add CD-Rhizotron study and protocol

studies/CD-Rhizotron/protocols/CD-RhizotronProtocol.md

+## CD-Rhizotron
+
+To assemble a CD-Rhizotron, a small opening, measuring approximately 1.5-2 cm, was cut on the top of a slimline jewel CD case (14.3 cm x 12.4 cm x 0.52 cm; Figure S1A). The teeth of the tray were snipped off and sanded down to produce a smooth surface. The resulting hole was sealed on both sides with packing tape. CD-Rhizotrons were filled with soil (Cologne Agricultural Soil, CAS (Bulgarelli, D. et al., 2012)) and wrapped with aluminum foil to provide a dark environment for proper root growth (Figures S1A–S1D). Up to four sterilized *A. thaliana* Col-0 seeds were sown directly onto each CD-Rhizotron from the top aperture of the CD-Rhizotron. CD-Rhizotrons were incubated under standard growth conditions. After 5-7 days, germinated seedlings were removed to leave each CD-Rhizotron with a single seedling. Plants were grown for another 3 weeks before they were harvested for microbiota profiling. Preparation of SynCom was adapted from (Durán et al., 2018). The 60-member SynCom was curated based on differences in 16S rRNA sequence with a 97% threshold. Briefly, bacterial strains (Table S5) were cultivated in 50% Tryptic Soy Broth (Sigma) for one week at 28°C with shaking at 200 rpm. The bacterial cultures were pooled in equal ratio and centrifuged at 4000x g for 10 mins. The bacterial pellet was re-suspended in 10 mM MgCl2 to remove residual media and bacteria-derived metabolites. The washing step was repeated three times. The washed bacterial suspension was adjusted to an OD600 of 0.02 (107 cells/mL) prior to inoculation onto sterile peat soil.
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