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Biology 355 - Microbial Ecology

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Welcome to BIO387B (Bio355) Microbial Ecology

I look forward to sharing this fascinating topic with you over the next semester. In the meantime, here is some helpful background.

Course Format

We will meet MWF from 10:00 - 10:50 AM in Hudson 209. Please refer to the course calendar for weekly topics. We will discuss and introduce general concepts for each topic on Monday and Wednesday, with an emphasis on group discussion and current readings. On Fridays, we will delve into scientific papers related to each topic and examine applications and research as well as case studies.

Course Grading

We will have a weekly quiz on Mondays (except for exam days) worth 10 points, generally asking 2 questions pertaining to material discussed in class the week before. Quizzes cannot be made up. Your best 10 quiz grades will be counted.

We will have 3 in-class exams (see calendar), each on a Monday. Exams cover topics discussed during the previous 4-5 weeks. Exams are 100 points each and include short-answer, multiple choice and case study questions.

You will also submit a term paper worth 100 points at the end of the semester. Papers should be 3000 words in length and cover a topic related to Microbial Ecology.


Book chapters are assigned as according to the class calendar. Please read each chapter before Monday's class. Additional reading assignments will be posted for each week, to be discussed in class.

Tentative outline of topics

I.        The nature of microorganisms

A.     Diversity of microbes

1.       Bacteria

2.       Archaea

3.       Viruses

4.       Protists

5.       Fungi

B.      Microbial structure

C.      Microbial metabolism and its effects

II.      Methods of studying microbial ecology

A.     Identification of microbes

1.       Culture methods

2.       Microscopy

3.       Genomics, proteomics, metabolomics

B.      Measures of abundance and diversity

III.   Interactions between microbes and other organisms

A.     Types of interactions between microbes

1.       Commensalism

2.       Mutualism

3.       Parasitism

4.       Amensalism

5.       Syntrophism

6.       Competition

7.       Predation

B.      Microbe-plant interactions

1.       Mycorrhizae

2.       Root nodules

3.       Hormone production

4.       Surface biomes

5.       Parasites and pathogens

C.      Microbe-animal interactions

1.       Parasitism

2.       Pathogenesis

3.       Mutualistic associations

(1)    Gut microbes

(2)    Tube worm symbioses

(3)    Bioluminescence

IV.   Community structure and interactions

A.     Types and composition of communities

1.       Soil

2.       Aquatic

(1)    Fresh water

(2)    Saline

3.       Rock/subsurface

4.       Atmospheric

B.      Measuring community structure

C.      Quorum sensing and communication

D.     Biofilms and biomats

V.     Microbes and Geochemical cycling

A.     Nitrogen cycle

B.      Sulfur cycle

C.      Metal cycling

D.     Carbon cycle

VI.   Biomineralization and decomposition

A.     Ores, silicates, metal deposits

B.      Wood and cellulose

C.      Bionutrients & fermentation

D.     Waste water treatment


A.     Hydrocarbons

B.      Xenobiotics

      C.   Inorganics


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