Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

The overall goal of this experiment is to characterize three compartments of the root microbiome, soil, rhizosphere, and root endosphere, using community profiling of the 16S ribosomal RNA gene. This method can help answer key questions in microbial ecology, such as the biotic and abiotic factors that are the significant drivers of microbiome structure. The main advantage of this technique is that it standardizes each step, from the separation of root and rhizosphere to DNA's extraction to preparing a sequencing library.

Demonstrating this procedure will be Tuesday Simmons, a graduate student in the Coleman-Derr Laboratory. To begin the protocol, collect bulk soil samples with an ethanol-sterilized soil core collector to obtain soil that is free of plant roots. Collect a core approximately 23 to 30 centimeters from the base of the plant.