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Viktoria Petrova authoredViktoria Petrova authored
Figure 1. Differential spatial colonization by root microbiota along the longitudinal root axis
(A) Phenotype of wild-type A. thaliana Col-0 grown on CD-Rhizotron, with root segments marked. CPCoA of the Bray-Curtis dissimilarities of endospheric (n = 63) or rhizosphere samples (n = 65), constrained by the distance to the tip from which they were harvested. Different colors represent respective longitudinal segments or whole root samples, with colors of clusters corresponding to the root segments depicted in the plant cartoon. Centroids are indicated for each cluster of root region. (B) Phenotype of wild-type A. thaliana Col-0 grown on ArtSoil. CPCoA of the Bray-Curtis dissimilarities of root endosphere (n = 39) or rhizosphere samples (n = 40), constrained by the distance to the tip from which they were harvested. Colors of clusters correspond to segments of the root depicted in the plant cartoon. Centroids are indicated for each cluster of root region.
Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Deposited Data | ||
| 16S sequencing data | This paper | https://www.ebi.ac.uk/ena/browser/home (Accession number: PRJEB63568) |
| Metabolomics data | This paper | https://www.metabolomicsworkbench.org/ (Study ID: ST002779) |
| Arabidopsis root spatial microarray | [https://doi.org/10.1126/science.1146265] | GEO dataset: GSE8934 ID: 200008934 |
| NIST14 Mass Spectral Library | https://www.nist.gov/srd/nist-standard-reference-database-1a-v14 | N/A |
| Arabidopsis thaliana Col-0 metabolic pathways | https://pmn.plantcyc.org/organism-summary?object=ARA | N/A |
| Software and Algorithms | ||
| iGraph | https://CRAN.R-project.org/package=igraph. | RRID:SCR_019225 |
| COBRApy | http://opencobra.sourceforge.net | RRID:SCR_012096 |
| GUROBI | https://www.gurobi.com/ | N/A |
| statsmodels | https://www.statsmodels.org/stable/index.html | RRID:SCR_016074 |
| Vegan | https://cran.r-project.org/web/packages/vegan/index.html | RRID:SCR_011950 |
| Qiime2 | https://qiime2.org/ | RRID:SCR_008249 |
| Flash2 | https://github.com/dstreett/FLASH2 | RRID:SCR_005531 |
| Dada2 | https://benjjneb.github.io/dada2 | RRID:SCR_008205 |
| Others | ||
| 16S data analyses | This work | GitHub https://github.com/duranpa/sweet_collaboration |