1887

Abstract

An anaerobic hyperthermophilic archaeon was isolated from a black smoker chimney with a snail attachment at a water depth of 2 739 m in the Southwest Indian Ocean. The sample was taken from the chimney exterior wall. The enrichment was conducted under a continuous culture with temperature fluctuation of 80–130 °C over 24 h for 42 days at 28 MPa. The isolation was performed at 90 °C at 0.1 MPa. Cells of the isolated strain 813A4 were irregular cocci. Strain 813A4 grew at 60–94 °C (optimal growth at 85 °C) at 0.1 MPa, and growth was detected at up to 99 °C at 28 MPa. At 85 °C, the strain was able to grow at pressures ranging from 0.1 to 110 MPa (optimal pressure, 0.1–40 MPa). At 85 °C, the cells of 813A4 grew at pH 5.5–9 (optimal, pH 7.0) and a NaCl concentration of 1.0–4.0 % (w/v; optimum concentration, 2.5 % NaCl). Strain 813A4 utilized yeast extract, tryptone and peptone as single carbon sources for growth. Elemental sulphur stimulated its growth. The G+C content of the complete genome was 53.48 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 813A4 belonged to the genus , with the highest sequence similarity to SHCK-94 (99.73 %). The average nucleotide identity between strains 813A4 and SHCK-94 was 82.56 %. All these data indicated that strain 813A4 should be classified as representing a novel species of the genus , for which sp. nov. is proposed. The type strain is 813A4 (=JCM 39367=MCCC M28628).

Funding
This study was supported by the:
  • Natural Science Foundation of China (Award 42106087)
    • Principle Award Recipient: WeishuZhao
  • Natural Science Foundation of China (Award 41921006)
    • Principle Award Recipient: XiangXiao
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2023-12-01
2024-05-08
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References

  1. Price MT, Fullerton H, Moyer CL. Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific. Front Microbiol 2015; 6:968 [View Article] [PubMed]
    [Google Scholar]
  2. Martin W, Baross J, Kelley D, Russell MJ. Hydrothermal vents and the origin of life. Nat Rev Microbiol 2008; 6:805–814 [View Article] [PubMed]
    [Google Scholar]
  3. Zillig W, Holz I, Janekovic D, Schäfer W, Reiter WD. The archaebacterium Thermococcus celer represents, a novel genus within the thermophilic branch of the archaebacteria. Syst Appl Microbiol 1983; 4:88–94 [View Article] [PubMed]
    [Google Scholar]
  4. Fiala G, Stetter KO. Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100°C. Arch Microbiol 1986; 145:56–61 [View Article]
    [Google Scholar]
  5. Takai K, Sugai A, Itoh T, Horikoshi K. Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol 2000; 50 Pt 2:489–500 [View Article] [PubMed]
    [Google Scholar]
  6. Zhao W, Zeng X, Xiao X. Thermococcus eurythermalis sp. nov., a conditional piezophilic, hyperthermophilic archaeon with a wide temperature range for growth, isolated from an oil-immersed chimney in the Guaymas Basin. Int J Syst Evol Microbiol 2015; 65:30–35 [View Article] [PubMed]
    [Google Scholar]
  7. Marteinsson VT, Birrien JL, Reysenbach AL, Vernet M, Marie D et al. Thermococcus barophilus sp. nov., a new barophilic and hyperthermophilic archaeon isolated under high hydrostatic pressure from a deep-sea hydrothermal vent. Int J Syst Bacteriol 1999; 49 Pt 2:351–359 [View Article] [PubMed]
    [Google Scholar]
  8. Hensley SA, Jung J-H, Park C-S, Holden JF. Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents. Int J Syst Evol Microbiol 2014; 64:3655–3659 [View Article] [PubMed]
    [Google Scholar]
  9. Holden JF, Baross JA. Enhanced thermotolerance by hydrostatic pressure in the deep-sea hyperthermophile Pyrococcus strain ES4. FEMS Microbiol Ecol 1995; 18:27–34 [View Article]
    [Google Scholar]
  10. Jannasch HW, Wirsen CO, Molyneaux SJ, Langworthy TA. Comparative physiological studies on hyperthermophilic archaea isolated from deep-sea hot vents with emphasis on Pyrococcus strain GB-D. Appl Environ Microbiol 1992; 58:3472–3481 [View Article] [PubMed]
    [Google Scholar]
  11. Zeng X, Birrien J-L, Fouquet Y, Cherkashov G, Jebbar M et al. Pyrococcus CH1, an obligate piezophilic hyperthermophile: extending the upper pressure-temperature limits for life. ISME J 2009; 3:873–876 [View Article] [PubMed]
    [Google Scholar]
  12. SIEGEL LM. A direct microdetermination for sulfide. Anal Biochem 1965; 11:126–132 [View Article] [PubMed]
    [Google Scholar]
  13. Natarajan VP, Zhang X, Morono Y, Inagaki F, Wang F. A modified SDS-based DNA extraction method for high quality environmental DNA from seafloor environments. Front Microbiol 2016; 7:986 [View Article] [PubMed]
    [Google Scholar]
  14. Chin C-S, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 2016; 13:1050–1054 [View Article] [PubMed]
    [Google Scholar]
  15. Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N et al. Consensus generation and variant detection by celera assembler. Bioinformatics 2008; 24:1035–1040 [View Article] [PubMed]
    [Google Scholar]
  16. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011; 43:491–498 [View Article] [PubMed]
    [Google Scholar]
  17. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 2007; 23:673–679 [View Article] [PubMed]
    [Google Scholar]
  18. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108
    [Google Scholar]
  19. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
    [Google Scholar]
  20. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
    [Google Scholar]
  21. Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol 2017; 34:2115–2122 [View Article] [PubMed]
    [Google Scholar]
  22. Søndergaard D, Pedersen CN, Greening C. HydDB: a web tool for hydrogenase classification and analysis. Sci Rep 2016; 6:34212
    [Google Scholar]
  23. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
    [Google Scholar]
  24. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  25. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425
    [Google Scholar]
  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  27. Rzhetsky A, Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 1992; 35:367–375 [View Article] [PubMed]
    [Google Scholar]
  28. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
    [Google Scholar]
  29. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  30. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]
  31. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
    [Google Scholar]
  32. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
    [Google Scholar]
  33. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
    [Google Scholar]
  34. Duffaud GD, d’Hennezel OB, Peek AS, Reysenbach AL, Kelly RM. Isolation and characterization of Thermococcus barossii, sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent flange formation. Syst Appl Microbiol 1998; 21:40–49 [View Article] [PubMed]
    [Google Scholar]
  35. Pikuta EV, Marsic D, Itoh T, Bej AK, Tang J et al. Thermococcus thioreducens sp. nov., a novel hyperthermophilic, obligately sulfur-reducing archaeon from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2007; 57:1612–1618 [View Article] [PubMed]
    [Google Scholar]
  36. Jolivet E, Corre E, L’Haridon S, Forterre P, Prieur D. Thermococcus marinus sp. nov. and Thermococcus radiotolerans sp. nov., two hyperthermophilic archaea from deep-sea hydrothermal vents that resist ionizing radiation. Extremophiles 2004; 8:219–227 [View Article] [PubMed]
    [Google Scholar]
  37. Godfroy A, Lesongeur F, Raguénès G, Quérellou J, Antoine E et al. Thermococcus hydrothermalis sp. nov., a new hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Int J Syst Bacteriol 1997; 47:622–626 [View Article] [PubMed]
    [Google Scholar]
  38. Kuwabara T, Minaba M, Iwayama Y, Inouye I, Nakashima M et al. Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic archaeon from Suiyo Seamount. Int J Syst Evol Microbiol 2005; 55:2507–2514 [View Article] [PubMed]
    [Google Scholar]
  39. Grote R, Li L, Tamaoka J, Kato C, Horikoshi K et al. Thermococcus siculi sp. nov., a novel hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent at the Mid-Okinawa Trough. Extremophiles 1999; 3:55–62 [View Article] [PubMed]
    [Google Scholar]
  40. Bae S, Kim YJ, Yang S, Lim JK, Jeon J et al. Thermococcus onnurineus sp nov., a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent area at the Pacmanus field. J Microbiol Biotechnol 2006; 16:1826–1831
    [Google Scholar]
  41. Dalmasso C, Oger P, Selva G, Courtine D, L’Haridon S et al. Thermococcus piezophilus sp. nov., a novel hyperthermophilic and piezophilic archaeon with a broad pressure range for growth, isolated from a deepest hydrothermal vent at the Mid-Cayman Rise. Syst Appl Microbiol 2016; 39:440–444 [View Article] [PubMed]
    [Google Scholar]
  42. González JM, Kato C, Horikoshi K. Thermococcus peptonophilus sp. nov., a fast-growing, extremely thermophilic archaebacterium isolated from deep-sea hydrothermal vents. Arch Microbiol 1995; 164:159–164 [PubMed]
    [Google Scholar]
  43. Gorlas A, Alain K, Bienvenu N, Geslin C. Thermococcus prieurii sp. nov., a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2013; 63:2920–2926 [View Article] [PubMed]
    [Google Scholar]
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