Shotgun Metagenomics of Environmental Samples

For each treatment, three samples were selected for shotgun metagenomics, resulting in a total of 18 sequenced samples. Libraries were prepared with a TruSeq PCR-free kit (Illumina). Samples were sequenced on a NovaSeq 6000 with a 2 × 151 setup, resulting in 800 million pair-reads. Low quality reads and adapters were removed with Trimmomatic v0.39^{70 (link)}. Co-assembly of short reads was done with Megahit^{71 (link)} using the --presets meta-large setting, resulting in 1,975,712 contigs of ≥1 kb, and N50 of 4375 bp. Reads were mapped to the co-assembly using Bowtie2 v2.3.5^{72 (link)}. Protein coding sequences in all the assembled contigs were identified with Prodigal v.2.6.3^{73 (link)}, using the meta prediction mode.