Additional file 2 of Environmental drivers of the resistome across the Baltic Sea

Additional file 2 (Supplementary-Tables.xls): Supplementary Table S1 Metadata: Sample information and environmental factors from Broman et al. (2022). Metagenomics sequence codes, site descriptors, i.e. region, station, haversine distance (km), coordinates, and physicochemical factors, i.e., water depth (m), salinity, temperature, dissolved O2 (mg/L), concentrations of total carbon (TC) and total nitrogen (TN) (µmol/g), and their ratio—C/N, and isotopic signatures, i.e., stable 13C and 15N isotope compositions (‰). Supplementary Table S2 Metagenomics data processing information: Sequence codes, raw read counts, quality-filtered and adapter trimmed, contaminant filtered, error corrected read counts, and contig assembly stat values. Supplementary Table S3 Relative abundance table of the microbial community based on mOTUs profiler. Supplementary Table S4 Comparison of methods for antimicrobial resistance gene (ARG) profiling. Supplementary Table S5 Antimicrobial resistance gene (ARG) data: Reads per kilobase million (RPKM) absolute counts. Supplementary Table S6 Mobile resistance gene (MRG) data: RPKM absolute counts. Supplementary Table S7 Mobile genetic elements (MGE) data: RPKM absolute counts. Supplementary Table S8 Virulence factor gene (VFG) data: RPKM absolute counts. Supplementary Table S9 Differential abundance test by Random Forests for ARG subtypes per region. Supplementary Table S10 Antimicrobial resistance genes (ARG) alpha diversity estimates per sample. Supplementary Table S11 Statistical results of Levene’s test for homogeneity of variance of the alpha diversity estimates. Supplementary Table S12 Statistical results of the permutation test for homogeneity of multivariate dispersions and permutation test for adonis under a reduced model for the microbial composition, ARG, MRG, MGE, and VFG data. Supplementary Table S13 Differential abundance test by Random Forests for the species per region. Supplementary Table S14 Summary statistics of the partial least squares path model (PLS-PM) in R of the latent variables—microbial communities, MGEs, VFGs, ARGs, and MRGs. Supplementary Table S15 Statistical results of the Procrustes analysis in R of ARG composition based on Bray-Curtis distance against the microbial communities, MRGs, MGEs, and VFGs. Supplementary Table S16 Statistical results of the Mantel test in R of ARG composition based on Bray-Curtis distance against the microbial communities, MRGs, MGEs, and VFGs. Supplementary Table S17 Statistical results of the General additive models (GAMs) in R of the alpha diversity and environmental factors. Supplementary Table S18 Statistical results of the permutation test for dbRDA analyses in R of the ARG composition and environmental factors. Supplementary Table S19 Spearman’s rank correlation between ARG alpha diversity metrics and environmental factors.