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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 4

gen. nov., sp. nov., a hydrogenotrophic methanogen, isolated from a hydrothermal vent chimney in the Mid-Cayman Spreading Center, the Caribbean Sea Free

Abstract

A novel hydrogenotrophic methanogen, strain HHB, was isolated from a deep-sea hydrothermal vent chimney sample collected from Beebe Vent Field at the Mid-Cayman Spreading Center, Caribbean Sea. The cells were non-motile regular to irregular cocci possessing several flagella. The novel isolate grew at 60–80 °C, pH 5.0–7.4 and with 1–4 % of NaCl (w/v). The isolate utilized H/CO as the only substrates for growth and methane production. The results of phylogenetic analyses of both 16S rRNA and gene sequences and comparative genome analysis indicated that HHB represented a member of the order , and was closely related to the members of the genera and . The most closely related species were IH1 and Kol 5 in comparison of 16S rRNA gene sequences (each with 93 % identity), and Mc-S-70 in the case of deduced amino acid sequence similarity of genes (92 % similarity). The ANI and AAI values between HHB and the members of the genera and were 69–72 % and 66–70 %, respectively. Although many of the morphological and physiological characteristics were quite similar between HHB and the species of the genera and , they were distinguishable by the differences in susceptibility to antibiotics, formate utilization, growth temperature and NaCl ranges. On the basis of these phenotypic, phylogenetic and genomic properties, we propose that strain HHB represents a novel species, of a novel genus, gen. nov., sp. nov. The type strain is HHB (=JCM 32161=DSM 105918).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): deep-sea , hydrothermal vent , methanogen and thermophilic
© 2019 IUMS
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2019-03-07
2024-04-26
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References

  1. Ferry JG. Methanogenesis Boston, MA: Springer Science & Business Media; 1993
     [Google Scholar]
  2. Whitman WB, Boone DR. Order I. Methanococcales . In Boone DR, Castenholz RW, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. Vol.1 New York: Springer; 2001 pp. 236–246
     [Google Scholar]
  3. Stadtman TC, Barker HA. Studies on the methane fermentation. X. A new formate-decomposing bacterium, Methanococcus vannielii . J Bacteriol 1951; 62:269–280[PubMed]
     [Google Scholar]
  4. Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. Methanogens: reevaluation of a unique biological group. Microbiol Rev 1979; 43:260–296[PubMed]
     [Google Scholar]
  5. Huber H, Thomm M, König H, Thies G, Stetter KO. Methanococcus thermolithotrophicus, a novel thermophilic lithotrophic methanogen. Arch Microbiol 1982; 132:47–50 [View Article]
     [Google Scholar]
  6. Jones WJ, Paynter MJB, Gupta R. Characterization of Methanococcus maripaludis sp. nov., a new methanogen isolated from salt marsh sediment. Arch Microbiol 1983; 135:91–97 [View Article]
     [Google Scholar]
  7. 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]
  8. Burggraf S, Fricke H, Neuner A, Kristjansson J, Rouvier P et al. Methanococcus igneus sp. nov., a novel hyperthermophilic methanogen from a shallow submarine hydrothermal system. Syst Appl Microbiol 1990; 13:263–269 [View Article][PubMed]
     [Google Scholar]
  9. 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; 48:913–919 [View Article][PubMed]
     [Google Scholar]
  10. 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; 49:583–589 [View Article][PubMed]
     [Google Scholar]
  11. Whitman W. “Genus II. Methanothermococcus gen. nov.,”. In Boone DR, Castenholz RW, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 1 New York: Springer; 2001 pp. 241–242
     [Google Scholar]
  12. Takai K, Inoue A, Horikoshi K. Methanothermococcus okinawensis sp. nov., a thermophilic, methane-producing archaeon isolated from a Western Pacific deep-sea hydrothermal vent system. Int J Syst Evol Microbiol 2002; 52:1089–1095 [View Article][PubMed]
     [Google Scholar]
  13. 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][PubMed]
     [Google Scholar]
  14. Takai K, Nealson KH, Horikoshi K. Methanotorris formicicus sp. nov., a novel extremely thermophilic, methane-producing archaeon isolated from a black smoker chimney in the Central Indian Ridge. Int J Syst Evol Microbiol 2004; 54:1095–1100 [View Article][PubMed]
     [Google Scholar]
  15. Kendall MM, Liu Y, Sieprawska-Lupa M, Stetter KO, Whitman WB et al. Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments. Int J Syst Evol Microbiol 2006; 56:1525–1529 [View Article][PubMed]
     [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][PubMed]
     [Google Scholar]
  17. Stewart LC, Jung JH, Kim YT, Kwon SW, Park CS 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]
  18. Connelly DP, Copley JT, Murton BJ, Stansfield K, Tyler PA et al. Hydrothermal vent fields and chemosynthetic biota on the world's deepest seafloor spreading centre. Nat Commun 2012; 3:620 [View Article][PubMed]
     [Google Scholar]
  19. Takai K, Inoue A, Horikoshi K. Thermaerobacter marianensis gen. nov., sp. nov., an aerobic extremely thermophilic marine bacterium from the 11,000 m deep Mariana Trench. Int J Syst Bacteriol 1999; 49 Pt 2:619–628 [View Article][PubMed]
     [Google Scholar]
  20. Delong EF. Archaea in coastal marine environments. Proc Natl Acad Sci USA 1992; 89:5685–5689 [View Article][PubMed]
     [Google Scholar]
  21. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
     [Google Scholar]
  22. Imachi H, Aoi K, Tasumi E, Saito Y, Yamanaka Y et al. Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor. Isme J 2011; 5:1913–1925 [View Article][PubMed]
     [Google Scholar]
  23. Yashiro Y, Sakai S, Ehara M, Miyazaki M, Yamaguchi T et al. Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge. Int J Syst Evol Microbiol 2011; 61:53–59 [View Article][PubMed]
     [Google Scholar]
  24. Nunoura T, Nishizawa M, Hirai M, Shimamura S, Harnvoravongchai P et al. Microbial diversity in sediments from the bottom of the challenger deep, the mariana trench. Microbes Environ 2018; 33:186–194 [View Article][PubMed]
     [Google Scholar]
  25. Zillig W, Holz I, Janekovic D, Klenk HP, Imsel E et al. Hyperthermus butylicus, a hyperthermophilic sulfur-reducing archaebacterium that ferments peptides. J Bacteriol 1990; 172:3959–3965 [View Article][PubMed]
     [Google Scholar]
  26. Yamaguchi M, Okada H, Namiki Y. Smart specimen preparation for freeze substitution and serial ultrathin sectioning of yeast cells. J Electron Microsc 2009; 58:261–266 [View Article][PubMed]
     [Google Scholar]
  27. 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]
  28. Tamaoka J, Komagata K. Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 1984; 25:125–128 [View Article]
     [Google Scholar]
  29. Takai K, Inoue A, Horikoshi K. Methanothermococcus okinawensis sp. nov., a thermophilic, methane-producing archaeon isolated from a Western Pacific deep-sea hydrothermal vent system. Int J Syst Evol Microbiol 2002; 52:1089–1095 [View Article][PubMed]
     [Google Scholar]
  30. Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res 2010; 38:e132e132 [View Article][PubMed]
     [Google Scholar]
  31. Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL. Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res 2012; 40:e9e9 [View Article][PubMed]
     [Google Scholar]
  32. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 2017; 45:D353–D361 [View Article][PubMed]
     [Google Scholar]
  33. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  34. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
     [Google Scholar]
  35. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article][PubMed]
     [Google Scholar]
  36. Farrer RA. Synima: a Synteny imaging tool for annotated genome assemblies. BMC Bioinformatics 2017; 18:507 [View Article][PubMed]
     [Google Scholar]
  37. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389–3402 [View Article][PubMed]
     [Google Scholar]
  38. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004; 32:1363–1371 [View Article][PubMed]
     [Google Scholar]
  39. Uniprot Consortium T. UniProt: the universal protein knowledgebase. Nucleic Acids Res 2018; 46:2699 [View Article][PubMed]
     [Google Scholar]
  40. Chen IA, Markowitz VM, Chu K, Palaniappan K, Szeto E et al. IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res 2017; 45:D507–D516 [View Article][PubMed]
     [Google Scholar]
  41. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  42. 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]
  43. Nakagawa S, Takai K. Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance. FEMS Microbiol Ecol 2008; 65:1–14 [View Article][PubMed]
     [Google Scholar]
  44. Slobodkina GB, Kolganova TV, Chernyh NA, Querellou J, Bonch-Osmolovskaya EA et al. Deferribacter autotrophicus sp. nov., an iron(III)-reducing bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2009; 59:1508–1512 [View Article][PubMed]
     [Google Scholar]
  45. Whitman WB. Genus II. Methanotorris gen. nov. In Boone DR, Castenholz RW, Garrity GM. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. Vol.1 New York: Springer; 2001 pp. 245–246
     [Google Scholar]
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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 69, 1225 (2019); https://doi.org/10.1099/ijsem.0.003297
/content/journal/ijsem/10.1099/ijsem.0.003297
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