Instructor: Jeffrey Marlow


Microorganisms are the most abundant form of life in the ocean. From the sun-drenched surface waters to the dark abyssal plains, microbes play essential roles in recycling nutrients, supporting higher trophic levels, and absorbing climate and environmental changes. In recent years, scientists have discovered a stunning array of new microbial life thanks to rapidly advancing DNA sequencing technology. However, high-throughput sequencing often lacks quantitative replicability, and by sacrificing spatial arrangements, key symbioses or other microbial interactions are easily missed. Fluorescence in situ hybridization (FISH) is a critical tool in any microbiologist’s repertoire that uses sequencing as a springboard to develop a deeper sense of specific species’ roles in an ecosystem. The technique introduces fluorescent oligonucleotide probes that bind with target organisms and can be seen under the microscope. By visualizing distinct lineages with strategically designed fluorescent probes, a more quantitative understanding of abundance and potential inter-species relationships is possible.

This project-based course will introduce upper-level undergraduate and graduate students to a range of FISH techniques and the research questions they can address, unfolding key topics of molecular biology, microbial ecology, and microscopy in the process. By focusing on microorganisms found in local salt marsh sediments, students will contribute new primary data to a marine ecosystem on the front lines of climate change.