Additional file 1 of Conserved environmental adaptations of stream microbiomes in the hyporheic zone across North America

Supplementary Material 1: Stach_et_al_2025_Supplememtary_information: Figure S1: Visualization of the statistical comparison of microbial energy metabolism in sediment and surface water, encoded by the metagenome and expressed by the metatranscriptome. Figure S2: Phylogenetic analysis of homologous genes annotated as methane monooxygenase (mmo) and ammonia monooxygenase (amo), respectively, to decipher the functional annotation of genes retrieved from river metagenomes. Figure S3: Phylogenetic analysis of homologous genes annotated as nitrate reductase (nar) and nitrite oxidoreductase (nxr), respectively, to decipher proper annotation of homologous genes from river ecosystems. Table S1: Statistical testing of environmental impact on gene expression of the microbial community structure in stream sediments. Figure S4 and S5: Significantly upregulated (S4) and downregulated (S5) genes with abs(LFC) > 1 and adj. p-value < 0.05 due to stream order increase. Supplementary Material 2: Table SI1: Meta information of metatranscriptomic and metagenomic samples used in this study. Table SI2: Information on MAGs analyzed in this study. Table SI3: Metagenomic datasets used for building the gene database. Table SI4: Gene identity of genes displayed in UpSetPlot (Figure 4B). Table SI5: List of up- and downregulated genes displayed in Figure 5. Table SI6: Metagenomic and metatranscriptomic counts of metabolic pathways displayed in Figure 2. Table SI7: DRAM distill classification of energy pathways. SI8: Supplementary data for phylogenetic analysis of homologous genes as displayed in Figures S2 and S3. Table SI9: Data on encoded and expressed nitrogen and sulfur pathways as support for Figure 3.