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Microbes in the Wild: Environmental Microbiology Lab - EEB 401

The Class

Advancement in microbial sciences has been tightly coupled with technological innovation since the discovery of microbial life by Antonie van Leeuwenhoek in the 1670s using a self-made microscope.

This relationship holds today, as we are swept into a “big data fast” era, whereby novel microorganisms, metabolisms, life histories, and interactions are described at an increasing rate using advanced technologies. Yet, there is a need for microbiologists to simultaneously master classical approaches to culturing and observation.

In the lecture component of this course, you will learn the theory behind classical and state-of-the-art techniques used to study the ecology and evolution of microorganisms.

In the laboratory, your project development and hypothesis testing will drive the application of methods, which may include: advanced microscopy, culturing to target specific metabolisms, functional diversity descriptions, isolation and identification of microbes and their viruses, analysis of sequence data to study microbial community ecology (e.g., 16S rRNA gene sequencing) and genomics of viral isolates.

You will master skills needed to (i) build your microbial methods tool-set to develop deeper and more specific questions and hypotheses, and (ii) increase competitiveness for future academic and professional pursuits in environmental, human, and public health sciences, engineering, and sustainability sciences.

Note: This fall term advanced lab course will follow a 2-week field course held at the UM Biological Station (UMBS) in the second half of August that will include an overnight field expedition on a research vessel in the Great Lakes. The fall term will focus on the analysis of student projects developed at UMBS. These two courses are designed to be taken in sequence, but if needed can be taken independently.






Credits: 3

Meets: Fall Semester (September 5 - December 21, 2017)

Location: U-M Ann Arbor Campus

Instructor: Melissa Duhaime

The Extension

This project-based course extension will emulate how scientists study environmental microbes in the context of real-world sustainability issues in Northern Michigan—while making novel scientific contributions.

For the Biological Station (UMBS) segment of the course, you will gain exposure to water microbe-relevant sustainability issues in Northern Michigan. We will work with local partners (wastershed councils, managers, citizen science groups) to answer: “What are the real world issues?”

Simultaneously, you will master microbiological concepts and skills needed for field sample collection and analysis, answering: “How could we rigorously address those issues?”


The first week will be devoted to project development: hypothesis generation and study design.

Between the first and second weeks, you will spend two nights on Lake Michigan in a tall-masted schooner to learn how to work on a research vessel, sampling equipment and collection, navigation, and the science of regional ecosystem monitoring programs.


The second week will be devoted to student project development, continued sample collection as needed, data analysis, and preserving the projects until the on-campus course component begins.

You will master: field sampling techniques for the collection of microbes and their viruses in both the water column and sediment, fluorescent microscopy of microbes and viruses, development of enrichment cultures targeting specific microbial metabolisms, isolation of environmental microbes and viruses, nucleic acids extractions, and concepts of community genomics (actual analysis to be performed in fall term on campus).

Note: The course extension will take August 14-25, 2017. Most students will enroll for the 2-credit extension in the Fall 2017 semester. However, students for whom the additional fall extension credits will result in increased tuition should contact the instructor or the Program in Biology to discuss other registration options. The extension should not cost extra tuition for any participants.




Copyright Dennis Kunkel Microscopy, Inc. PHAGES IN ACTION.




Credits: 2

Meets: August 14-25, 2017

Location: U-M Biological Station

Instructor: Melissa Duhaime