Weiss, S. et al. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. ISME J. 10, 1669–1681 (2016).
Google Scholar
Djokic, T., Kranendonk, M. J. V., Campbell, K. A., Walter, M. R. & Ward, C. R. Earliest signs of life on land preserved in ca. 3.5 Ga hot spring deposits. Nat. Commun. 8, 1–9 (2017).
Damer, B. & Deamer, D. The Hot Spring Hypothesis for an origin of life. Astrobiology 20, 429–452 (2020).
Google Scholar
Van Kranendonk, M. J. et al. Elements for the origin of life on land: a deep-time perspective from the Pilbara Craton of Western Australia. Astrobiology 21, 39–59 (2021).
Google Scholar
Colman, D. R. et al. Phylogenomic analysis of novel Diaforarchaea is consistent with sulfite but not sulfate reduction in volcanic environments on early Earth. ISME J. 14, 1316–1331 (2020).
Google Scholar
Anbar, A. D. & Knoll, A. H. Proterozoic ocean chemistry and evolution: a bioinorganic bridge? Science 297, 1137–1142 (2002).
Google Scholar
Lloyd, K. G. et al. Phylogenetically novel uncultured microbial cells dominate Earth microbiomes. mSystems 3, 431 (2018).
Hedlund, B. P. et al. Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’. Curr. Opin. Microbiol. 25, 136–145 (2015).
Google Scholar
Nunoura, T. et al. Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragments. Environ. Microbiol. 7, 1967–1984 (2005).
Google Scholar
Nunoura, T. et al. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res. 39, 3204–3223 (2010).
Google Scholar
Rinke, C. et al. A standardized archaeal taxonomy for the Genome Taxonomy Database. Nat. Microbiol. 6, 946–959 (2021).
Google Scholar
Hua, Z.-S. et al. Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Nat. Commun. 9, 1–11 (2018).
Google Scholar
Takami, H., Arai, W., Takemoto, K., Uchiyama, I. & Taniguchi, T. Functional classification of uncultured ‘Candidatus Caldiarchaeum subterraneum’ using the Maple system. PLoS ONE 10, e0132994 (2015).
Google Scholar
Beam, J. P. et al. Ecophysiology of an uncultivated lineage of Aigarchaeota from an oxic, hot spring filamentous ‘streamer’ community. ISME J. 10, 210–224 (2016).
Google Scholar
Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013).
Google Scholar
Cole, J. K. et al. Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities. ISME J. 7, 718–729 (2013).
Google Scholar
Peacock, J. P. et al. Pyrosequencing reveals high-temperature cellulolytic microbial consortia in Great Boiling Spring after in situ lignocellulose enrichment. PLoS ONE 8, e59927 (2013).
Google Scholar
Kletzin, A. & Adams, M. W. W. Tungsten in biological systems. FEMS Microbiol. Rev. 18, 5–63 (1996).
Google Scholar
Hagedoorn, P. L. et al. Purification and characterization of the tungsten enzyme aldehyde:ferredoxin oxidoreductase from the hyperthermophilic denitrifier Pyrobaculum aerophilum. J. Biol. Inorg. Chem. 10, 259–269 (2005).
Google Scholar
de Vries, S. et al. Adaptation to a high-tungsten environment: Pyrobaculum aerophilum contains an active tungsten nitrate reductase. Biochemistry 49, 9911–9921 (2010).
Google Scholar
Bräsen, C., Esser, D., Rauch, B. & Siebers, B. Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation. Microbiol. Mol. Biol. Rev. 78, 89–175 (2014).
Kato, S. et al. Long-term cultivation and metagenomics reveal ecophysiology of previously uncultivated thermophiles involved in biogeochemical nitrogen cycle. Microbes Environ. 33, 107–110 (2018).
Google Scholar
Costa, K. C. et al. Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin. Extremophiles 13, 447–459 (2009).
Google Scholar
Mukund, S. & Adams, M. W. The novel tungsten-iron-sulfur protein of the hyperthermophilic archaebacterium, Pyrococcus furiosus, is an aldehyde ferredoxin oxidoreductase. Evidence for its participation in a unique glycolytic pathway. J. Biol. Chem. 266, 14208–14216 (1991).
Google Scholar
Mukund, S. & Adams, M. W. W. Glyceraldehyde-3-phosphate ferredoxin oxidoreductase, a novel tungsten-containing enzyme with a potential glycolytic role in the hyperthermophilic archaeon Pyrococcus furiosus. J. Biol. Chem. 270, 8389–8392 (1995).
Google Scholar
Roy, R. et al. Purification and molecular characterization of the tungsten-containing formaldehyde ferredoxin oxidoreductase from the hyperthermophilic archaeon Pyrococcus furiosus: the third of a putative five-member tungstoenzyme family. J. Bacteriol. 181, 1171–1180 (1999).
Google Scholar
Roy, R. & Adams, M. W. W. Characterization of a fourth tungsten-containing enzyme from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 184, 6952–6956 (2002).
Google Scholar
Bevers, L. E., Bol, E., Hagedoorn, P.-L. & Hagen, W. R. WOR5, a novel tungsten-containing aldehyde oxidoreductase from Pyrococcus furiosus with a broad substrate specificity. J. Bacteriol. 187, 7056–7061 (2005).
Google Scholar
Habib, U. & Hoffman, M. Effect of molybdenum and tungsten on the reduction of nitrate in nitrate reductase, a DFT study. Chem. Cent. J. 11, 1–12 (2017).
Liao, R.-Z. Why is the molybdenum-substituted tungsten-dependent formaldehyde ferredoxin oxidoreductase not active? A quantum chemical study. J. Biol. Inorg. Chem. 18, 175–181 (2013).
Google Scholar
Qian, H.-X. & Liao, R.-Z. QM/MM study of tungsten-dependent benzoyl-coenzyme A reductase: rationalization of regioselectivity and predication of W vs Mo selectivity. Inorg. Chem. 57, 10667–10678 (2018).
Google Scholar
Liu, Y.-F., Liao, R.-Z., Ding, W.-J., Yu, J.-G. & Liu, R.-Z. Theoretical investigation of the first-shell mechanism of acetylene hydration catalyzed by a biomimetic tungsten complex. JBIC 16, 745–752 (2011).
Google Scholar
Kerr, P. F. Tungsten-bearing manganese deposit at Golconda, Nevada. Geol. Soc. Am. Bull. 51, 1359–1390 (1940).
Google Scholar
Mukund, S. & Adams, M. W. W. Molybdenum and vanadium do not replace tungsten in the catalytically active forms of the three tungstoenzymes in the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 178, 163–167 (1996).
Google Scholar
Debnar-Daumler, C., Seubert, A., Schmitt, G. & Heider, J. Simultaneous involvement of a tungsten-containing aldehyde:ferredoxin oxidoreductase and a phenylacetaldehyde dehydrogenase in anaerobic phenylalanine metabolism. J. Bacteriol. 196, 483–492 (2014).
Google Scholar
Scott, I. M. et al. A new class of tungsten-containing oxidoreductase in Caldicellulosiruptor, a genus of plant biomass-degrading thermophilic bacteria. Appl. Environ. Microbiol. 81, 7339–7347 (2015).
Google Scholar
Scott, I. M. et al. The thermophilic biomass-degrading bacterium Caldicellulosiruptor bescii utilizes two enzymes to oxidize glyceraldehyde 3-phosphate during glycolysis. J. Biol. Chem. 294, 9995–10005 (2019).
Google Scholar
Johnson, J. L., Rajagopalan, K. V., Mukund, S. & Adams, M. W. Identification of molybdopterin as the organic component of the tungsten cofactor in four enzymes from hyperthermophilic Archaea. J. Biol. Chem. 268, 4848–4852 (1993).
Google Scholar
Chan, M. K., Mukund, S., Kletzin, A., Adams, M. W. & Rees, D. C. Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase. Science 267, 1463–1469 (1995).
Google Scholar
Glass, J. B. et al. Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane‐oxidizing microbial consortia in sulphidic marine sediments. Environ. Microbiol. 16, 1592–1611 (2014).
Google Scholar
Li, G.-W., Burkhardt, D., Gross, C. & Weissman, J. S. Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157, 624–635 (2014).
Google Scholar
Behrens, S. et al. Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeling-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and NanoSIMS. Appl. Environ. Microbiol. 74, 3143–3150. https://doi.org/10.1128/AEM.00191-08 (2008).
Knapik, K., Becerra, M. & González-Siso, M.-I. Microbial diversity analysis and screening for novel xylanase enzymes from the sediment of the Lobios Hot Spring in Spain. Sci. Rep. 9, 11195 (2019).
Google Scholar
Roy, R., Dhawan, I. K., Johnson, M. K., Rees, D. C. & Adams, M. W. Aldehyde Ferredoxin Oxidoreductase. 266 (American Cancer Society, 2011).
Sevcenco, A.-M. et al. The tungsten metallome of Pyrococcus furiosus. Metallomics 1, 395–402 (2009).
Google Scholar
Sakuraba, H. & Ohshima, T. Novel energy metabolism in anaerobic hyperthermophilic archaea: a modified Embden-Meyerhof pathway. J. Biosci. Bioeng. 93, 441–448 (2002).
Google Scholar
Ma, K., Hutchins, A., Sung, S.-J. S. & Adams, M. W. W. Pyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon, Pyrococcus furiosus, functions as a CoA-dependent pyruvate decarboxylase. Proc. Natl Acad. Sci. USA 94, 9608–9613 (1997).
Google Scholar
Mai, X. & Adams, M. W. Characterization of a fourth type of 2-keto acid-oxidizing enzyme from a hyperthermophilic archaeon: 2-ketoglutarate ferredoxin oxidoreductase from Thermococcus litoralis. J. Bacteriol. 178, 5890–5896 (1996).
Google Scholar
Adams, M. W. W. & Kletzin, A. Oxidoreductase-type enzymes and redox proteins involved in fermentative metabolisms of hyperthermophilic archaea. Adv. Prot. Chem. 48, 101–180 (1996).
Google Scholar
Mulkidjanian, A. Y., Galperin, M. Y., Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Evolutionary primacy of sodium bioenergetics. Biol. Direct 3, 1–19 (2008).
Heider, J., Ma, K. & Adams, M. W. W. Purification, characterization, and metabolic function of tungsten-containing aldehyde ferredoxin oxidoreductase from the hyperthermophilic and proteolytic archaeon Thermococcus strain ES-1. J. Bacteriol. 177, 4757–4764 (1995).
Google Scholar
Schut, G. J. et al. The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications. FEMS Microbiol. Rev. 37, 182–203 (2013).
Google Scholar
Kuhns, M., Trifunović, D., Huber, H. & Müller, V. The Rnf complex is a Na+ coupled respiratory enzyme in a fermenting bacterium, Thermotoga maritima. Commun. Biol. 3, 1–10 (2020).
Sapra, R., Verhagen, M. F. J. M. & Adams, M. W. W. Purification and characterization of a membrane-bound hydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol. 182, 3423–3428 (2000).
Google Scholar
Sapra, R., Bagramyan, K. & Adams, M. W. W. A simple energy-conserving system: Proton reduction coupled to proton translocation. Proc. Natl Acad. Sci. USA 100, 7545–7550 (2003).
Google Scholar
Schut, G. J. et al. The role of geochemistry and energetics in the evolution of modern respiratory complexes from a proton-reducing ancestor. Biochim. Biophys. Acta Bioenerg. 1857, 958–970 (2016).
Google Scholar
Juszczak, A., Aono, S. & Adams, M. W. The extremely thermophilic eubacterium, Thermotoga maritima, contains a novel iron-hydrogenase whose cellular activity is dependent upon tungsten. J. Biol. Chem. 266, 13834–13841 (1991).
Google Scholar
Selig, M., Xavier, K. B., Santos, H. & Schönheit, P. Comparative analysis of Embden-Meyerhof and Entner-Doudoroff glycolytic pathways in hyperthermophilic archaea and the bacterium Thermotoga. Arch. Microbiol. 167, 217–232 (1997).
Google Scholar
Zhang, Y. & Gladyshev, V. N. Molybdoproteomes and evolution of molybdenum utilization. J. Mol. Biol. 379, 881–899 (2008).
Google Scholar
Anbar, A. D. et al. A whiff of oxygen before the Great Oxidation Event? Science 317, 1903–1906 (2007).
Neubert, N., Nägler, T. F. & Böttcher, M. E. Sulfidity controls molybdenum isotope fractionation into euxinic sediments: evidence from the modern Black Sea. Geology 36, 775–778 (2008).
Google Scholar
Helz, G. R. et al. Mechanism of molybdenum removal from the sea and its concentration in black shales: EXAFS evidence. Geochim. Cosmochim. Acta 60, 3631–3642 (1996).
Google Scholar
Shen, Y., Buick, R. & Canfield, D. E. Isotopic evidence for microbial sulphate reduction in the early Archaean era. Nature 410, 77–81 (2001).
Google Scholar
Dodsworth, J. A. et al. Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov. Int. J. Sys. Evol. Microbiol. 64, 2119–2127 (2014).
Google Scholar
Hanada, S., Hiraishi, A., Shimada, K. & Matsuura, K. Chloroflexus aggregans sp. nov., a filamentous phototrophic bacterium which forms dense cell aggregates by active gliding movement. Int. J. Sys. Evol. Microbiol. 45, 676–681 (1995).
Google Scholar
Murugapiran, S. K. et al. Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling. Stand. Genom. Sci. 7, 449–468 (2013).
Google Scholar
Kozich, J. J., Westcott, S. L., Baker, N. T., Highlander, S. K. & Schloss, P. D. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina Sequencing Platform. Appl. Environ. Microbiol. 79, 5112–5120 (2013).
Friel, A. D. et al. Microbiome shifts associated with the introduction of wild atlantic horseshoe crabs (Limulus polyphemus) into a touch-tank exhibit. Front. Microbiol. 11, 1398 (2020).
Hamilton, T. L., Peters, J. W., Skidmore, M. L. & Boyd, E. S. Molecular evidence for an active endogenous microbiome beneath glacial ice. ISME J. 7, 1402–1412 (2013).
Google Scholar
Courtois, S. et al. Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ. Microbiol. 3, 431–439 (2001).
Google Scholar
Pernthaler, A. & Pernthaler, J. In Protocols for Nucleic Acid Analysis by Nonradioactive Probes 353, 153–164 (Humana Press, 2007).
Pett-Ridge, J. & Weber, P. K. In Microbial Systems Biology 91–136 (Humana, New York, NY, 2022). https://doi.org/10.1007/978-1-0716-1585-0_6
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
Google Scholar
Chaumeil, P. A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2020).
Google Scholar
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 1–11 (2010).
Cantalapiedra, C. P., Hernández-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38, 5825–5829 (2021).
Aziz, R. K. et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9, 1–15 (2008).
Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27, 1164–1165 (2011).
Google Scholar
Kück, P. & Longo, G. C. FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Front. Zool. 11, 1–8 (2014).
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
Google Scholar
Jacox, E., Chauve, C., Szöllősi, G. J., Ponty, Y. & Scornavacca, C. ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. Bioinformatics 32, 2056–2058 (2016).
Google Scholar
Chevenet, F. et al. SylvX: a viewer for phylogenetic tree reconciliations. Bioinformatics 32, 608–610 (2016).
Google Scholar
Csűös, M. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics 26, 1910–1912 (2010).
Yang, J. et al. The I-TASSER Suite: protein structure and function prediction. Nat. Methods 12, 7–8 (2015).
Google Scholar
Wu, S., Skolnick, J. & Zhang, Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol. 5, 17 (2007).
Google Scholar
Holm, L. & Rosenstrïm, P. I. Dali server: conservation mapping in 3D. Nucleic Acids Res. 38, W545–W549 (2010).
Google Scholar
Holm, L. Benchmarking fold detection by DaliLite v.5. Bioinformatics 35, 5326–5327 (2019).
Google Scholar
MacQueen, J. In Some Methods for Classification and Analysis of Multivariate Observations 1, 281–297 (1967).
Ma, K. & Adams, M. W. W. Sulfide dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus: a new multifunctional enzyme involved in the reduction of elemental sulfur. J. Bacteriol. 176, 6509–6517 (1994).
Google Scholar
Source: Ecology - nature.com
