Fig. 3: Transcriptome profiling shows distinct expression responses of co-existing planktonic and attached syntrophic communities.
From: Origin of biogeographically distinct ecotypes during laboratory evolution
A Heatmap (rows: genes) of z-scored expression (TPMs) of sequentially ordered significantly expressed genes (Fold Change > 2, p-value < 0.01, DESeq2 Wald test) for each day (planktonic vs attached) and split between up- or downregulated genes for Mm and Dv. All p-values can be found in supplementary data file 3. Right side annotation represents the log10 mean expression level for each gene across all samples (n = 35). B PCA of transcriptomic data of the evolved community from this study and cocultured planktonic WT Dv and Mm cells from a previously published study showing transcriptional states changes resulting from 1000 generations of syntrophic growth and between phases. C Genes encoding central functions (lactate permeases: n = 3, Flagella: n = 13, Dv Hydrogenases: n = 12, Mm High-Affinity Hydrogenases: n = 23, Mm Low-Affinity Hydrogenases: n = 4) for syntrophic interactions between Dv (orange) and Mm (gray) have distinct expression patterns across planktonic and the sediment attached phase. All error bars indicate the standard deviation (95% Confidence Interval) from the mean (marker) across 3 replicate FBRs. Source data are provided as a Source Data file.
