DOI: 10.6084/m9.figshare.25294811
title: Additional file 2 of Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil

description: Additional file 2: Table S1. Forward and reverse primers used in qPCR and RT-qPCR. Table S2. Sequencing statistics of metatranscriptomic datasets. Table S3. Sequencing statistics of near full-length 16S rRNA sequences. Table S4. Sequencing statistics of mRNA sequences. Table S5. Sequencing statistics of the metagenomic datasets. Table S6. Significance analysis for the quantification of bacterial 16S rRNA gene copy numbers. Table S7. Significance analysis for the quantification of mcrA gene copy numbers. Table S8. Significance analysis for the quantification of bacterial 16S rRNA transcripts. Table S9. Significance analysis for the quantification of mcrA transcripts. Table S10a. Analysis of the taxon-specific abundance on rRNA level, using the software STAMP. PFDR values ≤ 0.05 are indicative of signficant changes in family-level abundance across the complete 120-day incubation period. The resulting p values were corrected (PFDR) for multiple testing using the Benjamini-Hochberg method. Table S10b. Analysis for incubation time-dependent abundance changes of dominant family-level taxa on rRNA level, using the package DESeq2 in R. The resulting p values were corrected (PFDR) for multiple testing using the Benjamini-Hochberg method. PFDR values ≤ 0.05 are indicative of signficant difference in taxon-specific rRNA abundance between two particular incubation time points. Table S11a. Analysis of the taxon-specific abundance on mRNA level, using the software STAMP. The resulting p values were corrected (PFDR) for multiple testing using the Benjamini-Hochberg method. PFDR values ≤ 0.05 are indicative of signficant changes in family-level abundance across the complete 120-day incubation period. Table S11b. Analysis for incubation time-dependent abundance changes of dominant family-level taxa on mRNA level, using the package DESeq2 in R.The resulting p values were corrected (PFDR) for multiple testing using the Benjamini-Hochberg method. PFDR values ≤ 0.05 are indicative of signficant difference in taxon-specific mRNA abundance between two particular incubation time points. Table S12. List of CAZyme families whose transcripts were detected in the metatranscriptomic datasets during the 120-day incubation period. Table S13a. Analysis for the mapping-independent abundance of genes involved in methanogenesis, using the software STAMP. The resulting p values were corrected (PFDR) for multiple testing using the Benjamini-Hochberg method. PFDR  values ≤ 0.05 are indicative of significant difference in relative transcript abundance across all the incubation times tested. Table S13b. Analysis for the mapping-independent abundance of genes involved in methanogenesis, using the package DESeq2 in R. The resulting p values were corrected (PFDR) for multiple testing using the Benjamini-Hochberg method. PFDR values ≤ 0.05 are indicative of signficant difference in relative transcript abundance between two particular incubation time points. Table S14. The full name of enzymes involved acetoclastic, hydrogenotrophic, and  methylotrophic methanogenesis. Table S15. List of KEGG-annotated genes detected in the three Methanosarcina MAGs (21, 28, 35), but not in the Methanosarcina Groups I to IV reference genomes. Table S16. Copy number of KEGG-annotated genes present in both the three Methanosarcina MAGs (21, 28, 35) and the Methanosarcina Groups I to IV reference genomes. Table S17. KEGG level 2 analysis of mRNA mapped to the three Methanosarcina MAGs (21, 28, 35). The relative abundance values (%) are given in relation to total mapped mRNA functionally annotated by KEGG. The relative expression levels were calculated based on TPM values (means ± SE, n = 3). Table S18. KEGG level 3 analysis of mRNA mapped to the three Methanosarcina MAGs (21, 28, 35). The relative abundance values (%) are given in relation to total mapped mRNA functionally annotated by KEGG. The relative expression levels were calculated based on TPM values (means ± SE, n = 3). Table S19a. Analysis for the mapping-dependent abundance of genes involved in methanogenesis, using the software STAMP. The resulting p values were corrected (PFDR) for multiple testing using the Benjamini-Hochberg method. PFDR values ≤ 0.05 are indicative of significant difference in transcript mapping accross all three MAGs. Table S19b. Analysis for the mapping-dependent abundance of genes involved in methanogenesis, using the package DESeq2 in R. The resulting p values were corrected (PFDR) for multiple testing using the Benjamini-Hochberg method. PFDR values ≤ 0.05 are indicative of significant difference in transcript mapping between two particular incubation time points. Table S20. Statistics of transcript mapping to the three MAGs (21, 28, 25) and the Methanosarcina Groups I to IV reference genomes. Table S21a. Contigs of putative laccase-like genes (GeoLacc) expressed by members of the Geobacteraceae. Table S21b. TPM values of putative laccase-like genes (GeoLacc) expressed by members of the Geobacteraceae.