Fig 1.
Phylogenetic position of “Candidatus Caldiarchaeum subterraneum” based on concatenated common protein sequences.
A maximum-likelihood tree was constructed using MEGA [25]. The phylogenetic trees were collapsed at the family level except for Nanoarchaeum, “Ca. Korarchaeum,” and “Ca. Caldiarchaeum.” (A) Concatenated alignment of the sequences of 22 common proteins with no paralogs and domain splitting (hisS, pheS, valS, rpl11p, rpl14p, rpl1P, rpl22p, rpl2p, rpl3p, rpl5p, rpl6p, rplW, rps10p, rps11p, rps19p, rps2P, rps3p, rps4p, rps5p, rps7p, rps8p, and rps9p) among 142 archaea, including “Ca. A. autotrophicum” and two bacteria as an outgroup, as listed in S1 Table. (B) Concatenated alignment of the sequences of 12 common protein sequences without paralogs and domain splitting (eif2G, rfcL, eif6, rpl10e, rpl15p, rpl18p, rpl7ae, rplP0, rps19p, rps3p, rps5p, and rio1) among 137 archaea, including “Ca. C. subterraneum” and 13 unicellular eukaryotes as the outgroup (S1 Table). The numbers indicate the bootstrap support expressed as percentages. Bootstrap values of less than 50% were omitted.
Fig 2.
Functional classification of archaea based on the MCR patterns of the KEGG modules.
csu, Ca. Caldiarchaeum subterraneum; nga, Ca. Nitrososphaera gargensis; nmr, Nitrosopumilus maritimus; csy, Cenarchaeum symbiosum. Full species names for all other abbreviations are listed in S2 Table. Orange circle, methanogens; yellow-green circle, halophiles; gray circle, hyperthermophilic facultative autotrophic sulfur reducers; blue circle, heterotrophic (hyper)-thermophilic acidophiles or neutrophiles; brown circle, chemolithoautotrophic or facultative autotrophic (hyper)-thermophilic acidophiles; green circle, facultative autotrophic ammonia oxidizers. *, methanogens, which can generate methane from all possible substrates (CO2, acetate, methanol, and methylamine); #, methanogens isolated from the human gut, which can generate methane only from methanol.
Fig 3.
Distribution of “Ca. C. subterraneum” along the first and second PCA axes based on MCR patterns.
Obligate and facultative anaerobes are denoted by triangles and squares, respectively. Aerobes are denoted by circles. X indicates uncultivated species. Light brown, Euryarchaeota; light blue, Crenarchaeota; green, Thaumarchaeota; gray, “Korarchaeota”; purple, Nanoarchaeota; csu, “Ca. Caldiarchaeum subterraneum”. Full species names for all other abbreviations are listed in S2 Table. MCR patterns of 273 modules (pathway: 161, structural complex: 101, and functional set: 11), except for those with the same MCR values, among 79 archaea were subjected to this analysis.
Fig 4.
Comparison of MCR patterns for carbon fixation in “Ca. C. subterraneum” and three thaumarchaeotic species.
1. MCR patterns of six major carbon fixation pathways. 3–HP bicycle, 3–hydroxypropionate bicycle; HP–HB cycle, hydroxypropionate–hydroxybutyrate cycle; dicarboxylate HB cycle, dicarboxylate hydroxybutyrate cycle; 2, Mapping patterns of genes to two carbon fixation modules. Numbers in parentheses show the order of reaction steps in each module. In each “K number” set of components of the module, the vertically connected and horizontally located K numbers indicate complexes and alternatives, respectively [19]. (A) Reductive TCA cycle (M00173). *Specific enzymes for this pathway; §found only in Cenarchaeum symbiosum. (B) HP–HB cycle (M00375). Numbers in red show the reaction steps for which the corresponding genes were not identified in the genomes of the three thaumarchaeotic species, although their enzymatic activities have been detected experimentally [44]. *The gene responsible for step 3 has been experimentally identified in the N. maritimus genome very recently, whereas the K number has not yet been assigned to the gene (Nmar_1110) by KEGG [48]. **Because the K numbers were incorrectly assigned to the genes of thaumarchaeotic species, the genes responsible for steps 10 and 11 have not yet been identified in their genomes.
Fig 5.
Major central carbohydrate metabolism in “Ca. C. subterraneum.”
1. Comparison of the MCR patterns between aigarchaeotic and thaumarchaeotic species. csu, Ca. Caldiarchaeum subterraneum; nmr, Nitrosopumilus maritimus; nga, Ca. Nitrososphaera gargensis; csy, Cenarchaeum symbiosum. 2. Pathway map for central carbohydrate metabolism (left side) and mapping pattern of the modules corresponding to the pathway map in Ca. C. subterraneum (right side). In each “K number” set of components of the module, the vertically connected and horizontally located K numbers indicate complexes and alternatives, respectively [19]. K numbers in blue boxes indicate the orthologous genes identified in Ca. C. subterraneum. Grayish dashed lines and arrows show missing reaction steps in the pathway. Numbers in parentheses on each module component correspond to those on the pathway map. A1, glycolysis (M0001): (1), glucokinase; (2), glucose/mannose-6-phosphate isomerase; (3), 6-phosphofructokinase or ADP-dependent phosphofructokinase/glucokinase; (4), fructose-bisphosphate aldolase; (5), triosephosphate isomerase; (6), glyceraldehyde-3-phosphate dehydrogenase; (7), phosphoglycerate kinase; (8), 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; (9), enolase; (10), pyruvate kinase. A2, gluconeogenesis (M0003): (1), ADP-dependent phosphofructokinase/glucokinase; (2), enolase; (3), 2,3-bisphosphoglycerate- independent phosphoglycerate mutase; (4), phosphoglycerate kinase; (5), glyceraldehyde-3-phosphate dehydrogenase, (6), triosephosphate isomerase; (7), fructose 1,6-bisphosphate aldolase/phosphatase. B, pyruvate oxidation (M00307): (1), pyruvate dehydrogenase. C, TCA (Krebs) cycle (M0009): (1), citrate synthase; (2), aconitate hydratase; (3), isocitrate dehydrogenase; (4), 2-oxoglutarate dehydrogenase; (5), succinyl-CoA synthetase; (6), succinate dehydrogenase; (7), fumarate hydratase, class II; (8), malate dehydrogenase. D, glyoxylate cycle (M00012): (1), citrate synthase; (2), aconitate hydratase; (3), isocitrate lyase; (4), malate synthase; (5), malate dehydrogenase. M number shows identifier of each KEGG module. E, Crassulacean acid metabolism–light (M00169): (1), malate dehydrogenase; (2), pyruvate, orthophosphate dikinase. K numbers shown in red have not been assigned to the KEGG module, but similar enzymatic reactions to the K numbers assigned to the module have been confirmed. The reaction component shown by the red frame in the TCA cycle shows αβ-heterodimeric 2-oxoacid:ferredoxin oxidoreductase [55, 56], which is not yet reflected in the KEGG module.
Fig 6.
Sugar and blanched chain amino acid (BCAA) ABC transporters module abundance in Ca. C. subterraneum and thaumarchaeotic species.
K numbers in blue boxes indicate the orthologous genes identified in each species. csu, Ca. Caldiarchaeum subterraneum; nmr, Nitrosopumilus maritimus; nga, Ca. Nitrososphaera gargensis; csy, Cenarchaeum symbiosum. Grayish characters indicate the species with no gene set in the module. M numbers indicate the module IDs defined by KEGG.