Additional file 2 of Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin

Additional file 2: Table S1. Characteristics of metagenomic samples analyzed in this study. Perc_reads_* columns indicate the percentage of reads that map stringently (95% identity) to the dereplicated archaeal/bacterial or phage genome set, respectively. Table S2. Phylogenetic affiliation and relative abundance of ribosomal protein S3 (rps3) 'species groups' used to define community composition. Table S3. Characteristics of bacterial and archaeal genomes analyzed in this study. Table S4. Metabolic HMMs involved in carbon metabolism and manually-assigned score thresholds. Table S5. Presence of metabolic HMMs/pathways across the bacterial/archaeal genome set, and their abundance by sample percentage_relative_coverage refers to the percent of total coverage of all genomes in the quality-filtered, non-redundant set within a sample attributable to a given genome. Table S6. Phylogenetic affiliation, form affiliation, and relative abundance of RuBisCO genes across samples percentage_relative_coverage refers to the percent of all coverage to RuBisCO-containing scaffolds within a sample attributable to a given scaffold. Table S7. Relative abundance (percentage relative coverage of all genomes in the non-redundant set) of CPR bacteria genomes across samples. Table S8. Metrics of enrichment for CPR protein families by lake compartment. Table S9. Characteristics of phage genomes analyzed in this study. Table S10. Relative abundance (percentage relative coverage of all genomes in the non-redundant set) of phage genomes across samples. Table S11. Metrics of enrichment for phage protein families by lake compartment. Table S12. Characteristics of Methylobacter/phage pmoC sequences analyzed in this study.