## 2 Materials and Methods
### DNA Extraction and Whole Genome Shotgun Sequencing  
Replicates of soil samples were collected from the plant rhizosphere every day, on the one hand, and those of the surrounding bulk soil were gathered at each watering time point, on the other hand. DNAs were extracted using the CTAB/SDS method. Then, purity and integrity were checked by electrophoresis on 1% agarose gels as the first layer of quality control (QC). DNA concentration was adjusted to 10 ng/\(\,\mu\)L using a dsDNA Assay kit in 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) prior shipment to Novogene Co., Ltd., Singapore, for whole genome sequencing. An amount of 1 ug DNA per sample was used as an input material for mWGS sequencing. Physical fractionation was done by a Covaris Sonicator and microbiomes were checked for enrichment by Agilent2100 and qPCR. A second layer of QC was done in terms of data pre-processing by trimming low quality bases (Q-value \(\leq\) 38) exceeding a 40-bp threshold, and removing reads with N nucleotides over a 10-bp threshold and overlapped reads with adapter > 15-bp threshold by default. Then, filtered effective clean data were obtained and used further for processing and bioinformatics analysis. Sequencing libraries were generated from clean data using an Ultra DNA Library Prep kit for Illumina (NEB, Ipswich, MA, USA) following the manufacturer's instructions. DNA samples were fragmented by sonication to obtain 350 bp-band size, then DNA fragments were end-polished, adenine-tailed and ligated with the full-length adaptor to approach PCR. Then, amplicons were purified (AMPure XP System) and libraries were analyzed for size distribution by an Agilent2100 Bioanalyzer and quantified using qPCR. The clustering with paired-end reads of the index-coded samples was performed on a cBot Cluster Generation System according to the manufacturer's instructions. Then, the library preparations were sequenced on the Illumina HiSeq 2500 platform. Generated datasets were assembled using MEGAHIT (K-mer = 55) and the chimera was removed following standard methods as an extra layer of QC. The unutilized reads of each sample were mixed together in one sample (namely, NOVO_MIX) and assembled in order to explore the information of low-abundance species of the different samples. Generated scaffolds from utilized and unutilized reads were cut off at \"N\" to get N-free fragments or scaftigs [32], and those with <500 bp length were removed as a further QC step. Clean data were mapped to assembled scaftigs using Soap 2.21, then, effective scaftigs (found in \(\geq\)2 samples) were used for further analysis. Gene prediction was carried out by MetaGeneMark based on the assembled scarfigs to predict >100 nt ORFs [32; 33; 34; 35; 36]. Predicted genes with identity of 95% and coverage of 90%, by default, were subjected to dereplication using Cluster Database at High Identity with Tolerance (CD-HIT) [37; 38] in order to cluster and construct initial non-redundant gene catalogues (nrGC). The longest ORFs were chosen as the representative genes (Unigene), while ORFs with \(\leq\)100 nt length were removed. Non-redundant genes were constructed from predicted genes after redundant genes were removed using a greedy pairwise comparison, with highly stringent criteria of 95% identity over 90% of the shorter gene length [39]. Then, non-redundant genes were further incorporated in gene abundance analysis and assigned to taxonomic groups using a pipeline provided by Novogene Co. As an extra layer of CQ, metagenomic contigs were assigned taxonomically if 95% of its reads were annotated to the same species. Less than this percentage is considered chimeric contigs and removed. Taxonomic profiling was generated by the mapping of sequencing contigs/reads against catalogues generated from different microbiome samples in order to link genes to metagenome-assembled genomes (MAGs) and reconstruct the full-length 16S rRNA gene.