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BEE 6570

Mixed-Culture Engineered Systems: Bioenergy and Microbial Ecology


Instructor of record.  Lars Angenent, Ph. D.

Department of Biological and Environmental Engineering

Phone: 607-255-2480; E-mail: la249 [at]

Office: 214 Riley-Robb Hall

Course Webpage.

Credits.  3

Time of Class.               Lectures: Tuesdays and Thursdays from 10:10 - 11:25 am

Location of Class.          Room 105, Riley-Robb Hall


  • Lars Angenent (214 RR, 5-2480, la249 [at]
  • Jeff Werner (jjw58 [at]


  • Elliot Friedman (esf59 [at]

Office Hours: Setup a meeting with me via e-mail or during the lecture.

Pre-requisite.  Be a graduate student.

Course Description. During this course, we will perform an in-depth analysis of classic or the latest peer-reviewed publications that describe undefined mixed cultures in engineered systems.  We will especially discuss different organic waste treatment options, such as anaerobic digestion, aerobic digestion, composting, bioelectrochemical systems (such as microbial fuel cells), and carboxylic-acid fermentation systems.  After reading about more classical techniques, we will focus on the latest and most powerful molecular biology techniques (e.g., 16S rRNA gene surveys, metagenomics, proteomics, metatranscriptomics) and how statistics can inform us about community structure-function relationships.  Some bioinformatic and microbial ecology tools will also be discussed and used.  After completing this course, you should be able to critically read and evaluate scientific papers that show results obtained with molecular techniques from engineered systems.  More specifically, you should be able to know the limitations of the utilized techniques and be able to give other techniques that may complement or improve the knowledge gained from the study.

Required Text.  No textbook required, research papers and reviews will be posted as password-protected pdf files on the course web page.  The instructor will give the password to you during the first lecture.  You are expected to read the posted paper before coming to class, your involvement in discussing the paper is necessary and this will determine for the largest part your grade.  Some helpful books to lookup information relevant to this course:

  • Brock Biology of Microorganisms, tenth edition, Madigan, Martinko, and Parker, Prentice Hall, Pearson Education, Inc. Upper Saddle River, NJ.
  • Analysis of Genes and Genomes, John Wiley and Sons, Ltd, Chichester, West Sussex, England.
  • Environmental Molecular Microbiology: Protocols and Applications. Edited by Paul A. Rochelle, Horizon Press, Norfolk, England.
  • Molecular Biotechnology: Principles and Applications of Recombinant DNA, third edition.  Glick and Pasternack, ASM Press, Washington, DC.
  • Microbial Genetics, David Freifelder, Jones and Bartlett Publishers, Boston, MA (1987).

Phylogeny Projects.  Two phylogeny projects will be performed with small groups of students.  The result will be a phylogenetic (evolutionary relationships) tree with additional text describing how the tree was obtained (approximately 1-page description).  This description will be performed in a format that is similar to a materials and methods section of a peer-reviewed paper.

Teaching of a Molecular Technique + Term Paper.  You will teach a lecture about a Molecular Technique for 30-45 minutes and will then discuss a research paper.  First the basic mechanisms of the technique need to be taught and subsequently a peer-reviewed paper will be discussed.  The student is expected to choose a paper that uses a molecular technique to solve an engineering-related problem that uses an undefined mixed culture; if the technique is exciting and can be translated, we can be flexible on this.  A 5-page, single space term paper needs to be handed in before the lecture starts.  This term paper needs to summarize, discuss, and critically evaluate the chosen peer-reviewed research paper.  For example, the limitations of the utilized molecular technique needs to be assessed and other techniques that may complement or improve the knowledge gained from the study may be discussed.


Phylogeny Projects:                                                    30% (10% of grade per project part)

Teaching of Molecular Technique + Term Paper:      30%

Class Participation and Professional Evaluation        40%

Students agree that by taking this course all required papers may be subject to submission for textual similarity review to for the detection of plagiarism. All submitted papers will be included as source documents in the reference database solely for the purpose of detecting plagiarism of such papers. Use of service is subject to the Usage Policy posted on the site.


Except when explicitly told otherwise, you are expected to work independently.  Plagiarizing from either the primary literature (by copying and pasting text) or from another student (or from yourself from a previous course) will result in a failing grade, or, in more egregious cases, an appearance before the Academic Integrity Committee.  For example, cheating on an exam will result in an immediate failing grade for the exam, an appearance before the Academic Integrity Committee, and potentially a failing grade for the course.  We do not have an exam, but here your five-page paper and the discussion of the method must be executed according to the above rules.

Academic Integrity.  Each student in this course is expected to abide by the Cornell University Code of Academic Integrity.  Students must in no way misrepresent their work, fraudulently or unfairly advance their academic status, or be a party to another student's failure to maintain academic integrity.  A full statement of this code may be found at:

Accommodations for Students with Disabilities.  In compliance with the Cornell University policy and equal access laws, Lars Angenent is available to discuss appropriate academic accommodations that may be required for student with disabilities. Except for unusual circumstances, requests for academic accommodations must be made during the first three weeks of the semester so that appropriate arrangements can be made.  Students are encouraged to register with Student Disability Services to verify their eligibility for appropriate accommodations.