## 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                 |