| Chemicals, Peptides, and Recombinant Proteins |
|
| Tryptic Soy Broth |
Sigma-Aldrich |
Cat# T8907 |
| Potato Glucose Agar |
Sigma-Aldrich |
Cat# 70139 |
| Murashige Skoog |
Sigma-Aldrich |
Cat# M5519 |
|
| Deposited Data |
|
| MiSeq reads from natural site samples |
https://www.ebi.ac.uk/ena |
ENA: PRJEB27146 |
| MiSeq reads from microbiota reconstitution experiments |
https://www.ebi.ac.uk/ena |
ENA: PRJEB27147 |
|
| Experimental Models: Organisms/Strains |
|
| Root-associated bacterial, fungal and oomycetal strains |
See Table S3
|
See Table S3
|
|
Arabidopsis thaliana wild-type, Columbia (Col-0) |
TAIR |
CS60000 |
|
| Oligonucleotides |
|
| Primers used in this study |
See Table S2
|
See Table S2
|
|
| Software and Algorithms |
|
| QIIME |
Caporaso et al., 2010b |
http://qiime.org/ |
| USEARCH |
Edgar, 2013 |
https://www.drive5.com/usearch/ |
| PyNAST |
Caporaso et al., 2010a |
http://biocore.github.io/pynast/ |
| ITSx |
Bengtsson-Palme et al., 2013 |
http://microbiology.se/software/itsx/ |
| BLAST |
N/A |
https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| RDP |
Wang et al., 2007 |
https://rdp.cme.msu.edu/index.jsp |
| MAFFT (web) |
Katoh et al., 2017 |
https://mafft.cbrc.jp/alignment/server/ |
| RAxML (web) |
Boc et al., 2012 |
http://www.trex.uqam.ca/index.php?action=raxml |
| iTOL |
Letunic and Bork., 2016 |
https://itol.embl.de/ |
| CoNet |
Faust and Raes, 2016 |
http://apps.cytoscape.org/apps/conet |
| SparCC |
Friedman and Alm, 2012 |
http://psbweb05.psb.ugent.be/conet/microbialnetworks/sparcc.php |
| Cytoscape |
Shannon et al., 2003 |
https://cytoscape.org/ |
| R |
N/A |
https://www.r-project.org/ |
| R, vegan package |
N/A |
https://cran.r-project.org/web/packages/vegan/index.html |
| Plotting and analyses |
N/A |
https://github.com/ththi/Microbial-Interkingdom-Suppl |
