Microbes Across Environments
Instructor: David Mark Welch (MBL)
Course Description:
This course provides a comprehensive introduction to the theory and techniques of microbiome science, an emerging field that bridges disciplines, merging microbiology with genomics, ecology, population and evolutionary biology, phylogenetics, ecosystem science, and biogeochemistry, and has broad applications in medicine, agriculture, and ecosystem health. Through a combination of faculty and guest lectures and student-led discussion of primary literature we will explore the vast biochemical and metabolic diversity of the microbial world and its relationships with multicellular life. The major component of the course is an independent research project investigating the microbiomes of marine organisms collected by the students or resident in the ƬƬ Marine Resources Center, or of a salt marsh ecosystem in Woods Hole. Students develop their own hypotheses and sampling strategies, carry our sampling, extract DNA, and perform PCR for sequencing. The last third of the course is devoted to data analysis, where students learn to use the Unix-based bioinformatic tools necessary to find patterns in the hundreds of thousands of DNA sequences their project produced, a skill broadly applicable to any discipline in modern biology.
Learning Objectives and Outcomes:
At the end of the course students will have a solid understanding of the diversity of the microbial world and its role in shaping Earth processes and human and ecosystems health, as well as the physiological, phylogenetic, and functional differences between eubacteria, archaea, protists, and their viruses. Students will learn to read, evaluate, and discuss primary literature and how to formulate and test hypotheses. In addition to basic field and laboratory skills in microbiology and molecular biology, students will gain extensive experience using the Unix command line and the bioinformatic tools of microbiome science.
Course Structure:
Week 1: Morning lectures on microbial diversity and processes; afternoons in the lab with basic techniques of micro- and molecular biology, or in the field (Little Sippewissett Marsh, R/V Gemma, Marine Resources Center) collecting samples.
Week 2: Morning lectures on molecular biology and student-led discussion of review papers. Afternoons in the lab processing samples (DNA extraction, PCR, quantification), building Winogradsky columns, staining and microscopy of viruses and bacteria. Introduction to Unix and bioinformatics.
Week 3: Morning lectures by experts in microbiomes, student-led discussion of primary papers.
Afternoons finishing microbiology experiments, data analysis of independent projects, and preparation of final oral presentations.