Fig. 6
Relative mRNA abundance dynamics of individual methanogenic pathways over incubation time a, transcript dynamics of related key pathway genes b, and taxonomic assignment of the transcripts c. A list of the full gene names is shown in Table S14. The relative abundance values are given in relation to total mRNA affiliated to the KEGG level 3 category “methane metabolism”. The relative expression levels were calculated based on TPM values. Data are means ± SE (n = 3). Asterisks * (PFDR≤0.05), ** (PFDR≤0.01), and *** (PFDR≤0.001) indicate significant differences. Asterisks shown aside from the gene names indicate that in STAMP, the relative mRNA abundance significantly changed through the whole incubation period. Asterisks directly shown in the heatmap (b) indicate that in DESeq2, the mRNA abundance in that particular sampling time point significantly differed from the original abundance at the first sampling (day 3) or vice versa that the relative mRNA abundance (ack) at day 3 significantly differed from all other sampling time points. Significance values (PFDR) are only indicated for the peak transcript abundance(s) of each key pathway gene. c The percentage of acs transcripts affiliated with Methanocellaceae (acetate assimilation) was 68.1% on day 120, while those affiliated with Methanotrichaceae (acetoclastic methanogenesis) contributed 31.9%. The complete set of PFDR values obtained in DESeq2 analysis for all sampling time points is shown in Table S13