From b575f53256278f845cd538a4b8b64f4a5b244a0f Mon Sep 17 00:00:00 2001 From: Viktoria Petrova <vipet103@hhu.de> Date: Sun, 3 Nov 2024 12:44:09 +0100 Subject: [PATCH] add CD-Rhizotron study and protocol --- studies/CD-Rhizotron/README.md | 0 studies/CD-Rhizotron/isa.study.xlsx | Bin 0 -> 7497 bytes studies/CD-Rhizotron/protocols/.gitkeep | 0 .../protocols/CD-RhizotronProtocol.md | 3 +++ studies/CD-Rhizotron/resources/.gitkeep | 0 5 files changed, 3 insertions(+) create mode 100644 studies/CD-Rhizotron/README.md create mode 100644 studies/CD-Rhizotron/isa.study.xlsx create mode 100644 studies/CD-Rhizotron/protocols/.gitkeep create mode 100644 studies/CD-Rhizotron/protocols/CD-RhizotronProtocol.md create mode 100644 studies/CD-Rhizotron/resources/.gitkeep diff --git a/studies/CD-Rhizotron/README.md b/studies/CD-Rhizotron/README.md new file mode 100644 index 0000000..e69de29 diff --git a/studies/CD-Rhizotron/isa.study.xlsx b/studies/CD-Rhizotron/isa.study.xlsx new file mode 100644 index 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0000000..e69de29 diff --git a/studies/CD-Rhizotron/protocols/CD-RhizotronProtocol.md b/studies/CD-Rhizotron/protocols/CD-RhizotronProtocol.md new file mode 100644 index 0000000..09014bb --- /dev/null +++ b/studies/CD-Rhizotron/protocols/CD-RhizotronProtocol.md @@ -0,0 +1,3 @@ +## 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. \ No newline at end of file diff --git a/studies/CD-Rhizotron/resources/.gitkeep b/studies/CD-Rhizotron/resources/.gitkeep new file mode 100644 index 0000000..e69de29 -- GitLab