Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs


Nitrifying microorganisms occur across a wide temperature range from 4 to 84 °C and previous studies in geothermal systems revealed their activity under extreme conditions. Archaea were detected to be responsible for the first step of nitrification, but it is still a challenging issue to clarify the identity of heat-tolerant nitrite oxidizers. In a long-term cultivation approach, we inoculated mineral media containing ammonium and nitrite as substrates with biofilms and sediments of two hot springs in Yellowstone National Park (USA). The nitrifying consortia obtained at 70 °C consisted mostly of novel Chloroflexi as revealed by metagenomic sequencing. Among these, two deep-branching novel Chloroflexi were identified as putative nitrite-oxidizing bacteria (NOB) by the presence of nitrite oxidoreductase encoding genes in their genomes. Stoichiometric oxidation of nitrite to nitrate occurred under lithoautotrophic conditions, but was stimulated by organic matter. Both NOB candidates survived long periods of starvation and the more abundant one formed miniaturized cells and was heat resistant. This detection of novel thermophilic NOB exemplifies our still incomplete knowledge of nitrification, and indicates that nitrite oxidation might be an ancient and wide-spread form of energy conservation.

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Data availability

Metagenomic and 16S rRNA gene amplicon sequence data are available in the European Nucleotide Archive (ENA) under accession number PRJEB28556. Requests for bacterial enrichment cultures are subject to the “General Permit Conditions” and cannot be shared by the authors without permission from U.S. National Park Service.


  1. 1.

    Alawi M, Lipski A, Sanders T, Eva-Maria-Pfeiffer, Spieck E. Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic. ISME J. 2007;1:256–64.

    CAS  PubMed  Google Scholar 

  2. 2.

    Reigstad LJ, Richter A, Daims H, Urich T, Schwark L, Schleper C. Nitrification in terrestrial hot springs of Iceland and Kamchatka. FEMS Microbiol Ecol. 2008;64:167–74.

    CAS  PubMed  Google Scholar 

  3. 3.

    Spieck E, Bock E. The lithoautotrophic nitrite-oxidizing bacteria. In: Garrity G, Brenner DJ, Krieg NR, Staley JT, editors. Bergey’s manual of systematic bacteriology. Berlin/Heidelberg, Germany: Springer-Verlag; 2005. p. 149–53.

    Google Scholar 

  4. 4.

    Ehrich S, Behrens D, Lebedeva E, Ludwig W, Bock E. A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Arch Microbiol. 1995;164:16–23.

    CAS  PubMed  Google Scholar 

  5. 5.

    Lücker S, Nowka B, Rattei T, Spieck E, Daims H. The genome of Nitrospina gracilis illuminates the metabolism and evolution of the major marine nitrite oxidizer. Front Microbiol. 2013;4:3–19.

    Google Scholar 

  6. 6.

    Sorokin DY, Lücker S, Vejmelkova D, Kostrikina NA, Kleerebezem R, WIC Rijpstra, et al. Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi. ISME J. 2012;6:2245–56.

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Hedlund B, Thomas S, Dodsworth J, Zhang C. Life in high-temperature environments. In: Yates M, Nakatsu C, Miller R, Pillai S, editors. Manual of environmental microbiology, 4th ed. Washington, DC., USA: ASM Press; 2016. p. 4.3.4-1–4.3.4-15. https://doi.org/10.1128/9781555818821.ch4.3.4.

  8. 8.

    Dodsworth J, Hungate B, Hedlund BP. Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea. Environ Microbiol. 2011;13:2371–86.

    CAS  PubMed  Google Scholar 

  9. 9.

    Inskeep WP, Ackerman GG, Taylor WP, Kozubal M, Korf S, Macur RE. On the energetics of chemolithotropy in nonequilibrium systems: case studies of geothermal springs in Yellowstone National Park. Geobiology. 2005;3:297–317.

    CAS  Google Scholar 

  10. 10.

    Dodsworth JA, McDonald AI, Hedlund BP. Calculation of total free energy yield as an alternative approach for predicting the importance of potential chemolithotrophic reactions in geothermal springs. FEMS Microbiol Ecol. 2012;81:446–54.

    CAS  PubMed  Google Scholar 

  11. 11.

    de la Torre JR, Walker CB, Ingalls AE, Könneke M, Stahl DA. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ Microbiol. 2008;10:810–8.

    PubMed  Google Scholar 

  12. 12.

    Abby SS, Melcher M, Kerou M, Krupovic M, Stieglmeier M, Rossel C, et al. Candidatus Nitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile genome. Front Microbiol. 2018;9:1–19.

    Google Scholar 

  13. 13.

    Daebeler A, Herbold CW, Vierheilig J, Sedlacek CJ, Pjevac P, Albertsen M, 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;9:1–16.

    Google Scholar 

  14. 14.

    Becraft ED, Dodsworth JA, Murugapiran SK, Ohlsson JI, Briggs BR, Kanbar J, et al. Single-cell-genomics-facilitated read binning of candidate phylum EM19 genomes from geothermal spring metagenomes. Appl Environ Microbiol. 2016;82:992–1003.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. 15.

    Lebedeva EV, Off S, Zumbrägel S, Kruse M, Shagzhina A, Lücker S, et al. Isolation and characterization of a moderately thermophilic nitrite-oxidizing bacterium from a geothermal spring. FEMS Microbiol Ecol. 2011;75:195–204.

    CAS  PubMed  Google Scholar 

  16. 16.

    Edwards TA, Calica NA, Huang DA, Manoharan N, Hou W, Huang L, et al. Cultivation and characterization of thermophilic Nitrospira species from geothermal springs in the US Great Basin, China, and Armenia. FEMS Microbiol Ecol. 2013;85:283–92.

    CAS  PubMed  Google Scholar 

  17. 17.

    Kits KD, Sedlacek CJ, Lebedeva EV, Han P, Bulaev A, Pjevac P, et al. Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature. 2017;549:269–72.

    CAS  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol. 1998;180:366–76.

    CAS  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Meyer-Dombard DR, Shock EL, Amend JP. Archaeal and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA. Geobiology. 2005;3:211–27.

    Google Scholar 

  20. 20.

    Hedlund BP, Murugapiran SK, Alba TW, Levy A, Dodsworth JA, Goertz GB, et al. Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’. Curr Opin Microbiol. 2015;25:136–45.

    CAS  PubMed  Google Scholar 

  21. 21.

    Kato S, Sakai S, Hirai M, Tasumi E, Nishizawa M, Suzuki K, et al. Long-term cultivation and metagenomics reveal ecophysiology of previously uncultivated Thermophiles involved in biogeochemical nitrogen cycle. Microbes Environ. 2018;33:107–10.

    PubMed  PubMed Central  Google Scholar 

  22. 22.

    Krümmel A, Harms H. Effect of organic matter on growth and cell yield of ammonia-oxidizing bacteria. Arch Microbiol. 1982;133:50–54.

    Google Scholar 

  23. 23.

    Spieck E, Lipski A. Cultivation, growth physiology, and chemotaxonomy of nitrite-oxidizing bacteria. In: Klotz MG, editor. Methods in enzymology. 1st ed. Oxford, UK: Academic Press/Elsevier Inc.; 2011. p. 109–30.

    Google Scholar 

  24. 24.

    Widdel F, Bak F. Gram-negative mesophilic sulfate-reducing bacteria. The Prokaryotes. New York, NY, USA: Springer New York; 1992. p. 3352–78.

    Google Scholar 

  25. 25.

    Amann R, Ludwig W, Schleifer K. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995;59:143–69.

    CAS  PubMed  PubMed Central  Google Scholar 

  26. 26.

    Manz W, Amann R, Ludwig W, Wagner M, Schleifer K-H. Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. Syst Appl Microbiol. 1992;15:593–600.

    Google Scholar 

  27. 27.

    Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol. 1990;56:1919–25.

    CAS  PubMed  PubMed Central  Google Scholar 

  28. 28.

    Wallner G, Amann R, Beisker W. Optimizing fluorescent in situ hybridization with rRNA‐targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry. 1993;14:136–43.

    CAS  PubMed  Google Scholar 

  29. 29.

    Taylor S, Ninjoor V, Dowd DM, Tappel AL. Cathepsin B2 measurement by sensitive fluorometric ammonia analysis. Anal Biochem. 1974;60:153–62.

    CAS  PubMed  Google Scholar 

  30. 30.

    Corbin JL. Liquid chromatographic-fluorescence determination of ammonia from nitrogenase reactions: A 2 min assay. Appl Environ Microbiol. 1984;47:1027–30.

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Schmidt EL, Belser LW. Autotrophic nitrifying bacteria. In: Weaver RW, Angle JS, Bottomley PJ, editors. Methods of soil analysis. Part 2-microbiological and biochemical properties. Madison, WI, USA: Soil Science Society of America; 1994. p. 159–77.

    Google Scholar 

  32. 32.

    Sambrook J, Green MR, editors. Extracting DNA from gram-negative bacteria. Molecular cloning: a laboratory manual, 4th ed. New York, NY: Cold Spring Harbor Laboratory Press; 2012 p. 19–20.

  33. 33.

    Rotthauwe J, Witzel K, Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microbiol. 1997;63:4704–12.

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34.

    Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci USA. 2005;102:14683–8.

    CAS  PubMed  Google Scholar 

  35. 35.

    Pester M, Maixner F, Berry D, Rattei T, Koch H, Lücker S, et al. NxrB encoding the beta subunit of nitrite oxidoreductase as functional and phylogenetic marker for nitrite-oxidizing Nitrospira. Environ Microbiol. 2014;16:3055–71.

    CAS  PubMed  Google Scholar 

  36. 36.

    Poly F, Wertz S, Brothier E, Degrange V. First exploration of Nitrobacter diversity in soils by a PCR cloning-sequencing approach targeting functional gene nxrA. FEMS Microbiol Ecol. 2008;63:132–40.

    CAS  PubMed  Google Scholar 

  37. 37.

    Lane DJ. 16/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, editors. Nucleic acid techniques in bacterial systematics. Chichester, UK: John Wiley & Sons; 1991. p. 115–71.

    Google Scholar 

  38. 38.

    Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar A, et al. ARB: a software environment for sequence data. Nucleic Acids Res. 2004;32:1363–71.

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–D596.

    CAS  Google Scholar 

  40. 40.

    Herlemann DP, Labrenz M, Jürgens K, Bertilsson S, Waniek JJ, Andersson AF. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 2011;5:1571–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  41. 41.

    Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci. 2011;108:4516–22.

    CAS  PubMed  Google Scholar 

  42. 42.

    Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  43. 43.

    Dowd SE, Sun Y, Wolcott RD, Domingo A, Carroll JA. Bacterial tag–encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: Bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog Dis. 2008;5:459–72.

    CAS  PubMed  Google Scholar 

  44. 44.

    Bushnell B. BBMap short read aligner. Berkeley, CA.: University of California; 2016. http://sourceforge.net/projects/bbmap.

    Google Scholar 

  45. 45.

    Nikolenko SI, Korobeynikov AI, Alekseyev MA. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics. 2013;14:S7.

    PubMed  PubMed Central  Google Scholar 

  46. 46.

    Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. MetaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.

    CAS  PubMed  PubMed Central  Google Scholar 

  47. 47.

    Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–95.

    PubMed  PubMed Central  Google Scholar 

  48. 48.

    Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–9.

    PubMed  PubMed Central  Google Scholar 

  49. 49.

    Graham ED, Heidelberg JF, Tully BJ. BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation. PeerJ. 2017;5:e3035.

    PubMed  PubMed Central  Google Scholar 

  50. 50.

    Lu YY, Chen T, Fuhrman JA, Sun F, Sahinalp C. COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge. Bioinformatics. 2017;33:791–8.

    CAS  PubMed  Google Scholar 

  51. 51.

    Alneberg J, Bjarnason BS, De Bruijn I, Schirmer M, Quick J, Ijaz UZ, et al. Binning metagenomic contigs by coverage and composition. Nat Methods. 2014;11:1144–6.

    CAS  PubMed  Google Scholar 

  52. 52.

    Wu YW, Simmons BA, Singer SW. MaxBin 2.0: An automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2015;32:605–7.

    PubMed  Google Scholar 

  53. 53.

    Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:e1165.

    PubMed  PubMed Central  Google Scholar 

  54. 54.

    Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol. 2018;3:836–43.

    CAS  PubMed  PubMed Central  Google Scholar 

  55. 55.

    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.

    CAS  PubMed  PubMed Central  Google Scholar 

  56. 56.

    Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  57. 57.

    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.

    CAS  Google Scholar 

  58. 58.

    Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007;35:W182–W185.

    PubMed  PubMed Central  Google Scholar 

  59. 59.

    Guindon S, Delsuc F, Dufayard JF, Gascuel O. Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol. 2009;537:113–37.

    CAS  PubMed  Google Scholar 

  60. 60.

    Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003;19:1572–4.

    CAS  PubMed  Google Scholar 

  61. 61.

    Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.

    CAS  PubMed  PubMed Central  Google Scholar 

  62. 62.

    Na SI, Kim YO, Yoon SH, Ha Smin, Baek I, Chun J. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol. 2018;56:281–5.

    Google Scholar 

  63. 63.

    Olm MR, Brown CT, Brooks B, Banfield JF. DRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  64. 64.

    Lagkouvardos I, Joseph D, Kapfhammer M, Giritli S, Horn M, Haller D, et al. IMNGS: a comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies. Sci Rep. 2016;6:33721.

    CAS  PubMed  PubMed Central  Google Scholar 

  65. 65.

    Dodsworth JA, Gevorkian J, Despujos F, Cole JK, Murugapiran SK, Ming H, 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 Syst Evol Microbiol. 2014;64:2119–27.

    CAS  PubMed  Google Scholar 

  66. 66.

    Jackson TJ, Ramaley RF, Meinschein WG. Thermomicrobium, a new genus of extremely thermophilic bacteria. Int J Syst Bacteriol. 1973;23:28–36.

    Google Scholar 

  67. 67.

    King CE, King GM. Thermomicrobium carboxidum sp. nov., and Thermorudis peleae gen. nov., sp. nov., carbon monoxide-oxidizing bacteria isolated from geothermally heated biofilms. Int J Syst Evol Microbiol. 2014;64:2586–92.

    CAS  PubMed  Google Scholar 

  68. 68.

    Herbold CW, Lee CK, McDonald IR, Cary SC. Evidence of global-scale aeolian dispersal and endemism in isolated geothermal microbial communities of Antarctica. Nat Commun. 2014;5:1–10.

    Google Scholar 

  69. 69.

    Meincke M, Bock E, Kastrau D, Kroneck PMH. Nitrite oxidoreductase from Nitrobacter hamburgensis: redox centers and their catalytic role. Arch Microbiol. 1992;158:127–31.

    Google Scholar 

  70. 70.

    Lücker S, Wagner M, Maixner F, Pelletier E, Koch H, Vacherie B, et al. A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria. Proc Natl Acad Sci. 2010;107:13479–84.

    PubMed  Google Scholar 

  71. 71.

    Kirstein K, Bock E. Close genetic relationship between Nitrobacter hamburgensis nitrite oxidoreductase and Escherichia coli nitrate reductases. Arch Microbiol. 1993;160:447–53.

    CAS  PubMed  Google Scholar 

  72. 72.

    Kitzinger K, Koch H, Lücker S, Sedlacek CJ, Herbold C, Schwarz J, et al. Characterization of the first “Candidatus Nitrotoga” isolate reveals metabolic versatility and separate evolution of widespread nitrite-oxidizing bacteria. mBio. 2018;9:1–16.

    Google Scholar 

  73. 73.

    Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 2016;7:1–11.

    Google Scholar 

  74. 74.

    Hedlund BP, Dodsworth JA, Murugapiran SK, Rinke C, Woyke T. Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”. Extremophiles. 2014;18:865–75.

    CAS  PubMed  Google Scholar 

  75. 75.

    Takami H, Noguchi H, Takaki Y, Uchiyama I, Toyoda A, Nishi S, et al. A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem. PLoS ONE. 2012;7.

    CAS  PubMed  PubMed Central  Google Scholar 

  76. 76.

    Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J, Kazama H, 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. 2011;39:3204–23.

    CAS  PubMed  Google Scholar 

  77. 77.

    Hugenholtz P, Stackebrandt E. Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Microbiol. 2004;54:2049–51.

    PubMed  Google Scholar 

  78. 78.

    Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. 2016.

  79. 79.

    Daims H, Lücker S, Le Paslier D, Wagner M. Diversity, environmental genomics, and ecophysiology of nitrite-oxidizing bacteria. In: Ward BB, Klotz MG, Arp DJ, editors. Nitrification. Washington, DC, USA: ASM Press; 2011. p. 295–322.

    Google Scholar 

  80. 80.

    Bock E. Growth of Nitrobacter in the presence of organic matter. Arch Microbiol. 1976;108:305–12.

    CAS  PubMed  Google Scholar 

  81. 81.

    Lipski A, Spieck E, Makolla A, Altendorf K. Fatty acid profiles of nitrite-oxidizing bacteria reflect their phylogenetic heterogeneity. Syst Appl Microbiol. 2001;24:377–84.

    CAS  PubMed  Google Scholar 

  82. 82.

    Kim J-G, Park S-J, Sinninghe Damsté JS, Schouten S, Rijpstra WIC, Jung M-Y, et al. Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea. Proc Natl Acad Sci. 2016;113:7888–93.

    CAS  PubMed  Google Scholar 

  83. 83.

    Nunoura T, Chikaraishi Y, Izaki R, Suwa T, Sato T, Harada T, et al. A primordial and reversible TCA cycle in a facultatively chemolithoautotrophic thermophile. Science. 2018;359:559–63.

    CAS  PubMed  Google Scholar 

  84. 84.

    Mall A, Sobotta J, Huber C, Tschirner C, Kowarschik S, Bačnik K, et al. Reversibility of citrate synthase allows autotrophic growth of a thermophilic bacterium. Science. 2018;359:563–7.

    CAS  PubMed  Google Scholar 

  85. 85.

    Pati A, la Butti K, Pukall R, Nolan M, del Rio TG, Tice H, et al. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022 T). Stand Genom Sci. 2010;2:49–56.

    Google Scholar 

  86. 86.

    Yabe S, Aiba Y, Sakai Y, Hazaka M, Yokota A. A life cycle of branched aerial mycelium- and multiple budding spore-forming bacterium Thermosporothrix hazakensis belonging to the phylum Chloroflexi. J Gen Appl Microbiol. 2010;56:137–41.

    CAS  PubMed  Google Scholar 

  87. 87.

    Filippidou S, Junier T, Wunderlin T, Kooli WM, Palmieri I, Al-Dourobi A, et al. Adaptive strategies in a poly-extreme environment: differentiation of vegetative cells in Serratia ureilytica and resistance to extreme conditions. Front Microbiol. 2019;10:1–13.

    Google Scholar 

  88. 88.

    Suzina NE, Mulyukin AL, Kozlova AN, Shorokhova AP, Dmitriev VV, Barinova ES, et al. Ultrastructure of resting cells of some non-spore-forming bacteria. Microbiology. 2004;73:435–47.

    CAS  Google Scholar 

  89. 89.

    Meyer-Dombard DR, Swingley W, Raymond J, Havig J, Shock EL, Summons RE. Hydrothermal ecotones and streamer biofilm communities in the Lower Geyser Basin, Yellowstone National Park. Environ Microbiol. 2011;13:2216–31.

    CAS  PubMed  Google Scholar 

  90. 90.

    Yamada T, Sekiguchi Y. Cultivation of uncultured chloroflexi subphyla: significance and ecophysiology of formerly uncultured chloroflexi ‘subphylum i’ with natural and biotechnological relevance. Microbes Environ. 2009;24:205–16.

    PubMed  Google Scholar 

  91. 91.

    Miller SR, Strong AL, Jones KL, Ungerer MC. Bar-coded pyrosequencing reveals shared bacterial community properties along the temperature gradients of two alkaline hot springs in Yellowstone National Park. Appl Environ Microbiol. 2009;75:4565–72.

    CAS  PubMed  PubMed Central  Google Scholar 

  92. 92.

    Watsuji T, Kato T, Ueda K, Beppu T. CO2 supply induces the growth of Symbiobacterium thermophilum, a syntrophic bacterium. Biosci Biotechnol Biochem. 2006;70:753–6.

    CAS  PubMed  Google Scholar 

  93. 93.

    Stewart EJ. Growing unculturable bacteria. J Bacteriol. 2012;194:4151–60.

    CAS  PubMed  PubMed Central  Google Scholar 

  94. 94.

    Overmann J, Abt B, Sikorski J. Present and future of culturing bacteria. Annu Rev Microbiol. 2017;71:711–30.

    CAS  PubMed  Google Scholar 

  95. 95.

    Inskeep W. The YNP metagenome project: environmental parameters responsible for microbial distribution in the Yellowstone geothermal ecosystem. Front Microbiol. 2013;4:1–15.

    Google Scholar 

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The authors thank the National Park Service for permission to perform research in Yellowstone National Park (Permit YELL-2007-SCI-5698). Elke Woelken is acknowledged for excellent technical help in electron microscopy and Yvonne Bedarf and Christina Bietz for initial cultivation. We also thank Lia Burkhardt and Kerstin Reumann for sequencing assistance and we are grateful to Ilias Lagkouvardos and Antonios Kioukis for kindly enabling our analyses on the IMNGS platform.


This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation grant SP 667/7-1+2) and the Netherlands Organization for Scientific Research (Grants 863.14.019, 016.Vidi.189.050 and SIAM Gravitation Grant 024.002.002).

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EB and JS performed sampling at YNP, ES, JH, SL designed research, ES, KW, JH, DI performed research, JH, MA, MS, JF, SL analyzed data, and ES, JH and SL wrote the paper. All authors read and agreed on the final paper.

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Correspondence to Eva Spieck.

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Spieck, E., Spohn, M., Wendt, K. et al. Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs. ISME J 14, 364–379 (2020). https://doi.org/10.1038/s41396-019-0530-9

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