USDA ARS Plant Gene Expression Center 2 articles published in JoVE Genetics Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere Tuesday Simmons1, Daniel F. Caddell1, Siwen Deng1, Devin Coleman-Derr1,2 1Department of Plant and Microbial Biology, University of California, Berkeley, 2Plant Gene Expression Center, USDA ARS Here, we describe a protocol to obtain amplicon sequence data of soil, rhizosphere, and root endosphere microbiomes. This information can be used to investigate the composition and diversity of plant-associated microbial communities, and is suitable for the use with a wide range of plant species. Biology Visualizing Stromule Frequency with Fluorescence Microscopy Jacob O. Brunkard1, Anne M. Runkel2, Patricia Zambryski2 1Plant Gene Expression Center, Agricultural Research Service, USDA, 2Department of Plant and Microbial Biology, University of California, Berkeley Protocols to investigate the dynamics of chloroplast stromules, the stroma-filled tubules that extend from the surface of chloroplasts, are described.