MOESM2 of The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities

Additional file 1: Table S1. Type of environment, latitude and longitude for all sampled stations. Table S2. Overview of all samples included in the analyses. Table S3. PCR program for 16S rRNA gene amplicon sequencing. Table S4. The best-fit models of qPCR 16S rRNA gene copies for air samples and surface samples. Table S5. Top 20 phyla, families, and genera and species in surface samples collected on kiosks, benches, and railings. Table S6. Random forest classification models of samples collected from different surface types. Figure S1. The significant predictors of qPCR 16S rRNA gene copy yields in air samples. Figure S2. The significant predictors of qPCR 16S rRNA gene copy yields in surface samples. Figure S3. Quality profile of filtered reads. Figure S4. Rarefaction curves with observed diversity and Shannon’s Diversity Index. Figure S5. A) Relative abundances of the top 15 phyla across the three surface types and seasons. B) Heatmap of most abundant families. Figure S6. Top 20 most important genera in random forest classification analysis of samples collected in different seasons. Figure S7. Top 20 most important genera in random forest classification analysis of air and surface samples. Figure S8. Interaction effect between temperature (°C) and air/surface in the linear model of Shannon’s diversity index. Figure S9. PCoA plot of Bray Curtis dissimilarity distances with the only significant predictor (surface type) from the PERMANOVA model that included only surface-specific predictors

Analysis of multivariate homogeneity of group dispersions.

Analysis of multivariate homogeneity of group dispersions.</p

Effects of time and concentration on the diversity indices.

Effects of time and concentration on the diversity indices.</p

Differential abundance analysis of gut bacteria in <i>Daphnia magna</i> exposed to Ciprofloxacin.

Bacterial genera significantly associated with (a) exposure to Ciprofloxacin; (b) high somatic growth and fecundity of the host observed during the experiment. The fold change (log2FC) and the associated statistics were determined using the edgeR package.</p

Alpha diversity indices (Chao1, ACE, Shannon-Weiner and Fisher’s alpha) for gut microbiota in <i>Daphnia magna</i>.

Alpha diversity indices (Chao1, ACE, Shannon-Weiner and Fisher’s alpha) for gut microbiota in Daphnia magna.</p

Individual growth curves analyzed by empirical von Bertalanffy model.

Estimated BLmax and K values (Eq 1) and corresponding 95%-confidence limits for Daphnia magna grown in 0.01, 0.1 and 1 mg L-1 Ciprofloxacin and the control.</p

Principle Coordinate Analysis (PCoA) based on Bray Curtis dissimilarity metrics, showing the distance in the bacterial communities between the treatments.

Principle Coordinate Analysis (PCoA) based on Bray Curtis dissimilarity metrics, showing the distance in the bacterial communities between the treatments.</p

Effects of exposure (Ciprofloxacin, mg mL^-1) on the antioxidant capacity in <i>Daphnia magna</i>.

Effects of exposure (Ciprofloxacin, mg mL-1) on the antioxidant capacity in Daphnia magna.</p

Body growth parameters estimated by von Bertalanffy model.

Body growth parameters estimated by von Bertalanffy model.</p

Pairwise comparison of treatments using Bray-Curtis dissimilarity.

Pairwise comparison of treatments using Bray-Curtis dissimilarity.</p