Microbial Diversity

Course Description

Established in 1971 by Holger Jannasch, the Microbial Diversity summer course at the Marine Biological Laboratory (Woods Hole, MA) has provided advanced training for generations of early career researchers in microbiology. This intensive and transformative 6.5-week residential program trains 20 participants annually in the discovery, cultivation, and analysis of microorganisms that drive diverse biochemical and ecological processes. With roughly a 1:1 student–faculty ratio, participants receive individualized mentorship and close collaboration with leading researchers. Building on the program’s historic foundation in microbial physiology, the current directors, Drs. John R. Spear (Colorado School of Mines) and Scott C. Dawson (University of California, Davis), have expanded the curriculum to include modern genetic, biochemical, and computational approaches that advance the study of microbial diversity and function. Students isolate and characterize novel microbes from local marine and freshwater habitats, integrating physiological data with genomic and metabolic analyses and applying advanced sequencing and annotation pipelines to interpret genomic, transcriptomic, and biochemical datasets.

New course directions emphasize metagenomics-enabled cultivation, development of non-model genetic systems, and discovery of novel microbial metabolisms and biogeochemical pathways. Participants receive integrated training in microbial physiology, metabolism, and genomics, focusing on cultivation of bacteria, archaea, and microbial eukaryotes, as well as their associated viruses. Guided by metagenomic and physiological data, students design selective enrichment strategies to isolate new organisms and develop model systems for future studies. They also apply functional genomic, biochemical, and imaging approaches to investigate microbial innovation and cryptic pathways, with special emphasis on advanced imaging at microbial scales to explore the unique cell biology of diverse microbes. State-of-the-art microscopy and quantitative live-cell imaging are used to study biofilm and community development in both course-generated consortia and layered natural microbial ecosystems. Field and laboratory investigations are further integrated to link microbial activity with environmental processes, employing predictive machine-learning and statistical-learning tools to correlate metagenomic, geochemical, and physical datasets and uncover previously unrecognized relationships within microbial ecosystems.

Although the course focuses on local intertidal microbial systems, the technical and analytical frameworks developed are equally applicable to host-associated microbiomes, including those of plants, animals, and humans. Through these training modules, participants gain the conceptual and practical expertise to investigate microbial processes across molecular, cellular, and ecosystem scales. The program’s close mentorship and collaborative learning environment, supported by resident instructors, guest lecturers, and active researchers, foster interdisciplinary exchange and lasting professional relationships. Together, these initiatives ensure that Microbial Diversity remains at the forefront of graduate-level education in experimental microbiology, preparing trainees to address global scientific and environmental challenges through microbial discovery and innovation.