Microorganisms are vital to environmental health, yet their association with disease often overshadows these benefits. Building citizen-science activities around the positive role of microorganisms and an understanding of their ubiquity can begin to dispel misconceptions while simultaneously engaging the public in research. Here, we describe a citizen-science microbiology project geared toward implementation in middle and high school classrooms. Students culture environmental microorganisms and document microbial diversity of plant root systems compared with adjacent bulk soil. Results contribute data toward research on microbiome recruitment of weeds and other successful plants while addressing core topics in science education.