Fig. 2: Energy metabolism of strain 3DAC.

a Schematic diagram of the energetic process in strain 3DAC. Red shapes represent archaeal orthologs. Gray shapes represent bacterial orthologs. Solid lines represent enzymatic reactions. Dotted lines represent abiotic reactions. Differentially expressed genes were identified using DESeq2 (version 1.12.4). The default DESeq function with betaPrior = FALSE was applied, wherein a negative binomial generalized model with Wald test for significance was performed. The two-sided p-values were corrected for multiple testing using the Benjamini–Hochberg method. Blue arrows indicate significant up- or down-regulation with sulfur in the culture medium based on transcriptomic data [n = 3 per treatment, log2(fold change) >1, P value < 0.05] (Supplementary Data 1). This figure was created using BioRender (https://biorender.com/). b Growth capabilities on varied carbon sources of strain 3DAC. Computational predictions were simulated by the genome-scale metabolic model of 3DAC (Supplementary Data 1). “20aa”: all 20 amino acids supplemented as the sole carbon source. “20aa-X”: removal of individual amino acids X. “20aa+Y”: extra carbon source Y supplied with 20 amino acids. “+”: similar growth yields compared with the 20aa condition; “++”: at least 1.5-fold higher growth yields than 20aa; “-”: no growth. c Sulfide concentration and OD₆₀₀ during the growth of strain 3DAC. S: medium with elemental sulfur; NS: no elemental sulfur. Error bars represent the standard deviations (SDs) from independent biological triplicates (n = 3) during the experiments under 0.1 MPa. Data are presented as average values ± SD. d Experimental and computational growth yields of the 3DAC strain by utilizing various sulfur species. In the experimental group, error bars represent the standard deviations (SDs) from independent biological duplicates (n = 2) during the experiments under 0.1 MPa. Data are presented as average values ± SD. e Simulations of wild-type 3DAC (WT), single deletions (-MBS, -Nfn2, -SH1), double deletions (-MBS-Nfn2, -MBS-SH1 and -Nfn2-SH1) and triple deletions (-MBS-Nfn2-SH1) of archaea-derived complexes in energetic processes at 3DAC. Source data are provided as a Source Data file.