gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from ‘La Crouen’ alkaline thermal spring, New Caledonia No Access

Abstract

A novel anaerobic, alkaliphilic, mesophilic, Gram-stain-positive, endospore-forming bacterium was isolated from an alkaline thermal spring (42 °C, pH 9.0) in New Caledonia. This bacterium, designated strain LB2, grew at 25–50 °C (optimum, 37 °C) and pH 8.2–10.8 (optimum, pH 9.5). Added NaCl was not required for growth (optimum, 0–1 %) but was tolerated up to 7 %. Strain LB2 utilized a limited range of substrates, such as peptone, pyruvate, yeast extract and xylose. End products detected from pyruvate fermentation were acetate and formate. Both ferric citrate and thiosulfate were used as electron acceptors. Elemental sulphur, nitrate, nitrite, fumarate, sulphate, sulfite and DMSO were not used as terminal electron acceptors. The two major cellular fatty acids were iso-C and C. The genome consists of a circular chromosome (3.7 Mb) containing 3626 predicted protein-encoding genes with a G+C content of 36.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate is a member of the family , order within the phylum . Strain LB2 was most closely related to the thermophilic LBS3 (93.2 % 16S rRNA gene sequence identity). Genome-based analysis of average nucleotide identity and digital DNA–DNA hybridization of strain LB2 with LBS3 showed respective values of 70.8 and 13.4 %. Based on phylogenetic, genomic, chemotaxonomic and physiological properties, strain LB2 is proposed to represent the first species of a novel genus, for which the name gen. nov., sp. nov. is proposed (type strain LB2=DSM 100588=JCM 30958).

Funding
This study was supported by the:
  • ANR MICROPRONY (Award 19-CE02-0020-02)
    • Principle Award Recipient: NotApplicable
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2021-05-18
2024-03-29
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References

  1. Preiss L, Hicks DB, Suzuki S, Meier T, Krulwich TA. Alkaliphilic bacteria with impact on industrial applications, concepts of early life forms, and bioenergetics of ATP synthesis. Front Bioeng Biotech 2015; 3:75 [View Article][PubMed]
    [Google Scholar]
  2. Sarethy IP, Saxena Y, Kapoor A, Sharma M, Sharma SK et al. Alkaliphilic bacteria: applications in industrial biotechnology. J Ind Microbiol Biotechnol 2011; 38:769–790 [View Article][PubMed]
    [Google Scholar]
  3. Horikoshi K. Alkaliphiles: some applications of their products for biotechnology. Microbiol Mol Biol Rev 1999; 63:735–750 [View Article][PubMed]
    [Google Scholar]
  4. Kevbrin VV. Isolation and cultivation of alkaliphiles. Adv Biochem Eng Biotechnol 2020; 172:53–84 [View Article][PubMed]
    [Google Scholar]
  5. Wiegel J. Anaerobic alkaliphiles and alkaliphilic poly-extremophiles. Extremophiles Handbook 201181–97
    [Google Scholar]
  6. Cox ME, Launay J, Paris JP. Geochemistry of low temperature geothermal systems in New Caledonia. Pacific Geothermal Conference and 4th NZ Geothermal Workshop 1982 pp 453–459
    [Google Scholar]
  7. Maurizot P, Sevin B, Lesimple S, Collot J, Jeanpert J. Chapter 9: Mineral resources and prospectivity of non-ultramafic rocks of New-Caledonia. In Mortimer N. editor New Caledonia: Geology, Geodynamic Evolution and Mineral Resources 51 Geological Society, London, Memoirs: 2020 pp 215–245
    [Google Scholar]
  8. Deville E, Prinzhofer A. The origin of N2-H2-CH4-rich natural gas seepages in ophiolitic context: a major and noble gases study of fluid seepages in New Caledonia. Chem Geol 2016; 440:139–147 [View Article]
    [Google Scholar]
  9. Monnin C, Chavagnac V, Boulart C, Ménez B, Gérard M et al. Fluid chemistry of the low temperature hyperalkaline hydrothermal system of Prony Bay (New Caledonia). Biogeosciences 2014; 11:5687–5706 [View Article]
    [Google Scholar]
  10. Pinti DL. Serpentinization. Proc Natl Acad Sci 2015; 101:12818–12823
    [Google Scholar]
  11. Quéméneur M, Bes M, Postec A, Mei N, Hamelin J et al. Spatial distribution of microbial communities in the shallow submarine alkaline hydrothermal field of the Prony Bay, New Caledonia. Environ Microbiol Rep 2014; 6:665–674 [View Article][PubMed]
    [Google Scholar]
  12. Postec A, Quéméneur M, Bes M, Mei N, Benaïssa F et al. Microbial diversity in a submarine carbonate edifice from the serpentinizing hydrothermal system of the Prony Bay (New Caledonia) over a 6-year period. Front Microbiol 2015; 6:857 [View Article][PubMed]
    [Google Scholar]
  13. Pisapia C, Gérard E, Gérard M, Lecourt L, Lang SQ et al. Mineralizing filamentous bacteria from the Prony Bay hydrothermal field give new insights into the functioning of serpentinization-based subseafloor ecosystems. Front Microbiol 2017; 8:57 [View Article][PubMed]
    [Google Scholar]
  14. Frouin E, Bes M, Ollivier B, Quéméneur M, Postec A et al. Diversity of rare and abundant prokaryotic phylotypes in the Prony hydrothermal field and comparison with other serpentinite-hosted ecosystems. Front Microbiol 2018; 9:102 [View Article][PubMed]
    [Google Scholar]
  15. Mei N, Postec A, Monnin C, Pelletier B, Payri CE et al. Metagenomic and PCR-based diversity surveys of [FeFe]-hydrogenases combined with isolation of alkaliphilic hydrogen-producing bacteria from the serpentinite-hosted Prony Hydrothermal Field, New Caledonia. Front Microbiol 2016a; 7:1301 [View Article][PubMed]
    [Google Scholar]
  16. Ben Aissa F, Postec A, Erauso G, Payri C, Pelletier B et al. Vallitalea pronyensis sp. nov., isolated from a marine alkaline hydrothermal chimney. Int J Syst Evol Microbiol 2014; 64:1160–1165 [View Article][PubMed]
    [Google Scholar]
  17. Ben Aissa F, Postec A, Erauso G, Payri C, Pelletier B et al. Characterization of Alkaliphilus hydrothermalis sp. nov., a novel alkaliphilic anaerobic bacterium, isolated from a carbonaceous chimney of the Prony hydrothermal field, New Caledonia. Extremophiles 2015; 19:183–188 [View Article][PubMed]
    [Google Scholar]
  18. Bes M, Merrouch M, Joseph M, Quéméneur M, Payri C. Acetoanaerobium pronyense sp. nov., an anaerobic mesophilic bacterium isolated from the Prony alkaline Hydrothermal Field, New Caledonia. Int J Syst Evol Microbiol 2015; 65:2574–2580
    [Google Scholar]
  19. Mei N, Zergane N, Postec A, Erauso G, Ollier A et al. Fermentative hydrogen production by a new alkaliphilic Clostridium sp. (strain PROH2) isolated from a shallow submarine hydrothermal chimney in Prony Bay, New Caledonia. Int J Hydrogen Energ 2014; 39:19465–19473 [View Article]
    [Google Scholar]
  20. Mei N, Postec A, Erauso G, Joseph M, Pelletier B et al. Serpentinicella alkaliphila gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from the serpentinite-hosted Prony hydrothermal field, New Caledonia. Int J Syst Evol Microbiol 2016b; 66:4464–4470 [View Article][PubMed]
    [Google Scholar]
  21. Postec A, Quéméneur M, Lecoeuvre A, Chabert N, Joseph M et al. Alkaliphilus serpentinus sp. nov. and Alkaliphilus pronyensis sp. nov., two novel anaerobic alkaliphilic species isolated from the serpentinite-hosted Prony Bay Hydrothermal Field (New Caledonia). Syst Appl Microbiol 2021; 44:126175 [View Article][PubMed]
    [Google Scholar]
  22. Hungate RE. A roll tube method for cultivation of strict anaerobes. In Norris JR, Ribbons DW. (editors) Methods in Microbiology 3b London: Academic Press; 1969 pp 117–132
    [Google Scholar]
  23. Balch WE, Fox GE, Magrum LJ, Woese CR, Wolfe RS. Methanogens: reevaluation of a unique biological group. Microbiol Rev 1979; 43:260–296 [View Article][PubMed]
    [Google Scholar]
  24. Cord-Ruwisch R. A quick method for the determination of dissolved and precipitated sulfides in cultures of sulfate-reducing bacteria. J Microbiol Methods 1985; 4:33–36 [View Article]
    [Google Scholar]
  25. Quéméneur M, Erauso G, Frouin E, Zeghal E, Vandecasteele C et al. Hydrostatic pressure helps to cultivate an original anaerobic bacterium from the Atlantis Massif subseafloor (IODP Expedition 357): Petrocella atlantisensis gen. nov. sp. nov. Front Microbiol 2019; 10:1497 [View Article][PubMed]
    [Google Scholar]
  26. Kuykendall LD, Roy MA, O'Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
    [Google Scholar]
  27. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  28. Quéméneur M, Palvadeau A, Postec A, Monnin C, Chavagnac V et al. Endolithic microbial communities in carbonate precipitates from serpentinite-hosted hyperalkaline springs of the Voltri Massif (Ligurian Alps, Northern Italy). Environ Sci Pollut Res 2015; 22:13613–13624 [View Article]
    [Google Scholar]
  29. Lane DJ. Nucleic acid techniques in bacterial systematics. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Hoboken, NJ: Wiley; 1991 pp 115–175
    [Google Scholar]
  30. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  31. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  32. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  33. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  34. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  35. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article][PubMed]
    [Google Scholar]
  36. Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S et al. MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res 2013; 41:D636–D647 [View Article][PubMed]
    [Google Scholar]
  37. Chen I-MA, 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]
  38. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  39. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article][PubMed]
    [Google Scholar]
  40. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 2016; 17:1–14 [View Article]
    [Google Scholar]
  41. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article][PubMed]
    [Google Scholar]
  42. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
    [Google Scholar]
  43. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
    [Google Scholar]
  44. Kevbrin V, Boltyanskaya Y, Zhilina T, Kolganova T, Lavrentjeva E et al. Proteinivorax tanatarense gen. nov., sp. nov., an anaerobic, haloalkaliphilic, proteolytic bacterium isolated from a decaying algal bloom, and proposal of Proteinivoraceae fam. nov. Extremophiles 2013; 17:747–756 [View Article][PubMed]
    [Google Scholar]
  45. Prowe SG, Antranikian G. Anaerobranca gottschalkii sp. nov., a novel thermoalkaliphilic bacterium that grows anaerobically at high pH and temperature. Int J Syst Evol Microbiol 2001; 51:457–465 [View Article][PubMed]
    [Google Scholar]
  46. Engle M, Li Y, Woese C, Wiegel J. Isolation and characterization of a novel alkalitolerant thermophile, Anaerobranca horikoshii gen. nov., sp. nov. Int J Syst Bacteriol 1995; 45:454–461 [View Article][PubMed]
    [Google Scholar]
  47. Gorlenko V, Tsapin A, Namsaraev Z, Teal T, Tourova T et al. Anaerobranca californiensis sp. nov., an anaerobic, alkalithermophilic, fermentative bacterium isolated from a hot spring on Mono Lake. Int J Syst Evol Microbiol 2004; 54:739–743 [View Article][PubMed]
    [Google Scholar]
  48. Kevbrin V, Boltyanskaya Y, Garnova E, Wiegel J. Anaerobranca zavarzinii sp. nov., an anaerobic, alkalithermophilic bacterium isolated from Kamchatka thermal fields. Int J Syst Evol Microbiol 2008; 58:1486–1491 [View Article][PubMed]
    [Google Scholar]
  49. Boltyanskaya Y, Detkova E, Pimenov N, Kevbrin V. Proteinivorax hydrogeniformans sp. nov., an anaerobic, haloalkaliphilic bacterium fermenting proteinaceous compounds with high hydrogen production. Antonie van Leeuwenhoek 2018; 111:275–284 [View Article][PubMed]
    [Google Scholar]
  50. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
    [Google Scholar]
  51. Zhang P, Chen Y, Zhou Q, Zheng X, Zhu X et al. Understanding short-chain fatty acids accumulation enhanced in waste activated sludge alkaline fermentation: kinetics and microbiology. Environ Sci Technol 2010; 44:9343–9348 [View Article][PubMed]
    [Google Scholar]
  52. Antony CP, Shimpi GG, Cockell CS, Patole MS, Shouche YS. Molecular characterization of prokaryotic communities associated with Lonar crater basalts. Geomicrobiol J 2014; 31:519–528 [View Article]
    [Google Scholar]
  53. Rempfert KR, Miller HM, Bompard N, Nothaft D, Matter JM et al. Geological and geochemical controls on subsurface microbial life in the Samail Ophiolite, Oman. Front Microbiol 2017; 8:56 [View Article][PubMed]
    [Google Scholar]
  54. Purkamo L, Bomberg M, Kietäväinen R, Salavirta H, Nyyssönen M et al. Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids. Biogeosciences 2016; 13:3091–3108 [View Article]
    [Google Scholar]
  55. 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]
  56. Luscombe BM, Gray TRG. Characteristics of Arthrobacter grown in continuous culture. Microbiology 1974; 82:213–222
    [Google Scholar]
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