for approved accommodations can be obtained from DSPO. Please be sure the letter is delivered to the instructor (or the TA) as early in semester as possible. DSPO is located in STU 301 and is open 8:30am – 5:00pm, Monday through Friday. The phone number for DSPO is (213) 740-0776. (This statement is suggested by the office of the Provost).

Academic Integrity

The use of unauthorized material, communication with fellow students during an examination, attempting to benefit from the work of another student, and similar behavior that defeats the intent of an examination or other class work is unacceptable to the University. It is often difficult to distinguish between a culpable act and inadvertent behavior resulting from the nervous tension accompanying examinations. When the professor determines that a violation has occurred, appropriate action, as determined by the instructor, will be taken.

Although working together is encouraged, all work claimed as yours must in fact be your own effort. Students who plagiarize the work of other students will receive zero points and possibly be referred to Student Judicial Affairs and Community Standards (SJACS).

All students should read, understand, and abide by the University Student Conduct Code listed in SCampus, and available at:http://web-app.usc.edu/scampus/university-student-conduct-code/

CE 503

Microbiology for Environmental Engineers

Fall 2013

Collaborative Learning Strategy:

During the class we will be practicing the important concepts and skills of

collaborative learning in small group of three or four students. The strategy is

designed to increase you mastery of the course content. You will be expected to

actively participate in an effort to ensure your own and your “team-mates”

understanding of the ideas presented in the class. We need your commitment to

demonstrate willingness to contribute ideas, listen to others, and to be a constructive

force in the learning process.

Course Syllabus

I- Review of Basic Microbiological Concepts (1 week)

· Classification of Organisms

- Eubacteria

- The Archaea

- Fungi

- Slime Molds

- Protozoa

- Algae

- Viruses

- Other Biological Entities

II- Microbial Environments (3 weeks)

1- Soil Environment

· Soil Architecture and Characteristics

- Clay, silt, sand, etc.

- Size fractionation of soil constituent

- Soil cation-exchange capacity

- Soil pH

- Soil atmosphere

- Soil as a microbial environment

· Microorganisms in Surface Soil

- Bacteria

- Actinomycetes

- Fungi

- Algae

- Protozoa

· Microorganisms in Subsurface Soil

· Microorganisms in Shallow Subsurface Environment

· Microorganisms in Deep Subsurface Environment

2- Air Environment

· Important Airborne Pathogens

· Important Airborne Toxics

· Aeromicrobiological Pathways

- Launching

- Transport

- Deposition

· Microbial Survival in Air

· Bioaerosol Control

3 - Aquatic Environments

· Planktonic Environment

· Benthic Habitat

· Microbial Mats

· Biofilm

· Freshwater Environments

- Springs

- Rivers and Streams

- Lakes

- Microbial Characteristics

· Brackish Water

· Marine Water

- Microbial characteristics

III- Bacteria Growth (2 week)

Growth in Pure Culture in a Batch Reactor

- The Lag Phase

- The Exponential Phase

- The Stationary Phase

- The Death Phase

- Monod Equation

Continuous Culture in a Chemostat

Growth in the Environment

IV- Microscopic Techniques (1 week)

Visible Microscopy

Fluorescence Microscopy

Electron Microscopy

Scanning Probe Microscopy

V- Electron Transfer Chain (1 week)

· Overview

· Electron Donors

· Dehydrogenases

· Quinone Carriers

· Proton Pumps

· Cytochrome Electron Carriers

· Terminal Oxidases and Reductases

· Electron Acceptors

VI- Enzymes (1 week)

· Structure and Classification of Enzymes

· Mechanism of Enzyme reaction

· Environmental Effect on Enzyme Activity

· Enzyme inhibition

· Enzyme at a Glance

VII- Nucleic Acid-Based Methods of Analysis (2 weeks)

· Structure of Nucleic Acids

· Obtaining Microbial Nucleic Acid from the Environment

· Gene Probes and Probing

· Polymerase Chain reaction (PCR)

· Recombinant DNA Techniques

· Denaturing/Temperature Gradient Gel Electrophoreses (DGGE/TGGE)

VIII- Remediation of Organic and Metal Pollutants (2 weeks)

· Microorganisms and Organic Pollutants

- Contaminant Structure, Toxicity and Biodegradability

- Environmental Factors Affecting Biodegradation

- Biodegradation of Organic Pollutants

- Bioremediation

· Microorganisms and Metal Pollutants

- Metals in the Environment

- The Essential Metals

- The Toxic Metals

- The Nontoxic Nonessential Metals

- Metal Solubility, Bioavailability, and Speciation

- Metal Chemistry

v Cation Exchange Capacity

v Redox Potential

v pH

- Metal Toxicity Effects on Microbial Cell

- Mechanisms of Microbial Metal Resistance and Detoxification

XI- Remediation and Biotechnology Case Studies (1 week)

· Biofiltration of Industrial Gas Emissions

· Bioremediation of Soil Contaminated with Petroleum Hydrocarbons

· Biomembrane Treatment of Water for Reclamation and Reuse

CE 503

Microbiology for Environmental Engineers

Fall 2013

Term Project

Each student group will be required to present a term project, which will constitute 25% of the semester grade. A list of suggested topics is provided below. Students are required to submit a choice of topic by September 10, 2013.

A 25 minute Powerpoint presentation on the term project topic is mandatory. Student presentations will be made in class on Dec. 3rd , 2013. A sign up sheet will be passed around in class Nov. 26th, 2012.