Course Overview
Microbial Ecology and Diversity
11:680:491
Fall Semester
Meeting times: Mondays and Wednesdays 5:35–6:50 p.m.
Meeting Location TBD
Contact Information
Instructor: Costa Vetriani
848-932-3379
vetriani@marine.rutgers.edu
Office Hours: Upon request
Course Website, Resources, and Materials
- Text books:
- Madigan, Bender, Buckley, Sattley, and Stahl, Brock Biology of Microorganisms, 16th Edition, Pearson, NJ
- Maier, Pepper, and Gerba, Environmental Microbiology, 2nd edition 2009, Academic Press, San Diego.
Course Description
The course introduces the students to the enormous taxonomic, metabolic and ecological diversity of microorganisms on Earth. The course is organized in three sections of approximately equal proportion:
- Microbial diversity in which we “climb” the tree of life by first considering how life on Earth started and how it has evolved to the enormous diversity that we see now among the Bacteria, Archaea, and the microbial Eukarya and their viruses;
- Metabolic diversity in which we consider the magnificent diversity of the reactions that are carried out by microorganisms as revealed to us through various element cycles on Earth;
- Ecosystem diversity in which we describe how microbes live in communities and engage in interactions with each other, with plants and animals, and with their environments. We consider the uniqueness of microbial life in ecosystems and highlight the role of microbes in sustaining homeostasis on Earth;
Throughout the course we stress the importance of the processes that are discussed in class to human wellbeing and environmental sustainability. Grading consists of 3 midterm exams, a term paper, and class participation.
Learning Goals
- Graduates will gain a broad knowledge of the biology of microorganisms focusing on microbial processes and their effects on other organisms and the environment, microbial communities and biogeochemical cycles. Learning outcomes:
Graduates will be able to:- Appreciate the diversity of microorganisms and microbial communities and recognize how microorganisms solve the fundamental problems their environments present.
- Examine the impact of microbes on the biosphere.
- Graduates will be critical thinkers with effective written and oral communication skills; well prepared for positions in industry, government and graduate/professional study.
Learning outcomes:
Graduates will be able to:- Demonstrate the ability to communicate scientific information in writing.
- Demonstrate the ability to communicate orally in a clear, coherent and effective manner.
- Graduates will have a fundamental understanding of ethical and current issues in microbiology and appreciate a code of ethics for microbiologists including ethical conduct, scientific integrity and the dignity of the profession and practice of microbiology.
Leaning outcomes:- Evaluate the ethical implications of scientific issues in society.
Assignments/Responsibilities, Grading, and Assessment
Students are required to take three midterm exams and to submit a term paper on a topic related to the course. Each midterm exam consists of 8 short assay question which are graded by course instuctors. A draft term paper is reviewed and commented on by course instructors prior to final submission.
The first and second midterm exams constitute 50% of the final grade, the third which covers more material, 30%, the term paper 15% and class participation (presence and active contribution), 5%.
Accomodations for Students with Disabilities
Please follow the procedures outlined at ods.rutgers.edu/students/registration-form. Full policies and procedures are at ods.rutgers.edu.
Absence Policy
Students are expected to participate in all classes with the exception of emergencies such as health and family issues or in case of acceptional educational opportunities. An e-mail notification to the instructors should be submitted, if possibly, ahead of class time.
Course Schedule
|
Lec |
Topic | Instructor |
|---|---|---|---|
Introduction and microbial diversity |
1 |
Introduction and historical perspectives |
Barkay & Vetriani |
2 |
Origins of life |
Vetriani |
|
3 |
Microbial evolution |
Vetriani |
|
4 |
The prokaryotes (Bacteria and Archaea) |
Barkay |
|
5 |
Microbial Eukaryotes |
Barkay |
|
6 |
Viruses in microbial ecology |
Barkay |
|
7 |
Methods in microbial ecology |
Vetriani |
|
8 |
Microbial genetics and horizontal gene transfer |
Vetriani |
|
Metabolic diversity |
9 |
Modes of microbial metabolism in the environment |
Vetriani |
|
1st midterm (Lectures 1-8) |
|
|
10 |
The carbon cycle |
Barkay |
|
11 |
The nitrogen and sulfur cycles |
Vetriani |
|
12 |
Microbe-metal interactions |
Barkay |
|
13 |
Bioremediation |
Marinucci |
|
14 |
Cycles and humans |
Barkay |
|
Microbial interactions and ecosystems |
15 |
Microbe-animal interaction |
Vetriani |
16 |
Microbe-plant interactions |
Barkay |
|
|
2nd midterm (Lectures 9-16) |
|
|
17 |
Hydrothermal vent microbiology |
Vetriani |
|
18 |
-Omics approaches in microbial ecology |
Vetriani |
|
19 |
Microbiome and nutrition |
Zhao |
|
20 |
Microbiome and development |
Dominguez- Bello |
|
21 |
Microbial communities and ecosystems |
Barkay |
|
|
Thanksgiving recess |
|
|
22 |
Terrestrial environments |
Barkay |
|
23 |
Aquatic environments |
Vetriani |
|
24 |
Abiotic factors and life in extreme environments |
Barkay |
|
|
3rd exam (Lectures 17-24) |
|
Final Exam/Paper Date and Time
Online Final exam Schedule: finalexams.rutgers.edu
Academic Integrity
Read the university's policy on Academic Integrity . The principles of academic integrity require that a student:
- properly acknowledge and cite all use of the ideas, results, or words of others.
- properly acknowledge all contributors to a given piece of work.
- make sure that all work submitted as his or her own in a course or other academic activity is produced without the aid of impermissible materials or impermissible collaboration.
- obtain all data or results by ethical means and report them accurately without suppressing any results inconsistent with his or her interpretation or conclusions.
- treat all other students in an ethical manner, respecting their integrity and right to pursue their educational goals without interference. This requires that a student neither facilitate academic dishonesty by others nor obstruct their academic progress.
- uphold the canons of the ethical or professional code of the profession for which he or she is preparing.
Adherence to these principles is necessary in order to ensure that:
- everyone is given proper credit for his or her ideas, words, results, and other scholarly accomplishments.
- all student work is fairly evaluated and no student has an inappropriate advantage over others.
- the academic and ethical development of all students is fostered.
- the reputation of the University for integrity in its teaching, research, and scholarship is maintained and enhanced.
Failure to uphold these principles of academic integrity threatens both the reputation of the University and the value of the degrees awarded to its students. Every member of the University community therefore bears a responsibility for ensuring that the highest standards of academic integrity are upheld.
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