1887

Abstract

We isolated a Gram-stain-negative, pink-pigmented, motile, pleomorphic, extremely halophilic archaeon from the brine–seawater interface of Discovery Deep in the Saudi Arabian Red Sea. This strain, designated SB9, was capable of growth within a wide range of temperatures and salinity, but required MgCl2. Cells lysed in distilled water, but at 7.0 % (w/v) NaCl cell lysis was prevented. The major polar lipids from strain SB9 were phosphatidylglycerol, phosphatidylglycerolphosphate methyl ester, sulfated mannosyl glucosyl diether, mannosyl glucosyl diether, an unidentified glycolipid and two unidentified phospholipids. The major respiratory quinones of strain SB9 were menaquinones MK8 (66 %) and MK8 (VIII-H2) (34 %). Analysis of the 16S rRNA gene sequence revealed that strain SB9 was closely related to species in the genera Halogranum and Haloplanus ; in particular, it shared highest sequence similarity with the type strain of Halogranum rubrum (93.4 %), making it its closest known relative. The unfinished draft genome of strain SB9was 3 931 127 bp in size with a total G+C content of 62.53 mol% and contained 3917 ORFs, 50 tRNAs and eight rRNAs. Based on comparisons with currently available genomes, the highest average nucleotide identity value was 83 % to Halogranum salarium B-1 (GenBank accession no. GCA_000283335.1). These data indicate that this new isolate cannot be classified into any recognized genera of the family Haloferacaceae, and therefore strain SB9 is considered to be a representative of a novel species of a new genus within this family, for which the name Haloprofundus marisrubri gen. nov., sp. nov. is proposed. The type strain of Haloprofundus marisrubri is SB9 (=JCM 19565=CGMCC 1.14959).

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2017-02-20
2019-10-19
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References

  1. Gupta RS, Naushad S, Baker S. Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov. Int J Syst Evol Microbiol 2015;65:1050–1069 [CrossRef][PubMed]
    [Google Scholar]
  2. Torreblanca M, Rodriguez-Valera F, Juez G, Ventosa A, Kamekura M et al. Classification of non-alkaliphilic halobacteria based on numerical taxonomy and polar lipid composition, and description of Haloarcula gen. nov. and Haloferax gen. nov. Syst Appl Microbiol 1986;8:89–99[CrossRef]
    [Google Scholar]
  3. Oren A, Gurevich P, Gemmell RT, Teske A. Halobaculum gomorrense gen. nov., sp. nov., a novel extremely halophilic archaeon from the Dead Sea. Int J Syst Evol Microbiol 1995;45:747–754
    [Google Scholar]
  4. Cui HL, Yang X, Gao X, Xu XW. Halogranum gelatinilyticum sp. nov. and Halogranum amylolyticum sp. nov., isolated from a marine solar saltern, and emended description of the genus Halogranum. Int J Syst Evol Microbiol 2011;61:911–915 [CrossRef][PubMed]
    [Google Scholar]
  5. Montalvo-Rodríguez R, Vreeland RH, Oren A, Kessel M, Betancourt C et al. Halogeometricum borinquense gen. nov., sp. nov., a novel halophilic archaeon from Puerto Rico. Int J Syst Evol Microbiol 1998;48:1305–1312
    [Google Scholar]
  6. Elevi Bardavid R, Mana L, Oren A. Haloplanus natans gen. nov., sp. nov., an extremely halophilic, gas-vacuolate archaeon isolated from Dead Sea-Red Sea water mixtures in experimental outdoor ponds. Int J Syst Evol Microbiol 2007;57:780–783 [CrossRef][PubMed]
    [Google Scholar]
  7. Antunes A, Taborda M, Huber R, Moissl C, Nobre MF et al. Halorhabdus tiamatea sp. nov., a non-pigmented, extremely halophilic archaeon from a deep-sea, hypersaline anoxic basin of the Red Sea, and emended description of the genus Halorhabdus. Int J Syst Evol Microbiol 2008;58:215–220 [CrossRef][PubMed]
    [Google Scholar]
  8. Antunes A, Ngugi DK, Stingl U. Microbiology of the Red Sea (and other) deep-sea anoxic brine lakes. Environ Microbiol Rep 2011;3:416–433 [CrossRef][PubMed]
    [Google Scholar]
  9. Mitra A, Santra SC, Mukherjee J. Distribution of actinomycetes, their antagonistic behaviour and the physico-chemical characteristics of the world's largest tidal mangrove forest. Appl Microbiol Biotechnol 2008;80:685–695 [CrossRef][PubMed]
    [Google Scholar]
  10. Dyall-Smith ML. 2008; The Halohandbook: protocols for haloarchaeal genetics. www.haloarchaea.com/resources/halohandbook/
  11. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985;49:1–7[PubMed]
    [Google Scholar]
  12. Oren A, Ventosa A, Grant WD. Proposed minimal standards for description of new taxa in the order Halobacteriales. Int J Syst Evol Microbiol 1997;47:233–238
    [Google Scholar]
  13. Oren A. Diversity of halophiles. In: Horikoshi K. (editor) Extremophiles Handbook Japan: Springer; 2011; pp.309–325[CrossRef]
    [Google Scholar]
  14. Oren A. Taxonomy of halophilic Archaea: current status and future challenges. Extremophiles 2014;18:825–834 [CrossRef][PubMed]
    [Google Scholar]
  15. Glauert AM. Fixation, Dehydration and Embedding of Biological Specimens Amsterdam: Elsevier; 1991
    [Google Scholar]
  16. Bozzola JJ, Russell LD. Electron Microscopy: Principles and Techniques for Biologists, 2nd ed. Sudbury, MA: Jones & Bartlett; 1999
    [Google Scholar]
  17. Dussault HP. An improved technique for staining red halophilic bacteria. J Bacteriol 1955;70:484–485[PubMed]
    [Google Scholar]
  18. Smibert RM, Krieg NR. Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General, Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  19. Dong XZ, Cai MY. (editors) Chapter 14. Determination of biochemical characteristics. In Manual for the Systematic Identification of General Bacteria Beijing: Science Press (in Chinese); 2001; pp.370–398
    [Google Scholar]
  20. Gutiérrez C, González C. Method for simultaneous detection of proteinase and esterase activities in extremely halophilic bacteria. Appl Microbiol 1972;24:516–517[PubMed]
    [Google Scholar]
  21. Cui HL, Gao X, Sun FF, Dong Y, Xu XW et al. Halogranum rubrum gen. nov., sp. nov., a halophilic archaeon isolated from a marine solar saltern. Int J Syst Evol Microbiol 2010;60:1366–1371 [CrossRef][PubMed]
    [Google Scholar]
  22. Gutiérrez MC, Castillo AM, Kamekura M, Ventosa A. Haloterrigena salina sp. nov., an extremely halophilic archaeon isolated from a salt lake. Int J Syst Evol Microbiol 2008;58:2880–2884 [CrossRef][PubMed]
    [Google Scholar]
  23. Du ZJ, Wang Y, Dunlap C, Rooney AP, Chen GJ. Draconibacterium orientale gen. nov., sp. nov., isolated from two distinct marine environments, and proposal of Draconibacteriaceae fam. nov. Int J Syst Evol Microbiol 2014;64:1690–1696 [CrossRef][PubMed]
    [Google Scholar]
  24. CLSI Performance Standards for Antimicrobial Susceptibility Testing; 22nd Informational Supplement M100-S22 Wayne, PA: Clinical and Laboratory Standards Institute; 2012
    [Google Scholar]
  25. Cui HL, Gao X, Li XY, Xu XW, Zhou YG et al. Haloplanus vescus sp. nov., an extremely halophilic archaeon from a marine solar saltern, and emended description of the genus Haloplanus. Int J Syst Evol Microbiol 2010;60:1824–1827 [CrossRef][PubMed]
    [Google Scholar]
  26. Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011;27:863–864 [CrossRef][PubMed]
    [Google Scholar]
  27. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008;24:713–714 [CrossRef][PubMed]
    [Google Scholar]
  28. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010;20:265–272 [CrossRef][PubMed]
    [Google Scholar]
  29. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2014;25:1043–1055[CrossRef]
    [Google Scholar]
  30. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007;23:673–679 [CrossRef][PubMed]
    [Google Scholar]
  31. 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 [CrossRef][PubMed]
    [Google Scholar]
  32. 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[PubMed][CrossRef]
    [Google Scholar]
  33. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014;64:352–356 [CrossRef][PubMed]
    [Google Scholar]
  34. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57:81–91 [CrossRef][PubMed]
    [Google Scholar]
  35. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004;5:R12 [CrossRef][PubMed]
    [Google Scholar]
  36. Cui HL, Gao X, Yang X, Xu XW. Haloplanus aerogenes sp. nov., an extremely halophilic archaeon from a marine solar saltern. Int J Syst Evol Microbiol 2011;61:965–968 [CrossRef][PubMed]
    [Google Scholar]
  37. Kim KK, Lee KC, Lee JS. Halogranum salarium sp. nov., a halophilic archaeon isolated from sea salt. Syst Appl Microbiol 2011;34:576–580 [CrossRef][PubMed]
    [Google Scholar]
  38. Savage KN, Krumholz LR, Oren A, Elshahed MS. Halosarcina pallida gen. nov., sp. nov., a halophilic archaeon from a low-salt, sulfide-rich spring. Int J Syst Evol Microbiol 2008;58:856–860 [CrossRef][PubMed]
    [Google Scholar]
  39. Pesenti PT, Sikaroodi M, Gillevet PM, Sánchez-Porro C, Ventosa A et al. Halorubrum californiense sp. nov., an extreme archaeal halophile isolated from a crystallizer pond at a solar salt plant in California, USA. Int J Syst Evol Microbiol 2008;58:2710–2715 [CrossRef][PubMed]
    [Google Scholar]
  40. Allen MA, Goh F, Leuko S, Echigo A, Mizuki T et al. Haloferax elongans sp. nov. and Haloferax mucosum sp. nov., isolated from microbial mats from Hamelin Pool, Shark Bay, Australia. Int J Syst Evol Microbiol 2008;58:798–802 [CrossRef][PubMed]
    [Google Scholar]
  41. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997;25:4876–4882 [CrossRef][PubMed]
    [Google Scholar]
  42. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. mega6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  43. Jackson EE, Masood N, Ibrahim K, Urvoy N, Hariri S et al. Description of Siccibacter colletis sp. nov., a novel species isolated from plant material, and emended description of Siccibacter turicensis. Int J Syst Evol Microbiol 2015;65:1335–1341 [CrossRef][PubMed]
    [Google Scholar]
  44. Urdiain M, López-López A, Gonzalo C, Busse HJ, Langer S et al. Reclassification of Rhodobium marinum and Rhodobium pfennigii as Afifella marina gen. nov. comb. nov. and Afifella pfennigii comb. nov., a new genus of photoheterotrophic Alphaproteobacteria and emended descriptions of Rhodobium, Rhodobium orientis and Rhodobium gokarnense. Syst Appl Microbiol 2008;31:339–351 [CrossRef][PubMed]
    [Google Scholar]
  45. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  46. Haley BJ, Grim CJ, Hasan NA, Choi SY, Chun J et al. Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae. BMC Microbiol 2010;10:154 [CrossRef][PubMed]
    [Google Scholar]
  47. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014;64:346–351 [CrossRef][PubMed]
    [Google Scholar]
  48. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959;37:911–917 [CrossRef][PubMed]
    [Google Scholar]
  49. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR. (editors) Methods for General and Molecular Microbiology, 3rd ed. Washington, DC: ASM Press; 2007; pp.330–393
    [Google Scholar]
  50. Gutiérrez MC, Castillo AM, Corral P, Kamekura M, Ventosa A. Halorubrum aquaticum sp. nov., an archaeon isolated from hypersaline lakes. Int J Syst Evol Microbiol 2011;61:1144–1148 [CrossRef][PubMed]
    [Google Scholar]
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