add microbiota profiling assay and protocol

assays/MicrobiotaProfiling/protocols/MicrobiotaProfilingProtocol.md

+## Microbiota profiling
+
+Roots of 3-weeks-old plants grown via the CD-Rhizotrons were cut into 2-cm segments as described in “Root metabolite profiling” (Figures S1E and S1F). Each root segment was manually separated from the surrounding soil leaving only tightly adhered soil particles. The roots were then placed in 15 mL centrifuge tubes filled with 10 mL of deionized sterile water and inverted ten times to further displace residual soil from the roots. To harvest the root (endospheric) fraction, the roots were transferred to clean centrifuge tubes filled with 10 mL of detergent (0.1% Triton X-100 diluted in 1x TE) and shaken for two minutes. The roots were then transferred into clean centrifuge tubes filled with 10 mL of 80% ethanol and shaken for 30 seconds. The same step was repeated but replacing 80% ethanol with 2% bleach. Finally, roots were rinsed three times with deionized sterile water before they were dried on sterile filter papers and flash-frozen in liquid nitrogen and stored at -80 °C until further processing. To harvest the rhizospheric fraction, the soil wash-offs were centrifuged at 3000 × g for 10 min. The supernatants were discarded and the pellets were resuspended and transferred to clean 2 mL screwcap tubes. The tubes were centrifuged at 3000 × g for 10 min, after which the supernatant was discarded, and the pellets were flash-frozen in liquid nitrogen and stored in -80 °C for further processing. The similar protocol was applied for harvesting the root fraction of plants grown on ArtSoil. For rhizospheric fraction of plants grown on ArtSoil, a clean scalpel was used to scrape approximately 0.5 cm (wide) of agar along the surface where the roots grew. The agar scraps in clean microcentrifuge tubes were flash-frozen and stored at -80 °C for further processing.
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