SRX1526958 Seed inoculum biomass SRP068293 DNA and cDNA from Day 0 (Inoc), Days 105 (Phase 1), 301 (Phase 3), 454 (Phase 4A.c), 732 (End) and the filter upon take-down (FE) samples were used for 16S amplicon sequencing. The 16S rRNA gene V4 variable region was amplified using the ‘universal’ (for the co-amplification of archaeal and bacterial sequences) primer set 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R (5’GGACTACHVGGGTWTCT-AAT-3’) -Caporaso et al (2012) with barcodes for multiplexing on the forward primer. The PCR conditions included an initial denaturation step at 94°C for 3 min, followed by 28 cycles of denaturation at 94°C for 30 sec, annealing at 53°C for 40 sec, and extension at 72°C for 1 min, with a final elongation step at 72°C for 5 min using HotStarTaq Plus Master Mix Kit (Qiagen, USA) for the reaction. Amplicons were then pooled in equal proportions and purified using calibrated Ampure XP beads (Bechman Coulter). The combined and purified product was prepared using the Illumina TruSeq DNA library protocol. DNA amplification and sequencing was performed at MR DNA Molecular Research Laboratory (www.mrdnalab.com; Shallowater, TX, USA) using the Miseq reagent kit V3 (2x250bp) for paired-end reads on a Solexa Miseq machine following the manufacturer’s guidelines. SRS1244793 Seed inoculum biomass Tn-Seq METAGENOMIC unspecified 300 0 Application Read Forward 1 Illumina MiSeq SRX1534157 Biomass from Phase 1 SRP068293 DNA and cDNA from Day 0 (Inoc), Days 105 (Phase 1), 301 (Phase 3), 454 (Phase 4A.c), 732 (End) and the filter upon take-down (FE) samples were used for 16S amplicon sequencing. The 16S rRNA gene V4 variable region was amplified using the ‘universal’ (for the co-amplification of archaeal and bacterial sequences) primer set 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R (5’GGACTACHVGGGTWTCT-AAT-3’) -Caporaso et al (2012) with barcodes for multiplexing on the forward primer. The PCR conditions included an initial denaturation step at 94°C for 3 min, followed by 28 cycles of denaturation at 94°C for 30 sec, annealing at 53°C for 40 sec, and extension at 72°C for 1 min, with a final elongation step at 72°C for 5 min using HotStarTaq Plus Master Mix Kit (Qiagen, USA) for the reaction. Amplicons were then pooled in equal proportions and purified using calibrated Ampure XP beads (Bechman Coulter). The combined and purified product was prepared using the Illumina TruSeq DNA library protocol. DNA amplification and sequencing was performed at MR DNA Molecular Research Laboratory (www.mrdnalab.com; Shallowater, TX, USA) using the Miseq reagent kit V3 (2x250bp) for paired-end reads on a Solexa Miseq machine following the manufacturer’s guidelines. SRS1244794 Biomass from Phase 1 Tn-Seq METAGENOMIC unspecified 300 0 Application Read Forward 1 Illumina MiSeq SRX1534158 Biomass from Phase 3 SRP068293 DNA and cDNA from Day 0 (Inoc), Days 105 (Phase 1), 301 (Phase 3), 454 (Phase 4A.c), 732 (End) and the filter upon take-down (FE) samples were used for 16S amplicon sequencing. The 16S rRNA gene V4 variable region was amplified using the ‘universal’ (for the co-amplification of archaeal and bacterial sequences) primer set 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R (5’GGACTACHVGGGTWTCT-AAT-3’) -Caporaso et al (2012) with barcodes for multiplexing on the forward primer. The PCR conditions included an initial denaturation step at 94°C for 3 min, followed by 28 cycles of denaturation at 94°C for 30 sec, annealing at 53°C for 40 sec, and extension at 72°C for 1 min, with a final elongation step at 72°C for 5 min using HotStarTaq Plus Master Mix Kit (Qiagen, USA) for the reaction. Amplicons were then pooled in equal proportions and purified using calibrated Ampure XP beads (Bechman Coulter). The combined and purified product was prepared using the Illumina TruSeq DNA library protocol. DNA amplification and sequencing was performed at MR DNA Molecular Research Laboratory (www.mrdnalab.com; Shallowater, TX, USA) using the Miseq reagent kit V3 (2x250bp) for paired-end reads on a Solexa Miseq machine following the manufacturer’s guidelines. SRS1244795 Biomass from Phase 3 Tn-Seq METAGENOMIC unspecified 300 0 Application Read Forward 1 Illumina MiSeq SRX1534159 Biomass from Phase 4A.c SRP068293 DNA and cDNA from Day 0 (Inoc), Days 105 (Phase 1), 301 (Phase 3), 454 (Phase 4A.c), 732 (End) and the filter upon take-down (FE) samples were used for 16S amplicon sequencing. The 16S rRNA gene V4 variable region was amplified using the ‘universal’ (for the co-amplification of archaeal and bacterial sequences) primer set 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R (5’GGACTACHVGGGTWTCT-AAT-3’) -Caporaso et al (2012) with barcodes for multiplexing on the forward primer. The PCR conditions included an initial denaturation step at 94°C for 3 min, followed by 28 cycles of denaturation at 94°C for 30 sec, annealing at 53°C for 40 sec, and extension at 72°C for 1 min, with a final elongation step at 72°C for 5 min using HotStarTaq Plus Master Mix Kit (Qiagen, USA) for the reaction. Amplicons were then pooled in equal proportions and purified using calibrated Ampure XP beads (Bechman Coulter). The combined and purified product was prepared using the Illumina TruSeq DNA library protocol. DNA amplification and sequencing was performed at MR DNA Molecular Research Laboratory (www.mrdnalab.com; Shallowater, TX, USA) using the Miseq reagent kit V3 (2x250bp) for paired-end reads on a Solexa Miseq machine following the manufacturer’s guidelines. SRS1244796 Biomass from Phase 4A.c Tn-Seq METAGENOMIC unspecified 300 0 Application Read Forward 1 Illumina MiSeq SRX1534160 Biomass from the end of the trail SRP068293 DNA and cDNA from Day 0 (Inoc), Days 105 (Phase 1), 301 (Phase 3), 454 (Phase 4A.c), 732 (End) and the filter upon take-down (FE) samples were used for 16S amplicon sequencing. The 16S rRNA gene V4 variable region was amplified using the ‘universal’ (for the co-amplification of archaeal and bacterial sequences) primer set 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R (5’GGACTACHVGGGTWTCT-AAT-3’) -Caporaso et al (2012) with barcodes for multiplexing on the forward primer. The PCR conditions included an initial denaturation step at 94°C for 3 min, followed by 28 cycles of denaturation at 94°C for 30 sec, annealing at 53°C for 40 sec, and extension at 72°C for 1 min, with a final elongation step at 72°C for 5 min using HotStarTaq Plus Master Mix Kit (Qiagen, USA) for the reaction. Amplicons were then pooled in equal proportions and purified using calibrated Ampure XP beads (Bechman Coulter). The combined and purified product was prepared using the Illumina TruSeq DNA library protocol. DNA amplification and sequencing was performed at MR DNA Molecular Research Laboratory (www.mrdnalab.com; Shallowater, TX, USA) using the Miseq reagent kit V3 (2x250bp) for paired-end reads on a Solexa Miseq machine following the manufacturer’s guidelines. SRS1244797 Biomass from the end of the trail Tn-Seq METAGENOMIC unspecified 300 0 Application Read Forward 1 Illumina MiSeq SRX1534161 Pumice stone filter SRP068293 DNA and cDNA from Day 0 (Inoc), Days 105 (Phase 1), 301 (Phase 3), 454 (Phase 4A.c), 732 (End) and the filter upon take-down (FE) samples were used for 16S amplicon sequencing. The 16S rRNA gene V4 variable region was amplified using the ‘universal’ (for the co-amplification of archaeal and bacterial sequences) primer set 515F (5’-GTGCCAGCMGCCGCGGTAA-3’) and 806R (5’GGACTACHVGGGTWTCT-AAT-3’) -Caporaso et al (2012) with barcodes for multiplexing on the forward primer. The PCR conditions included an initial denaturation step at 94°C for 3 min, followed by 28 cycles of denaturation at 94°C for 30 sec, annealing at 53°C for 40 sec, and extension at 72°C for 1 min, with a final elongation step at 72°C for 5 min using HotStarTaq Plus Master Mix Kit (Qiagen, USA) for the reaction. Amplicons were then pooled in equal proportions and purified using calibrated Ampure XP beads (Bechman Coulter). The combined and purified product was prepared using the Illumina TruSeq DNA library protocol. DNA amplification and sequencing was performed at MR DNA Molecular Research Laboratory (www.mrdnalab.com; Shallowater, TX, USA) using the Miseq reagent kit V3 (2x250bp) for paired-end reads on a Solexa Miseq machine following the manufacturer’s guidelines. SRS1244798 Pumice stone filter Tn-Seq METAGENOMIC unspecified 300 0 Application Read Forward 1 Illumina MiSeq