Every summer, sixteen diverse undergraduate students from across the country participate in the Center for Dark Energy Biosphere Investigations (C-DEBI) sponsored Global Environmental Microbiology (GEM) course based at the University of Southern California (USC). The course is a four week, field-based, residential program where students gain first-hand experience in microbiological sample collection and laboratory techniques. Students finish the course having a new appreciation for the microbial world and of equal importance, collecting data and collaborating with peers. Students’ misconceptions about microbes are challenged through active participation to move their understanding beyond facts to “core concepts” (Bransford et al. 1999). This article outlines some of the conceptual changes microbiology can bring to science education as well as examines the GEM course from tenants of inquiry-based learning.