Methods In Microbial Ecology
Instructor: Joe Vallino (MBL)
Course Description:
This course offers a hands-on exploration of the microbial world, combining rigorous lectures with intensive, practical laboratory work. Students will master key techniques used to measure microbial processes in both natural environments and controlled experiments. Lectures will establish the theoretical foundation and context for the methods. Following each module's lecture, students will immediately execute the techniques in the lab, analyzing samples drawn from:
- Winogradsky columns that students construct early in the course.
- Samples collected during field excursions to nearby sites.
Learning Objectives and Outcomes
Upon completion of this intensive 3-week course, students will possess the necessary knowledge and technical expertise to independently use these methods for laboratory or field-based research. With a strong grasp of the underlying theories, students will be prepared to critically evaluate, modify, and extend these methods for novel applications in microbial ecology research.
Course Structure
The course is organized into focused two- or three-day modules, each integrating lecture and lab work on the following key topics:
- Fundamentals and Setup: Introduction to microbial ecology methods, construction of Winogradsky columns, and introduction to microscopy.
- Counting and Growth: Measuring bacterial biomass using direct counts (epifluorescence microscopy) and traditional bacterial growth on Petri plates.
- Rate Measurements: Estimating bacterial growth rates using radiolabeled metabolites (14C).
- Enzyme Activity: Assessment of extracellular enzyme activities using fluorogenic substrates.
- Biogeochemical Cycling: Exploration of biogeochemistry and redox chemistry of chemolithoautotrophs and other novel prokaryote metabolisms.
- Microbial Food Webs: Measuring bacterial predation rates by protists using fluorescently labeled particles.
- Community Dynamics: Using microcosms to study phytoplankton and bacterial competition and an introduction to time-series data analysis.
- Molecular Tools: Introduction to molecular techniques via Polymerase Chain Reaction (PCR) targeting key functional genes (methanogenesis, sulfate reduction).
Grading
95% Problem sets
5% Participation