Electives – Microbial Methods in Ecology


Collecting soil for Winogradsky Columns, 2010. Credit: Melissa Campbell

The usual methods of microbiology were developed to study microbes affecting human health (Lynch and Hobbie 1988). When these methods are used for field studies they have many problems; to begin with, less than one percent of the bacteria found in a sample of ocean water will grow on laboratory petri plates. Recent methodological advances, such as the application of fluorescently-labeled immunochemical or nucleic acid probes, provide a new way to taxonomically identify individual cells in the mixed populations of soils and waters. Yet, the application of these methods is limited to the detection of physiologically active cells with a large number of ribosomes, a rare occurrence in nature. Despite these and other problems, ecological microbiologists have developed a number of methods for enhancing our ability to measure the activities, abundances, and types of microbes found in soils, waters, and sediments of natural systems (e.g., the methods book of Kemp et al. 1993).

In this course, we will present the scientific rationale behind a number of methods suitable for determining the role of microbes in ecosystems. The methods will be described and students will carry out the procedures in a series of hands-on laboratories. One theme will be choosing methods and temporal and spatial scales appropriate to the question being asked (e.g., the review by Pearl and Pinckney 1996). The course will be taught, under the leadership of Joseph Vallino, in collaboration with scientists from the Ecosystems Center, the permanent staff of the Marine Biological Laboratory, and other Woods Hole institutions.


2016 SES student collects pink berries for microbial analysis. Credit: Joe Vallino

2016 SES student collects pink berry bacterial aggregates for microbial analysis. Credit: Joe Vallino

Lectures will describe the biology and logic that underlie the various methods used by microbial ecologists. In the laboratory, students will work with the latest techniques to measure microbial biomass, activity, extracellular enzymes, biogeochemistry and species diversity. These include epifluorescence microscopy, radioisotopic tracers for bacterial production, fluorescent substrates, hydrogen sulfide and methane production, and molecular probes for classes of bacteria. Students will be required to turn in answers and calculations to problem sets that are associated with each lab topic. These problem sets will form the basis of the grade. In addition, students will be asked to present their laboratory results and participate in group discussions on the findings by the entire class. Students will be encouraged to use the methods developed in this course for their individual research projects associated with the SES course.



For more information go to the Microbial Methods in Ecology website.

2019 Syllabus

Winogradsky Column Credit: Joe Vallino

Winogradsky Column Credit: Joe Vallino

Session 1: Introduction
Session 2: Construct Winogradsky Column: field trip to Little Sippewisset Marsh
Session 3: Bacterial Abundance: prepare dilution and coliform plates, fix samples for direct DAPI counts
Session 4: Bacterial Abundance: DAPI staining and counts; examine plates
Session 5: Bacterial Production: lecture on bacterial production method; count dilution plates
Session 6: Bacterial Production: measure bacterial production using C14
Session 7: Bacterial Production: 14C activity results, scintillation counter demonstration, explain calculations
Session 8: Extracellular Enzyme Assays: lecture on extracellular enzymes and fluorometry
Session 9: Extracellular Enzyme Assays: measure enzyme activities
Session 10: Chemolithotrophy: lecture on Winogradsky column, column observations
Session 11: Chemolithotrophy: measure hydrogen sulfide profiles in columns
Session 12: Chemolithotrophy: measure methane gradient in columns
Session 13: Microbial Food Webs: lecture on flagellate and ciliate grazing on bacteria
Session 14: Microbial Food Webs: lab on bacterial grazing with fluorescent beads
Session 15: Molecular Techniques: lab on DNA extraction
Session 16: Molecular Techniques: lab on electrophoresis and PCR
Session 17: Molecular Techniques: lecture on Molecular methods
Session 18: Microbial Food Webs: lecture on bacterial phytoplankton competition
Session 19: Microbial Food Webs: microcosm start-up and sample microcosm
Session 20: Microbial Food Webs: sample microcosm
Session 21: Microbial Food Webs: sample microcosm
Session 22: Microbial Food Webs: sample microcosm
Session 23: Microbial Food Webs: sample microcosm, analyze samples
Session 24: Microbial Food Webs: analyze microcosm samples
Session 25: Microbial Food Webs: present and discuss microcosm results and calculations
Session 26: Microbial Food Webs: bacteria phytoplankton competition