1887

Abstract

Three hyperthermophilic methanogens, designated strain SG7, strain SG1 and strain SLH, were isolated from the ABE and Tu’i Malila deep-sea hydrothermal vent fields along the Eastern Lau Spreading Center. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strains SG7, SG1 and SLH were affiliated with the genus within the family , order . They shared 95.5–99.48 % 16S rRNA gene sequence similarity to other species and were most closely related to . Cells of strains SG7, SG1 and SLH were cocci, with a diameter of 1.0–2.2 µm. The three strains grew between 45 and 93 °C (optimum, 80–85 °C), at pH 5.0–7.1 (optimum pH 6.2) and with 10–50 g l NaCl (optimum 20–25 g l). Genome analysis revealed the presence of a 5.1 kbp plasmid in strain SG7. Based on the results of average nucleotide identity and digital DNA–DNA hybridization analyses, we propose that strains SG1 and SG7 are representatives of a novel species, for which the name sp. nov. is proposed; the type strain is SG7 (=DSM 109608=JCM 39049).

Funding
This study was supported by the:
  • HORIZON EUROPE European Research Council (Award 340440)
    • Principle Award Recipient: NotApplicable
  • American Institute of Biological Sciences (Award OCE 1558795)
    • Principle Award Recipient: AnnaLouise Reysenbach
  • American Institute of Biological Sciences (Award OCE1235432)
    • Principle Award Recipient: AnnaLouise Reysenbach
  • Seventh Framework Programme (Award 311975)
    • Principle Award Recipient: StéphaneL'Haridon
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005646
2023-01-24
2024-12-03
Loading full text...

Full text loading...

References

  1. L’Haridon S, Goulaouic S, St. John E, Fouteau S, Reysenbach AL. Methanocaldococcus lauensis sp. nov., a novel deep-sea hydrothermal vent hyperthermophilic methanogen. Figshare 2022 [View Article]
    [Google Scholar]
  2. Whitman WB, Boone DR, Koga Y. Methanococcales. In Bergey’s Manual of Systematics of Archaea and Bacteria vol 1 Wiley;
    [Google Scholar]
  3. Rother M, Whitman WB, Boone DR, Koga Y. Methanococcaceae. In Bergey’s Man Syst Archaea Bact 2020 pp 1–2
    [Google Scholar]
  4. Dodsworth JA, Whitman WB. Methanocaldococcaceae. In Bergey’s Man Syst Archaea Bact 2021 pp 1–3
    [Google Scholar]
  5. Rother M, Whitman WB. Methanococcus. In Bergey’s Man Syst Archaea Bact 2019 pp 1–10 [View Article]
    [Google Scholar]
  6. Sakai S, Takaki Y, Miyazaki M, Ogawara M, Yanagawa K et al. Methanofervidicoccus abyssi gen. nov., sp. nov., a hydrogenotrophic methanogen, isolated from a hydrothermal vent chimney in the Mid-Cayman Spreading Center, the Caribbean Sea. Int J Syst Evol Microbiol 2019; 69:1225–1230 [View Article]
    [Google Scholar]
  7. Rother M, Whitman WB. Methanothermococcus. In Bergey’s Man Syst Archaea Bact 2019 pp 1–6
    [Google Scholar]
  8. Whitman WB. Methanotorris gen. nov. In Bergey’s Man Syst Archaea Bact 2015 pp 1–3
    [Google Scholar]
  9. Whitman WB. Methanocaldococcus gen. nov. In Bergey’s Man Syst Archaea Bact 2015 pp 1–5
    [Google Scholar]
  10. 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]
  11. Rinke C, Chuvochina M, Mussig AJ, Chaumeil PA, Davín AA et al. A standardized archaeal taxonomy for the genome taxonomy database. Nat Microbiol 2021; 6:946–959 [View Article]
    [Google Scholar]
  12. Jones WJ, Leigh JA, Mayer F, Woese CR, Wolfe RS. Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent. Arch Microbiol 1983; 136:254–261 [View Article]
    [Google Scholar]
  13. Jeanthon C, L’Haridon S, Reysenbach AL, Corre E, Vernet M et al. Methanococcus vulcanius sp. nov., a novel hyperthermophilic methanogen isolated from East Pacific Rise, and identification of Methanococcus sp. DSM 4213T as Methanococcus fervens sp. nov. Int J Syst Bacteriol 1999; 49 Pt 2:583–589 [View Article]
    [Google Scholar]
  14. Stewart LC, Jung J-H, Kim Y-T, Kwon S-W, Park C-S et al. Methanocaldococcus bathoardescens sp. nov., a hyperthermophilic methanogen isolated from a volcanically active deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2015; 65:1280–1283 [View Article] [PubMed]
    [Google Scholar]
  15. L’Haridon S, Reysenbach AL, Banta A, Messner P, Schumann P et al. Methanocaldococcus indicus sp. nov., a novel hyperthermophilic methanogen isolated from the Central Indian Ridge. Int J Syst Evol Microbiol 2003; 53:1931–1935 [View Article]
    [Google Scholar]
  16. Bellack A, Huber H, Rachel R, Wanner G, Wirth R. Methanocaldococcus villosus sp. nov., a heavily flagellated archaeon that adheres to surfaces and forms cell-cell contacts. Int J Syst Evol Microbiol 2011; 61:1239–1245 [View Article]
    [Google Scholar]
  17. Jeanthon C, L’Haridon S, Reysenbach AL, Vernet M, Messner P et al. Methanococcus infernus sp. nov., a novel hyperthermophilic lithotrophic methanogen isolated from a deep-sea hydrothermal vent. Int J Syst Bacteriol 1998; 48 Pt 3:913–919 [View Article]
    [Google Scholar]
  18. Flores GE, Shakya M, Meneghin J, Yang ZK, Seewald JS et al. Inter-field variability in the microbial communities of hydrothermal vent deposits from a back-arc basin. Geobiology 2012; 10:333–346 [View Article] [PubMed]
    [Google Scholar]
  19. Ferrini VL, Tivey MK, Carbotte SM, Martinez F, Roman C. Variable morphologic expression of volcanic, tectonic, and hydrothermal processes at six hydrothermal vent fields in the Lau back-arc basin. Geochem Geophys Geosyst 2008; 9:n [View Article]
    [Google Scholar]
  20. Takai KEN, Nakamura K, Suzuki K, Inagaki F, Nealson KH et al. Ultramafics-Hydrothermalism-Hydrogenesis-HyperSLiME (UltraH 3) linkage: a key insight into early microbial ecosystem in the Archean deep-sea hydrothermal systems. Paleontol Res 2006; 10:269–282 [View Article]
    [Google Scholar]
  21. McCollom TM. Geochemical constraints on sources of metabolic energy for chemolithoautotrophy in ultramafic-hosted deep-sea hydrothermal systems. Astrobiology 2007; 7:933–950 [View Article]
    [Google Scholar]
  22. Perner M, Kuever J, Seifert R, Pape T, Koschinsky A et al. The influence of ultramafic rocks on microbial communities at the Logatchev hydrothermal field, located 15 degrees N on the Mid-Atlantic Ridge. FEMS Microbiol Ecol 2007; 61:97–109 [View Article]
    [Google Scholar]
  23. Takai K, Compositional NK. Physiological and metabolic variability in microbial communities associated with geochemically diverse, deep-sea hydrothermal vent fluids. Geomicrobiol Mol Environ Perspect 2010251–283
    [Google Scholar]
  24. Flores GE, Campbell JH, Kirshtein JD, Meneghin J, Podar M et al. Microbial community structure of hydrothermal deposits from geochemically different vent fields along the Mid-Atlantic Ridge. Environ Microbiol 2011; 13:2158–2171 [View Article] [PubMed]
    [Google Scholar]
  25. Roussel EG, Konn C, Charlou J-L, Donval J-P, Fouquet Y et al. Comparison of microbial communities associated with three Atlantic ultramafic hydrothermal systems. FEMS Microbiol Ecol 2011; 77:647–665 [View Article] [PubMed]
    [Google Scholar]
  26. Reysenbach A-L, Liu Y, Lindgren AR, Wagner ID, Sislak CD et al. Mesoaciditoga lauensis gen. nov., sp. nov., a moderately thermoacidophilic member of the order Thermotogales from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2013; 63:4724–4729 [View Article] [PubMed]
    [Google Scholar]
  27. Widdel F, Bak F. Gram-negative mesophilic sulfate-reducing bacteria. In The Prokaryotes New York, NY: Springer New York; 1992 pp 3352–3378
    [Google Scholar]
  28. Pfennig N, Widdel F, Trüper HG. The dissimilatory sulfate-reducing bacteria. In The Prokaryotes 1981 pp 926–940
    [Google Scholar]
  29. Spring S. 15 preservation of thermophilic microorganisms. Methods Microbiol 2006; 35:349–368
    [Google Scholar]
  30. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes de novo assembler. Curr Protoc Bioinformatics 2020; 70:e102 [View Article]
    [Google Scholar]
  31. Gruber-Vodicka HR, Seah BKB, Pruesse E. phyloFlash: rapid small-subunit rRNA profiling and targeted assembly from metagenomes. mSystems 2020; 5:e00920-20 [View Article]
    [Google Scholar]
  32. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
    [Google Scholar]
  33. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002; 30:3059–3066 [View Article] [PubMed]
    [Google Scholar]
  34. 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]
  35. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article]
    [Google Scholar]
  36. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  37. Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res 2018; 46:W246–W251 [View Article]
    [Google Scholar]
  38. 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]
    [Google Scholar]
  39. Makarova KS, Haft DH, Barrangou R, Brouns SJJ, Charpentier E et al. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 2011; 9:467–477 [View Article]
    [Google Scholar]
  40. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK et al. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 2011; 39:D225–9 [View Article]
    [Google Scholar]
  41. St John E, Flores GE, Meneghin J, Reysenbach A-L. Deep-sea hydrothermal vent metagenome-assembled genomes provide insight into the phylum Nanoarchaeota. Environ Microbiol Rep 2019; 11:262–270 [View Article] [PubMed]
    [Google Scholar]
  42. St. John E, Liu Y, Podar M, Stott MB, Meneghin J et al. A new symbiotic nanoarchaeote (Candidatus nanoclepta minutus) and its host (Zestosphaera tikiterensis gen. nov., sp. nov.) from a New Zealand hot spring. Syst Appl Microbiol 2019; 42:94–106 [View Article]
    [Google Scholar]
  43. Ultsch A. Emergence in self organizing feature maps. In WSOM, 6th. edn Int Work Self-Organizing Maps; 2007
    [Google Scholar]
  44. 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; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  45. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article]
    [Google Scholar]
  46. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019:btz848 [View Article]
    [Google Scholar]
  47. 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]
  48. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  49. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
    [Google Scholar]
  50. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci 2005; 102:2567–2572 [View Article]
    [Google Scholar]
  51. Thauer RK. The Wolfe cycle comes full circle. Proc Natl Acad Sci 2012; 109:15084–15085 [View Article]
    [Google Scholar]
  52. Mukhopadhyay B, Johnson EF, Wolfe RS. A novel pH2 control on the expression of flagella in the hyperthermophilic strictly hydrogenotrophic methanarchaeaon Methanococcus jannaschii. Proc Natl Acad Sci 2000; 97:11522–11527 [View Article]
    [Google Scholar]
  53. Giometti CS, Tollaksen SL, Babnigg G, Reich CI, Olsen GJ et al. Structural modifications of Methanococcus Jannaschii flagellin proteins revealed by proteome analysis. Eur J Mass Spectrom 2001; 7:207–217 [View Article]
    [Google Scholar]
  54. Flores GE, Shakya M, Meneghin J, Yang ZK, Seewald JS et al. Inter-field variability in the microbial communities of hydrothermal vent deposits from a back-arc basin. Geobiology 2012; 10:333–346 [View Article] [PubMed]
    [Google Scholar]
  55. Boone DR, Whitman WB. Proposal of minimal standards for describing new taxa of methanogenic bacteria. Int J Syst Bacteriol 1988; 38:212–219 [View Article]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005646
Loading
/content/journal/ijsem/10.1099/ijsem.0.005646
Loading

Data & Media loading...

Supplements

Loading data from figshare Loading data from figshare
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error