Fig. 2 in Isolation of an archaeon at the prokaryote eukaryote interface

Fig. 2 | Syntrophic amino acid utilization of MK-D1. a, Genome-based metabolic reconstruction of MK-D1.Metabolic pathways identified (coloured or black) and not identified (grey) are shown.For identified pathways,each step (solid line) or process (dotted) is marked by whether it is oxidative (red), reductive (blue),ATP-yielding (orange) or ATP-consuming (purple).Wavy arrows indicate exchange of compounds:formate,H2, amino acids,vitamin B12, biotin, lipoate and thiamine pyrophosphate (TPP),which are predicted to be metabolized or synthesized by the partnering Halodesulfovibrio and/or Methanogenium. Biosynthetic pathways are indicated with a yellow background.Metatranscriptomics-detected amino-acid-catabolizing pathways are indicated (black dots above amino acids).DHDH,4,5-dihydroxy- 2,6-dioxohexanoate;DHDG,2-dehydro-3-deoxy-d-gluconate;DHDG6P, 3-dehydro-3-deoxy-d-gluconate 6-phosphate;Ac-CoA,acetyl-CoA;uro, urocanate;Fo-Glu,formyl glutamate;CH3=H4F,methylene-tetrahydrofolate; CH≡H4F,methenyl-tetrahydrofolate;Fo-H4F,formyl-tetrahydrofolate;2OB, 2-oxobutyrate;Prop-CoA,propionyl-CoA;ACAC,acetoacetate; GB-CoA, γ-amino-butyryl-CoA;But-CoA,butyryl-CoA;Fd,ferredoxin;XSH/X-S-S-X, thiol/disulfide pair; TCA,tricarboxylic acid cycle;PPP,pentose-phosphate pathway.b–e, NanoSIMS analysis of a highly purified MK-D1 culture incubated with a mixture of 13C- and 15N-labelled amino acids.b, Green fluorescent micrograph of SYBR Green I-stained cells.Aggregates are MK-D1,and filamentous cells are Methanobacterium sp. strain MO-MB1 (fluorescence can be weak owing to the high rigidity and low permeability of the cell membrane (Extended Data Fig.2m,n; see also ref.49). c, NanoSIMS ion image of 12C (cyan). d, NanoSIMS ion image of 12C15N/12C14N (magenta).e, Overlay image of b–d. d, The colour bar indicates the relative abundance of 15N expressed as 15N/14N. Scale bars 5 µm.The NanoSIMS analysis was performed without replicates due to its slow growth rate and low cell density.However,to ensure the reproducibility,we used two different types of highly purified cultures of MK-D1 (see Methods).Representative of n = 8 recorded images.The iTAG analysis of the imaged culture is shown in Supplementary Table 1.