, Volume 8, Issue 6, pp 431–439 | Cite as

Halobacterium noricense sp. nov., an archaeal isolate from a bore core of an alpine Permian salt deposit, classification of Halobacterium sp. NRC-1 as a strain of H. salinarum and emended description of H. salinarum

  • Claudia Gruber
  • Andrea Legat
  • Marion Pfaffenhuemer
  • Christian Radax
  • Gerhard Weidler
  • Hans-Jürgen Busse
  • Helga Stan-LotterEmail author
Original Paper


Two rod-shaped haloarchaeal strains, A1 and A2, were isolated from a bore core from a salt mine in Austria. The deposition of the salt is thought to have occurred during the Permian period (225–280 million years ago). The 16S rDNA sequences of the strains were 97.1% similar to that of the type species of the genus Halobacterium, which was also determined in this work. Polar lipids consisted of C20–C20 derivatives of phosphatidylglycerol, methylated phosphatidylglycerol phosphate, phosphatidylglycerol sulfate, triglycosyl diether and sulfated tetraglycosyl diether. Optimal salinity for growth was 15–17.5% NaCl; Mg++ was tolerated up to a concentration of 1 M. The DNA–DNA reassociation value of strain A1T was 25% with H. salinarum DSM 3754T and 41% with Halobacterium sp. NRC-1, respectively. Based on these results and other properties, e.g. whole cell protein patterns, menaquinone content and restriction patterns of DNA, strains A1 and A2 are members of a single species, for which we propose the name H. noricense. The type strain is A1 (DSM 15987T, ATCC BAA-852T, NCIMB 13967T). Since we present evidence that Halobacterium sp. NRC-1 is a member of H. salinarum, an emended description of H. salinarum is provided.


Halobacterium noricense Halobacterium salinarum Halobacterium sp. NRC-1 Haloarchaea Salt mine Bore core Longevity 



We acknowledge support from the Austrian Science Foundation (FWF), projects P13995-MOB and P16260-B07. We thank Mag. Michael Mayr (Salinen Austria) for help in obtaining the rock salt samples, Dr. Peter Schumann (DSMZ, Braunschweig, Germany) for determination of the G+C content and for DNA–DNA hybridization experiments, Chris Frethem (University of Minnesota) for electron microscopy and Günther Thüry (Lic. Phil., University of Salzburg) for suggesting the species name.


  1. Cashion P, Hodler-Franklin MA, McCully J, Franklin M (1977) A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81:461–466PubMedGoogle Scholar
  2. Collins MD, Ross HNM, Tindall BJ, Grant WD (1981) Distribution of isoprenoid quinones in halophilic bacteria. J Appl Bacteriol 50:559–565Google Scholar
  3. DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685–5689PubMedGoogle Scholar
  4. Denner EBM, McGenity TJ, Busse H-J, Wanner G, Grant WD, Stan-Lotter H (1994) Halococcus salifodinae sp. nov., an archaeal isolate from an Austrian salt mine. Int J Syst Bacteriol 44:774–780Google Scholar
  5. Dussault HP (1955) An improved technique for staining red halophilic bacteria. J Bacteriol 70:484–485PubMedGoogle Scholar
  6. Felsenstein J (1993) PHYLIP (phylogenetic interference package) ver.3.5.1c (distributed by the author). University of Seattle, Wash.Google Scholar
  7. Fish SA, Shepherd TJ, McGenity TJ, Grant WD (2002) Recovery of 16S ribosomal RNA gene fragments from ancient halite. Nature 417:432–436CrossRefPubMedGoogle Scholar
  8. Gochnauer MB, Kushawa SC, Kates M, Kushner DJ (1972) Nutritional control of pigment and isoprenoid compound formation in extremely halophilic bacteria. Arch Microbiol 84:339–349Google Scholar
  9. Grant WD, Larsen H (1989) Extremely halophilic archaeobacteria, order Halobacteriales ord. nov. In: Staley JT, Bryant MP, N. Pfennig N, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 3. Williams and Wilkins, Baltimore, pp 2216–2230Google Scholar
  10. Grant WD, Gemmell RT, McGenity TJ (1998) Halobacteria: the evidence for longevity. Extremophiles 2:279–287CrossRefPubMedGoogle Scholar
  11. Grant WD (2001) Genus I. Halobacterium Elazari-Volcani 1957, 207AL emend. Larsen and Grant 1989, 2222. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology, 2nd edn, vol 1. Springer, Berlin Heidelberg New York, pp 301–305Google Scholar
  12. Grant WD, Kamekura M, McGenity TJ, Ventosa A (2001) Order I. Halobacteriales Grant and Larsen 1989b, 495VP (effective publication: Grant and Larsen 1989a, 2216) In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology, 2nd edn, vol 1. Springer, Berlin Heidelberg New York, pp 294–299Google Scholar
  13. Hackett NR, Bobovnikova Y, Heyrovska N (1994) Conservation of chromosomal arrangement among three strains of the genetically unstable archaeon H. salinarium. J Bacteriol 176:7711–7718PubMedGoogle Scholar
  14. Hackett N (1995) Preparation of intact, agarose-embedded DNA from H. halobium and its digestion by restriction enzyme. In: DasSarma S, Fleischmann EM (eds) Archaea: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., pp 185–187Google Scholar
  15. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  16. Holt JG, Krieg NR, Sneath PHA, Staley JT, Williams ST (1994) Extremely halophilic, aerobic archaeobacteria (halobacteria). In: Bergey’s manual of determinative bacteriology, 9th edn. Williams and Wilkins, Baltimore, pp 739–746Google Scholar
  17. Humble MW, King A, Philips I (1977) API Zym, a simple rapid system for the detection of bacterial enzymes. J Clin Pathol 30:275–277PubMedGoogle Scholar
  18. Jackman PJH (1987) Microbial systematics based on electrophoretic whole-cell protein patterns. Methods Microbiol 19:209–225Google Scholar
  19. Jukes TH, Cantor RR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol 3. Academic, New York, pp 21–132Google Scholar
  20. Laemmli UK (1970) Cleave of structural proteins during the assembly of the head of the bacteriophage T4. Nature 227:684–685Google Scholar
  21. Lechner J, Sumper M (1987) The primary structure of a procaryotic glycoprotein: cloning and sequencing of the cell surface glycoprotein gene of halobacteria. J Biol Chem 262:9724–9729PubMedGoogle Scholar
  22. Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM, Tiedje JM (2001) The RDP-II (ribosomal database project). Nucleic Acids Res 29:173–174CrossRefPubMedGoogle Scholar
  23. Malik KA (1983) A modified method for the cultivation of phototrophic bacteria under anaerobic conditions. J Microbiol Methods 1:343–352CrossRefGoogle Scholar
  24. McGenity TJ, Gemmell RT, Grant WD (1998) Proposal of a new halobacterial genus Natrinema gen. nov., with two species Natrinema pellirubrum nom. nov. and Natrinema pallidum nom. nov. Int J Syst Bacteriol 48:1187–1196PubMedGoogle Scholar
  25. McGenity TJ, Gemmell RT, Grant WD, Stan-Lotter H (2000) Origins of halophilic microorganisms in ancient salt deposits (mini-review). Environ Microbiol 2:243–250CrossRefPubMedGoogle Scholar
  26. Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonski PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KW, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H, Lowe TM, Liang P, Riley M, Hood L, DasSarma S (2000) Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci USA 97:12176–12181CrossRefPubMedGoogle Scholar
  27. Ng WV, Yang CF, Halladay JT, Arora P, DasSarma S (1995) Isolation of genomic and plasmid DNAs from H. halobium. In: DasSarma S, Fleischmann EM (eds) Archaea: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., pp 179–184Google Scholar
  28. Norton CF, McGenity TJ, Grant WD (1993) Archaeal halophiles (halobacteria) from two British salt mines. J Gen Microbiol 139:1077–1081Google Scholar
  29. Oren A (1983) Halobacterium sodomense sp. nov., a Dead Sea halobacterium with an extremely high magnesium requirement. Int J Syst Bacteriol 33:381–386Google Scholar
  30. Oren A, Gurevich P, Gemmell RT, Teske A (1995) Halobaculum gomorrense gen. nov., sp. nov., a novel extremely halophilic archaeon from the Dead Sea. Int J Syst Bacteriol 45:747–754PubMedGoogle Scholar
  31. Oren A, Ventosa A, Grant WD (1997) Proposed minimal standards for description of new taxa in the order Halobacteriales. Int J Syst Bacteriol 47:233–238Google Scholar
  32. Oren A, Litchfield CD (1999) A procedure for the enrichment and isolation of Halobacterium. FEMS Microbiol Lett 173:353–358CrossRefGoogle Scholar
  33. Oren A, Trüper HG (1990) Anaerobic growth of halophilic archaeobacteria by reduction of dimethylsulfoxide and trimethylamine N-oxide. FEMS Microbiol Lett 70:33–36CrossRefGoogle Scholar
  34. Radax C, Gruber C, Stan-Lotter H (2001) Novel haloarchaeal 16S rRNA gene sequences from alpine Permo-Triassic rock salt. Extremophiles 5:221–228CrossRefPubMedGoogle Scholar
  35. Reistad R (1970) On the composition and nature of the bulk protein of extremely halophilic bacteria. Arch Mikrobiol 71:353–360PubMedGoogle Scholar
  36. Ross HNM, Grant WD, Harris JE (1985) Lipids in archaebacterial taxonomy. In: Goodfellow M, Minnekin DE (eds) Chemical methods in bacterial systematics. Academic, London, pp 289–299Google Scholar
  37. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  38. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Manual of methods for general microbiology. American Society for Microbiology, Washington, D.C., pp 607–654Google Scholar
  39. Stan-Lotter H, Lang FJ Jr, Hochstein LI (1989) Electrophoresis and isoelectric focusing of whole cell membrane proteins from the extremely halophilic archaebacteria. Appl Theor Electrophor 1:147–153PubMedGoogle Scholar
  40. Stan-Lotter H, Sulzner M, Egelseer E, Norton CF, Hochstein LI (1993) Comparison of membrane ATPases from extreme halophiles isolated from ancient salt deposits. Orig Life Evol Biosph 23:53–64PubMedGoogle Scholar
  41. Stan-Lotter H, McGenity TJ, Legat A, Denner EBM, Glaser K, Stetter KO, Wanner G (1999) Very similar strains of Halococcus salifodinae are found in geographically separated Permo-Triassic salt deposits. Microbiology 145:3565–3574PubMedGoogle Scholar
  42. Stan-Lotter H, Radax C, Gruber C, McGenity TJ, Legat A, Wanner G, Denner EBM (2000) The distribution of viable microorganisms in Permo-Triassic rock salt. In: Geertman RM (ed) SALT 2000: 8th world salt symposium, vol 2. Elsevier, Amsterdam, pp 921–926Google Scholar
  43. Stan-Lotter H, Pfaffenhuemer M, Legat A, Busse H-J, Radax C, Gruber C (2002) Halococcus dombrowskii sp. nov., an archaeal isolate from a Permo-Triassic alpine salt deposit. Int J System Evol Microbiol 52:1807–1814CrossRefGoogle Scholar
  44. Stan-Lotter H, Radax C, Gruber C, Legat A, Pfaffenhuemer M, Wieland H, Leuko S, Weidler G, Kömle N, Kargl G (2003) Astrobiology with haloarchaea from Permo-Triassic rock salt. Int J Astrobiol 1:271–284CrossRefGoogle Scholar
  45. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefPubMedGoogle Scholar
  46. Ventosa A, Oren A (1996) Halobacterium salinarum nom. corrig., a name to replace Halobacterium salinarium (Elazari-Volcani) and to include Halobacterium halobium and Halobacterium cutirubrum. Int J Syst Bacteriol 46:347Google Scholar
  47. Wainø M, Tindall BJ, Ingvorsen K (2000) Halorhabdus utahensis gen. nov., sp. nov., an aerobic, extremely halophilic member of the Archaea from Great Salt Lake, Utah. Int J Syst Evol Microbiol 50:183–190PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Claudia Gruber
    • 1
  • Andrea Legat
    • 1
  • Marion Pfaffenhuemer
    • 1
  • Christian Radax
    • 1
  • Gerhard Weidler
    • 1
  • Hans-Jürgen Busse
    • 2
    • 3
  • Helga Stan-Lotter
    • 1
    Email author
  1. 1.Fachbereich für Molekulare Biologie, Abteilung MikrobiologieSalzburgAustria
  2. 2.Institut für Bakteriologie, Mykologie und HygieneViennaAustria
  3. 3.Institut für Mikrobiologie und GenetikViennaAustria

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