University of Florida

ABE 5663
Applied Microbial Biotechnology

Semester Taught - Spring

Catalog Description

Credits: 3

The course will focus on quantification of microbial growth and microbially mediated degradation and transformation processes emphasizing the application of these tools to develop mathematical models for industrial processes for pollution control, waste treatment, biofuel and bioproducts production and bioremediation.


Bioprocess Engineering

Course Objectives

  • develop concepts and mathematical tools required to understand and analyze microbial growth, and microbially mediated  degradation and transformation processes,
  • quantify and analyze bioreactor operation and performance through mathematical process modeling and simulation,
  • learn about some industrially important bioprocesses used for waste treatment, biofuel production and bioremediation,
  • construct mathematical process models to simulate operation of these bioprocesses. 


Pratap Pullammanappillil
Office - 203 Frazier Rogers Hall
Telephone (352) 392-1864 x203
E-mail address:

Material/Supply Fees


Class Materials Required

There is no required textbook.  Material will be covered from original research papers and from the following books:

  1. Rittmann, B. E. and McCarty, P. L.  2001.  Environmental Biotechnology: Principles and Applications,  McGraw Hill, New York.
  2. Biochemical Engineering, Bailey and Ollis, 1986, McGraw Hill
  3. Bu'lock, J. and Kristiansen, B., eds.  1997.  Basic Biotechnology, Academic Press, New York.

Lecture notes will be handed out.

Course Outline

  • Introduction
  • Stoichiometry and energetics
  • Phenomenological models
  • Mechanistic models
  • Structured models
  • Mixed culture interactions
  • Mixed product fermentation and mixed substrate utilization
  • Attached growth
  • Mathematical modeling of suspended growth and attached growth bioreactors
  • Case studies (Anaerobic digestion, Activated sludge process, Composting, Phototrophic processes, Microbial corrosion, Microbial Fuel Cells, Bioremediation)


Grades will be based upon field trip reports, homework problems, and class participation.

A 91-100
A- 86-90
B+ 81-85
B 76-80
B- 71-75
C+ 66-70
C 61-65
C- 56-60
D+ 51-55
D 46-50
D- 40-45
E <40
Grading Method Percentage
Homework 50%
Exam 20%
Project 30%

Attendance and Expectations: Attendance is expected at all lectures. It is expected that students will have knowledge and access to a numerical analysis software package. Homework is due within one week of when assigned or as indicated.

Make-up Exam Policy:  No make-up exams will be given except for valid medical reasons or unless prior arrangements have been made.

Academic Honesty

As a student at the University of Florida, you have committed yourself to uphold the Honor Code, which includes the following pledge: “We, the members of the University of Florida community, pledge to hold ourselves and our peers to the highest standards of honesty and integrity.”  You are expected to exhibit behavior consistent with this commitment to the UF academic community, and on all work submitted for credit at the University of Florida, the following pledge is either required or implied: "On my honor, I have neither given nor received unauthorized aid in doing this assignment." 
It is assumed that you will complete all work independently in each course unless the instructor provides explicit permission for you to collaborate on course tasks (e.g. assignments, papers, quizzes, exams). Furthermore, as part of your obligation to uphold the Honor Code, you should report any condition that facilitates academic misconduct to appropriate personnel. It is your individual responsibility to know and comply with all university policies and procedures regarding academic integrity and the Student Honor Code.  Violations of the Honor Code at the University of Florida will not be tolerated. Violations will be reported to the Dean of Students Office for consideration of disciplinary action. For more information regarding the Student Honor Code, please see:  

UF Counseling Services

Resources are available on-campus for students having personal problems or lacking clear career and academic goals which interfere with their academic performance. These resources include:

  1. University Counseling Center, 301 Peabody Hall, 392-1575, personal and career counseling;
  2. Student Mental Health, Student Health Care Center, 392-1171, personal counseling;
  3. Center for Sexual Assault/Abuse Recovery and Education (CARE), Student Health Care Center, 392-1161, sexual assault counseling;
  4. Career Resource Center, Reitz Union, 392-1601, career development assistance and counseling.