Fig. 1

Differential gene expression of nutrient-rich (exponential phase) and nutrient-limited (stationary phase) cultures of Thermomicrobium roseum. a Volcano plot showing relative expression change of genes following nutrient limitation. The fold-change shows the ratio of normalised transcript abundance of three stationary phase cultures divided by three exponential phase cultures (biological replicates). Each gene is represented by a grey dot and respiratory genes are highlighted as per the legend. b, c Heat maps of normalised abundance of the putative operons encoding the structural subunits of the group 1h [NiFe]-hydrogenase (hhyLS; b) and type I carbon monoxide dehydrogenase (coxLSM; c). The read counts per kilobase million (RPKM) are shown for three exponentially growing and three stationary phase biological replicates. HP = hypothetical protein. d Differential regulation of the respiratory complexes mediating aerobic respiration of organic and inorganic compounds. Complexes are differentially shaded depending on whether they are significantly upregulated (green), downregulated (orange), or unchanged (grey) in nutrient-limited compared to nutrient-rich cultures. Gene names, loci numbers, and average fold changes in transcriptome abundance are shown for each complex. Shown are the structural subunits of type I NADH dehydrogenase (nuoA-E,H-N), type II NADH dehydrogenase (ndh), succinate dehydrogenase (sdhA-D), group 1h [NiFe]-hydrogenase (hhyLS), type I carbon monoxide dehydrogenase (coxLMS), heterodisulfide reductase (hdrABC), electron transfer flavoprotein (etfAB), sulfur-carrier protein (tusA), cytochrome aa₃ oxidase (coxABC), cytochrome bo₃ oxidase (cyoAB), and ATP synthase (atpA-H). Note that the physiological role of the highly upregulated hdrABC, etfAB, and tusA genes is yet to be experimentally validated in T. roseum