REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
AtSphere Arabidopsis thaliana-derived culture collection. Full list of strains in this study are in Table S2	Bai et al., 2015	http://www.at-sphere.com/
Biological Samples
Cologne agricultural soil	Bai et al., 2015	CAS
Italian soil	This study	IS
Chemicals, Peptides, and Recombinant Proteins
DFS Taq Polymerase	Bioron	CAT#101005
Agar Bacteriological	Difco	CAT#214530
FeEDTA	Sigma-Aldrich	CAT#E6760
FeCl3 hexahydrate	Merck	CAT#103943
HEPES buffer	Roth	CAT#6763.1
Scopoletin	Sigma-Aldrich	CAT#S2500
Fraxetin	Sigma-Aldrich	CAT#18224
Tryptic Soy Broth	Sigma-Aldrich	CAT#T8907
Critical Commercial Assays
FastDNA SPIN kit for Soil	MP Biomedicals	CAT# SKU 116560200
Quant_iT Pico Green dsDNA Assay	ThermoFischer	CAT#P7589
AMPure XP DNA purification beads	Beckman Coulter	CAT#A63881
RNEasy Plant Mini Kit	Qiagen	CAT#74904
Deposited Data
16S rRNA root profiling data	This paper https://www.ebi.ac.uk/ena	ENA: accession PRJEB38663
Raw and processed data, scripts for analysis and figure generation	This paper	Mendeley Data DOI: 10.17632/tkdn6zbw7k.1
Root RNA-Seq data	This paper https://www.ebi.ac.uk/ena	ENA: accession PRJEB38663
Silva 132 rRNA database, Released Dec. 2017	Quast et al., 2013	RRID: SCR_006423
Experimental Models: Organisms/Strains
A. thaliana: Col-0 wildtype	NASC	N60000
A. thaliana: f6’h1-1 TDNA insertion mutant	NASC	SALK_132418C
A. thaliana: s8h-2 TDNA insertion mutant	NASC	SM_3_23443
A. thaliana: cyp82c4-1 TDNA insertion mutant	NASC	SALK_001585
A. thaliana: pdr9-2 TDNA insertion mutant	NASC	SALK_050885
A. thaliana: irt1-1 TDNA insertion mutant	Vert et al., 2002	irt1-1
A. thaliana: fro2 (frd1-1) TDNA insertion mutant	NASC	N3777
A. thaliana: aha2-4 TDNA insertion mutant	NASC	SALK_082786
A. thaliana: bts-1 TDNA insertion mutant	NASC	SALK_016526
Oligonucleotides
All primers are found in Table S1		N/A
Software and Algorithms
R statistical environment	https://www.r-project.org/	V 4.0.1
DADA2	Callahan et al., 2016	V1.12.1
Interactive Tree of Life (iTOL)	Letunic and Bork, 2007	https://itol.embl.de/
Vegan, R package	Dixon, 2003	V 2.5-6
RVAideMemoire, R package	Hervé, 2020	V 0.9-77
edgeR, R package	Robinson et al., 2010	V 3.24.3
Fastp	Chen et al., 2018	RRID: SCR_016962
Kallisto	Bray et al., 2016	RRID: SCR_016582
Tximport, R package	Soneson et al., 2015	V 1.16.1
SVA, R package	Leek et al., 2012	V 3.36.0
DESeq2, R package	Love et al., 2014	V 1.28.1
ComplexHeatmap, R package	Gu et al. 2016	V 2.4.2
Goseq, R package	Young et al., 2010	V 1.40.0
Gene Ontology Consortium	Ashburner et al., 2000	RRID: SCR_002811
Ggpubr, R package	Kassambara, 2020	V 0.3.0
FSA, R package	Ogle et al., 2020	V 0.8.30
Rcompanion, R package	Mangiafico, 2020	V 2.3.25
Emmeans, R package	Lenth, 2020	V 1.4.8
BioRender (Graphical Abstract)	BioRender.com	RRID: SCR_018361