Microbes in the Wild: Environmental Microbiology Lab - EEB 401
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.
This fall term advanced lab course follows a 2-week field course held at the UM Biological Station (UMBS) in the second half of August. This field component includes daily field sampling and an overnight 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.
The UMBS Extension - August 12-24, 2018 (2 credits)
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. 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?”
WEEK 1: 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.
WEEK 2: 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).
This course runs August 12-24, 2018, but students will enroll for fall term credit. While students are financially responsible for these credits, they may not have to pay additional tuition if their total credits are within 12-18 hours. Students taking fewer than 12 or more than 18 credit hours will be assessed fees on those credits. Students will live at the Biological Station for the duration of the course. Their room and board is covered by a grant from the UM Provost’s Office.
Fall Term Campus Course (3 credits)
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.