The current and ongoing challenges brought on by climate change will require future scientists who have hands-on experience using advanced molecular techniques, can work with large data sets, and can make correlations between metadata and microbial diversity. A course-embedded research project can prepare students to answer complex research questions that might help plants adapt to climate change. The project described herein uses plants as a host to study the impact of climate change-induced drought on host-microbe interactions through next-generation DNA sequencing and analysis using a command-line program. Specifically, the project studies the impact of simulated drought on the rhizosphere microbiome of Fast Plants rapid cycling "Brassica rapa" using inexpensive greenhouse supplies and 16S rRNA V3/V4 Illumina sequencing. Data analysis is performed with the freely accessible Python-based microbiome bioinformatics platform QIIME 2.