1887

Abstract

A thermoacidophilic, anaerobic, and iron- and sulfur-reducing archaeon, strain NAS-02, was isolated from a terrestrial hot spring in Japan, as previously reported. This organism is the first non-ammonia-oxidizing isolate in the phylum . Here, we propose gen. nov., sp. nov. to accommodate this strain. The type strain of the type species is NAS-02 (=JCM 31663=DSM 105898). The values of 16S rRNA gene similarity and average amino acid identity between NAS-02 and its closest relatives are <86 and <42 %, respectively. Based on the phylogeny and physiology, we propose the family fam. nov., the order ord. nov. and the class class. nov. to accommodate the novel genus.

Funding
This study was supported by the:
  • RIKEN (Award interdisciplinary research program Integrated Symbiology)
    • Principle Award Recipient: MoriyaOhkuma
  • Japan Society for the Promotion of Science (Award 19H03310)
    • Principle Award Recipient: ShingoKato
  • Japan Society for the Promotion of Science (Award 19H05689)
    • Principle Award Recipient: MoriyaOhkuma
  • Japan Society for the Promotion of Science (Award 19H05679)
    • Principle Award Recipient: MoriyaOhkuma
  • RIKEN (Award Special Postdoctoral Researchers Program)
    • Principle Award Recipient: ShingoKato
  • Institute for Fermentation, Osaka
    • Principle Award Recipient: ShingoKato
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2020-12-09
2024-12-13
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References

  1. Spang A, Caceres EF, Ettema TJG. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 2017; 357:eaaf3883 [View Article][PubMed]
    [Google Scholar]
  2. Adam PS, Borrel G, Brochier-Armanet C, Gribaldo S. The growing tree of archaea: new perspectives on their diversity, evolution and ecology. Isme J 2017; 11:2407–2425 [View Article][PubMed]
    [Google Scholar]
  3. Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota . Nat Rev Microbiol 2008; 6:245–252 [View Article][PubMed]
    [Google Scholar]
  4. Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB et al. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 2005; 437:543–546 [View Article][PubMed]
    [Google Scholar]
  5. Qin W, Heal KR, Ramdasi R, Kobelt JN, Martens-Habbena W et al. Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota . Int J Syst Evol Microbiol 2017; 67:5067–5079 [View Article][PubMed]
    [Google Scholar]
  6. Bayer B, Vojvoda J, Reinthaler T, Reyes C, Pinto M et al. Nitrosopumilus adriaticus sp. nov. and Nitrosopumilus piranensis sp. nov., two ammonia-oxidizing archaea from the Adriatic Sea and members of the class Nitrososphaeria . Int J Syst Evol Microbiol 2019; 69:1892–1902 [View Article][PubMed]
    [Google Scholar]
  7. Tourna M, Stieglmeier M, Spang A, Könneke M, Schintlmeister A et al. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proc Natl Acad Sci U S A 2011; 108:8420–8425 [View Article][PubMed]
    [Google Scholar]
  8. Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A et al. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Natl Acad Sci U S A 2008; 105:2134–2139 [View Article][PubMed]
    [Google Scholar]
  9. Stieglmeier M, Klingl A, Alves RJ, Rittmann SK, Melcher M et al. Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota . Int J Syst Evol Microbiol 2014; 64:2738–2752 [View Article][PubMed]
    [Google Scholar]
  10. Jung MY, Islam MA, Gwak JH, Kim JG, Rhee SK. Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon member of the phylum Thaumarchaeota isolated from agricultural soil. Int J Syst Evol Microbiol 2018; 68:3084–3095 [View Article][PubMed]
    [Google Scholar]
  11. Abby SS, Melcher M, Kerou M, Krupovic M, Stieglmeier M et al. Candidatus Nitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile genome. Front Microbiol 2018; 9:28 [View Article][PubMed]
    [Google Scholar]
  12. Daebeler A, Herbold CW, Vierheilig J, Sedlacek CJ, Pjevac P et al. Cultivation and genomic analysis of “Candidatus Nitrosocaldus islandicus,” an obligately thermophilic, ammonia-oxidizing thaumarchaeon from a hot spring biofilm in Graendalur Valley, Iceland. Front Microbiol 2018; 9:193 [View Article][PubMed]
    [Google Scholar]
  13. de la Torre JR, Walker CB, Ingalls AE, Konneke M, Stahl DA. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol 2008; 10:810–818 [View Article][PubMed]
    [Google Scholar]
  14. Beam JP, Jay ZJ, Kozubal MA, Inskeep WP. Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park. ISME J 2014; 8:938–951 [View Article][PubMed]
    [Google Scholar]
  15. Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P et al. Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota . Trends Microbiol 2010; 18:331–340 [View Article][PubMed]
    [Google Scholar]
  16. Vetriani C, Jannasch HW, MacGregor BJ, Stahl DA, Reysenbach AL. Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl Environ Microbiol 1999; 65:4375–4384 [View Article][PubMed]
    [Google Scholar]
  17. Barns SM, Delwiche CF, Palmer JD, Pace NR. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci U S A 1996; 93:9188–9193 [View Article][PubMed]
    [Google Scholar]
  18. Eme L, Reigstad LJ, Spang A, Lanzén A, Weinmaier T et al. Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota . Res Microbiol 2013; 164:425–438 [View Article][PubMed]
    [Google Scholar]
  19. Takai K, Horikoshi K. Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 1999; 152:1285–1297[PubMed]
    [Google Scholar]
  20. Lin X, Handley KM, Gilbert JA, Kostka JE. Metabolic potential of fatty acid oxidation and anaerobic respiration by abundant members of Thaumarchaeota and Thermoplasmata in deep anoxic peat. Isme J 2015; 9:2740–2744 [View Article][PubMed]
    [Google Scholar]
  21. Kato S, Sakai S, Hirai M, Tasumi E, Nishizawa M et al. Long-term cultivation and metagenomics reveal ecophysiology of previously uncultivated thermophiles involved in biogeochemical nitrogen cycle. Microbes Environ 2018; 33:107–110 [View Article][PubMed]
    [Google Scholar]
  22. Kato S, Itoh T, Yuki M, Nagamori M, Ohnishi M et al. Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring. Isme J 2019; 13:2465–2474 [View Article][PubMed]
    [Google Scholar]
  23. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013; 41:D590–D596 [View Article][PubMed]
    [Google Scholar]
  24. Chen IA, Chu K, Palaniappan K, Pillay M, Ratner A et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res 2019; 47:D666–D677 [View Article][PubMed]
    [Google Scholar]
  25. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article][PubMed]
    [Google Scholar]
  26. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article][PubMed]
    [Google Scholar]
  27. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  28. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article][PubMed]
    [Google Scholar]
  29. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019btz848 [View Article][PubMed]
    [Google Scholar]
  30. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. Isme J 2017; 11:2399–2406 [View Article][PubMed]
    [Google Scholar]
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