SRX5622247 AfP2-CC SRP190066 PRJNA525709 Bacterial colonies were tooth-picked into a 2 ml centrifuge tube for each community containing sterilized water, then proteinase K and lysozyme (both from Sigma-Aldrich, St. Louis Missouri, United States) were added for an initial lysis (37C, 30 min). Then the tubes were centrifuged and the pellets were used as the source for DNA extraction with the MoBio PowerSoil extraction kit. PCR reactions were carried out to amplify the V3-V4 region (341F and 805R primers; 464 bp amplicon; Klindworth 2013) following the Illumina MiSeq protocol with 5 overhangs. We performed triplicated PCR reactions for each sample, using the high fidelity Pfx platinum polymerase (Invitrogen, Thermo Fisher Scientific Corporation, Carlsbad, California, USA). Finally, amplicons from each replicate were pooled and purified with the Wizard SV Gel and PCR Cleanup System kit (Promega Corporation, Madison, Wisconsin, USA). SRS4568090 SAMN11174946 AfP2-CC AMPLICON METAGENOMIC PCR Illumina MiSeq SRX5622248 Bc-CC SRP190066 PRJNA525709 Bacterial colonies were tooth-picked into a 2 ml centrifuge tube for each community containing sterilized water, then proteinase K and lysozyme (both from Sigma-Aldrich, St. Louis Missouri, United States) were added for an initial lysis (37C, 30 min). Then the tubes were centrifuged and the pellets were used as the source for DNA extraction with the MoBio PowerSoil extraction kit. PCR reactions were carried out to amplify the V3-V4 region (341F and 805R primers; 464 bp amplicon; Klindworth 2013) following the Illumina MiSeq protocol with 5 overhangs. We performed triplicated PCR reactions for each sample, using the high fidelity Pfx platinum polymerase (Invitrogen, Thermo Fisher Scientific Corporation, Carlsbad, California, USA). Finally, amplicons from each replicate were pooled and purified with the Wizard SV Gel and PCR Cleanup System kit (Promega Corporation, Madison, Wisconsin, USA). SRS4568091 SAMN11174947 Bc-CC AMPLICON METAGENOMIC PCR Illumina MiSeq SRX5622249 Gl SRP190066 PRJNA525709 Plant roots were vortex-shaked and sonicated on sterile PBS solution, to get the rhizospheric pellet as described elsewhere (Lundberg et al. 2012). The metagenomic DNA was extracted from the pellets with the MoBio PowerSoil extraction kit (MoBio Laboratories, Solana Beach, CA, USA). PCR reactions were carried out to amplify the V3-V4 region (341F and 805R primers; 464 bp amplicon; Klindworth 2013) following the Illumina MiSeq protocol with 5 overhangs. We performed triplicated PCR reactions for each sample, using the high fidelity Pfx platinum polymerase (Invitrogen, Thermo Fisher Scientific Corporation, Carlsbad, California, USA). Finally, amplicons from each replicate were pooled and purified with the Wizard SV Gel and PCR Cleanup System kit (Promega Corporation, Madison, Wisconsin, USA). SRS4568093 SAMN11174944 Gl AMPLICON METAGENOMIC PCR Illumina MiSeq SRX5622250 AfP1-CC SRP190066 PRJNA525709 Bacterial colonies were tooth-picked into a 2 ml centrifuge tube for each community containing sterilized water, then proteinase K and lysozyme (both from Sigma-Aldrich, St. Louis Missouri, United States) were added for an initial lysis (37C, 30 min). Then the tubes were centrifuged and the pellets were used as the source for DNA extraction with the MoBio PowerSoil extraction kit. PCR reactions were carried out to amplify the V3-V4 region (341F and 805R primers; 464 bp amplicon; Klindworth 2013) following the Illumina MiSeq protocol with 5 overhangs. We performed triplicated PCR reactions for each sample, using the high fidelity Pfx platinum polymerase (Invitrogen, Thermo Fisher Scientific Corporation, Carlsbad, California, USA). Finally, amplicons from each replicate were pooled and purified with the Wizard SV Gel and PCR Cleanup System kit (Promega Corporation, Madison, Wisconsin, USA). SRS4568092 SAMN11174945 AfP1-CC AMPLICON METAGENOMIC PCR Illumina MiSeq SRX5622251 Bc SRP190066 PRJNA525709 Plant roots were vortex-shaked and sonicated on sterile PBS solution, to get the rhizospheric pellet as described elsewhere (Lundberg et al. 2012). The metagenomic DNA was extracted from the pellets with the MoBio PowerSoil extraction kit (MoBio Laboratories, Solana Beach, CA, USA). PCR reactions were carried out to amplify the V3-V4 region (341F and 805R primers; 464 bp amplicon; Klindworth 2013) following the Illumina MiSeq protocol with 5 overhangs. We performed triplicated PCR reactions for each sample, using the high fidelity Pfx platinum polymerase (Invitrogen, Thermo Fisher Scientific Corporation, Carlsbad, California, USA). Finally, amplicons from each replicate were pooled and purified with the Wizard SV Gel and PCR Cleanup System kit (Promega Corporation, Madison, Wisconsin, USA). SRS4568094 SAMN11174942 Bc AMPLICON METAGENOMIC PCR Illumina MiSeq SRX5622252 Bs SRP190066 PRJNA525709 Plant roots were vortex-shaked and sonicated on sterile PBS solution, to get the rhizospheric pellet as described elsewhere (Lundberg et al. 2012). The metagenomic DNA was extracted from the pellets with the MoBio PowerSoil extraction kit (MoBio Laboratories, Solana Beach, CA, USA). PCR reactions were carried out to amplify the V3-V4 region (341F and 805R primers; 464 bp amplicon; Klindworth 2013) following the Illumina MiSeq protocol with 5 overhangs. We performed triplicated PCR reactions for each sample, using the high fidelity Pfx platinum polymerase (Invitrogen, Thermo Fisher Scientific Corporation, Carlsbad, California, USA). Finally, amplicons from each replicate were pooled and purified with the Wizard SV Gel and PCR Cleanup System kit (Promega Corporation, Madison, Wisconsin, USA). SRS4568095 SAMN11174943 Bs AMPLICON METAGENOMIC PCR Illumina MiSeq SRX5622253 AfP1 SRP190066 PRJNA525709 Plant roots were vortex-shaked and sonicated on sterile PBS solution, to get the rhizospheric pellet as described elsewhere (Lundberg et al. 2012). The metagenomic DNA was extracted from the pellets with the MoBio PowerSoil extraction kit (MoBio Laboratories, Solana Beach, CA, USA). PCR reactions were carried out to amplify the V3-V4 region (341F and 805R primers; 464 bp amplicon; Klindworth 2013) following the Illumina MiSeq protocol with 5 overhangs. We performed triplicated PCR reactions for each sample, using the high fidelity Pfx platinum polymerase (Invitrogen, Thermo Fisher Scientific Corporation, Carlsbad, California, USA). Finally, amplicons from each replicate were pooled and purified with the Wizard SV Gel and PCR Cleanup System kit (Promega Corporation, Madison, Wisconsin, USA). SRS4568096 SAMN11174940 AfP1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX5622254 AfP2 SRP190066 PRJNA525709 Plant roots were vortex-shaked and sonicated on sterile PBS solution, to get the rhizospheric pellet as described elsewhere (Lundberg et al. 2012). The metagenomic DNA was extracted from the pellets with the MoBio PowerSoil extraction kit (MoBio Laboratories, Solana Beach, CA, USA). PCR reactions were carried out to amplify the V3-V4 region (341F and 805R primers; 464 bp amplicon; Klindworth 2013) following the Illumina MiSeq protocol with 5 overhangs. We performed triplicated PCR reactions for each sample, using the high fidelity Pfx platinum polymerase (Invitrogen, Thermo Fisher Scientific Corporation, Carlsbad, California, USA). Finally, amplicons from each replicate were pooled and purified with the Wizard SV Gel and PCR Cleanup System kit (Promega Corporation, Madison, Wisconsin, USA). SRS4568097 SAMN11174941 AfP2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX5622255 Bs-CC SRP190066 PRJNA525709 Bacterial colonies were tooth-picked into a 2 ml centrifuge tube for each community containing sterilized water, then proteinase K and lysozyme (both from Sigma-Aldrich, St. Louis Missouri, United States) were added for an initial lysis (37C, 30 min). Then the tubes were centrifuged and the pellets were used as the source for DNA extraction with the MoBio PowerSoil extraction kit. PCR reactions were carried out to amplify the V3-V4 region (341F and 805R primers; 464 bp amplicon; Klindworth 2013) following the Illumina MiSeq protocol with 5 overhangs. We performed triplicated PCR reactions for each sample, using the high fidelity Pfx platinum polymerase (Invitrogen, Thermo Fisher Scientific Corporation, Carlsbad, California, USA). Finally, amplicons from each replicate were pooled and purified with the Wizard SV Gel and PCR Cleanup System kit (Promega Corporation, Madison, Wisconsin, USA). SRS4568098 SAMN11174948 Bs-CC AMPLICON METAGENOMIC PCR Illumina MiSeq SRX5622256 Gl-CC SRP190066 PRJNA525709 Bacterial colonies were tooth-picked into a 2 ml centrifuge tube for each community containing sterilized water, then proteinase K and lysozyme (both from Sigma-Aldrich, St. Louis Missouri, United States) were added for an initial lysis (37C, 30 min). Then the tubes were centrifuged and the pellets were used as the source for DNA extraction with the MoBio PowerSoil extraction kit. PCR reactions were carried out to amplify the V3-V4 region (341F and 805R primers; 464 bp amplicon; Klindworth 2013) following the Illumina MiSeq protocol with 5 overhangs. We performed triplicated PCR reactions for each sample, using the high fidelity Pfx platinum polymerase (Invitrogen, Thermo Fisher Scientific Corporation, Carlsbad, California, USA). Finally, amplicons from each replicate were pooled and purified with the Wizard SV Gel and PCR Cleanup System kit (Promega Corporation, Madison, Wisconsin, USA). SRS4568099 SAMN11174949 Gl-CC AMPLICON METAGENOMIC PCR Illumina MiSeq SRX5622257 Af-MG SRP190066 PRJNA525709 Plant roots were vortex-shaked and sonicated on sterile PBS solution, to get the rhizospheric pellet as described elsewhere (Lundberg et al. 2012). The metagenomic DNA was extracted from the pellets with the MoBio PowerSoil extraction kit (MoBio Laboratories, Solana Beach, CA, USA). SRS4568100 SAMN11174950 Af-MG WGS METAGENOMIC RANDOM Illumina HiSeq 2000 SRX5622258 SC SRP190066 PRJNA525709 Bacterial colonies were tooth-picked into a 2 ml centrifuge tube for each community containing sterilized water, then proteinase K and lysozyme (both from Sigma-Aldrich, St. Louis Missouri, United States) were added for an initial lysis (37C, 30 min). Then the tubes were centrifuged and the pellets were used as the source for DNA extraction with the MoBio PowerSoil extraction kit. SRS4568101 SAMN11174951 SC WGS METAGENOMIC RANDOM Illumina HiSeq 2000 SRX5622259 FSC SRP190066 PRJNA525709 Bacterial colonies were tooth-picked into a 2 ml centrifuge tube for each community containing sterilized water, then proteinase K and lysozyme (both from Sigma-Aldrich, St. Louis Missouri, United States) were added for an initial lysis (37C, 30 min). Then the tubes were centrifuged and the pellets were used as the source for DNA extraction with the MoBio PowerSoil extraction kit. SRS4568102 SAMN11174952 FSC WGS METAGENOMIC RANDOM Illumina MiSeq