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

• DOI: 10.3791/57561
• Publication Date: 2018-05-03T00:00:09Z
• Authors: Tuesday Simmons; Daniel F. Caddell; Siwen Deng; Devin Coleman-Derr
• Keywords: Amplicon; Amplicon sequencing

The intimate interaction between plant host and associated microorganisms is crucial in determining fitness, can foster improved tolerance to abiotic stresses diseases. As the microbiome be highly complex, low-cost, high-throughput methods such as amplicon-based sequencing of 16S rRNA gene are often preferred for characterizing its microbial composition diversity. However, selection appropriate methodology when conducting experiments critical reducing biases that make analysis comparisons samples studies difficult. This protocol describes detail a standardized collection extraction DNA from soil, rhizosphere, root samples. Additionally, we highlight well-established amplicon pipeline allows exploration bacterial communities these samples, easily adapted other marker genes. has been validated variety species, including sorghum, maize, wheat, strawberry, agave, help overcome issues with contamination organelles.