1887

Abstract

A novel and extremely halophilic archaeon, designated strain 2a_47_2, was isolated from a solar saltern sample collected in Indonesia. Cells of the strain were Gram-stain-negative, non-motile and pleomorphic and formed orange–red pigmented colonies. Strain 2a_47_2 grew at 20–48 °C (optimum 38–41 °C), pH 6.0–8.5 (optimum pH 7.5), >1.7 M NaCl (optimum 2.6 M) and <0.5 M MgCl2 (optimum 0.3 M). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two phospholipids and sulfated diglycosyl diether. The cells mainly contained menaquinone-8. The G+C content in the genomic DNA of the strain was 67.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 2a_47_2 represents a member of the family Halorubraceae and is different from any other known halophilic archaea. This finding was also demonstrated by phylogenetic analyses based on deduced RpoB′ amino acid sequences. Collectively, these results show that strain 2a_47_2 represents a novel genus and species in the family Halorubraceae , and the name Halobium palmae gen. nov., sp. nov. is proposed. The type strain is 2a_47_2 (=NBRC 111368=InaCC Ar34).

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2016-10-01
2019-10-15
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References

  1. Adachi J., Hasegawa M..( 1995;). Improved dating of the human chimpanzee separation in the mitochondrial-DNA tree – heterogeneity among amino-acid sites. . J Mol Evol 40: 622–628. [CrossRef] [PubMed]
    [Google Scholar]
  2. Amoozegar M. A., Makhdoumi-Kakhki A., Shahzadeh Fazeli S. A., Azarbaijani R., Ventosa A..( 2012;). Halopenitus persicus gen. nov., sp. nov., an archaeon from an inland salt lake. . Int J Syst Evol Microbiol 62: 1932–1936. [CrossRef] [PubMed]
    [Google Scholar]
  3. Amoozegar M. A., Makhdoumi-Kakhki A., Mehrshad M., Fazeli S. A., Ventosa A..( 2013;). Halopenitus malekzadehii sp. nov., an extremely halophilic archaeon isolated from a salt lake. . Int J Syst Evol Microbiol 63: 3232–3236. [CrossRef] [PubMed]
    [Google Scholar]
  4. Burns D. G., Janssen P. H., Itoh T., Kamekura M., Echigo A., Dyall-Smith M. L..( 2010;). Halonotius pteroides gen. nov., sp. nov., an extremely halophilic archaeon recovered from a saltern crystallizer. . Int J Syst Evol Microbiol 60: 1196–1199. [CrossRef] [PubMed]
    [Google Scholar]
  5. Corral P., de la Haba R. R., Sánchez-Porro C., Ali Amoozegar M., Thane Papke R., Ventosa A..( 2016;). Halorubrum halodurans sp. nov., an extremely halophilic archaeon isolated from a hypersaline lake. . Int J Syst Evol Microbiol 66: 435–444. [CrossRef] [PubMed]
    [Google Scholar]
  6. Cui H. L., Zhang W. J..( 2014;). Salinigranum rubrum gen. nov., sp. nov., a member of the family Halobacteriaceae isolated from a marine solar saltern. . Int J Syst Evol Microbiol 64: 2029–2033. [CrossRef] [PubMed]
    [Google Scholar]
  7. Cui H. L., Gao X., Sun F. F., Dong Y., Xu X. W., Zhou Y. G., Liu H. C., Oren A., Zhou P. J..( 2010;). Halogranum rubrum gen. nov., sp. nov., a halophilic archaeon isolated from a marine solar saltern. . Int J Syst Evol Microbiol 60: 1366–1371. [CrossRef] [PubMed]
    [Google Scholar]
  8. Cui H. L., Yang X., Gao X., Xu X. W..( 2011;). 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 61: 911–915. [CrossRef] [PubMed]
    [Google Scholar]
  9. Dittmer J. C., Lester R. L..( 1964;). A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. . J Lipid Res 15: 126–127.
    [Google Scholar]
  10. Gupta R. S., Naushad S., Baker S..( 2015;). 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 65: 1050–1069. [CrossRef] [PubMed]
    [Google Scholar]
  11. Gupta R. S., Naushad S., Fabros R., Adeolu M..( 2016;). A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae fam. nov. . Antonie van Leeuwenhoek 109: 565–587.[CrossRef]
    [Google Scholar]
  12. Hamada M., Iino T., Iwami T., Harayama S., Tamura T., Suzuki K..( 2010;). Mobilicoccus pelagius gen. nov., sp. nov. and Piscicoccus intestinalis gen. nov., sp. nov., two new members of the family Dermatophilaceae, and reclassification of Dermatophilus chelonae (Masters et al. 1995) as Austwickia chelonae gen. nov., comb. nov. . J Gen Appl Microbiol 56: 427–436. [CrossRef] [PubMed]
    [Google Scholar]
  13. Han D., Cui H. L..( 2014;). Haloplanus litoreus sp. nov. and Haloplanus ruber sp. nov., from a marine solar saltern and an aquaculture farm, respectively. . Antonie Van Leeuwenhoek 105: 679–685. [CrossRef] [PubMed]
    [Google Scholar]
  14. Hasegawa M., Kishino H., Yano T..( 1985;). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. . J Mol Evol 22: 160–174. [CrossRef] [PubMed]
    [Google Scholar]
  15. Henriet O., Fourmentin J., Delincé B., Mahillon J..( 2014;). Exploring the diversity of extremely halophilic archaea in food-grade salts. . Int J Food Microbiol 191: 36–44. [CrossRef] [PubMed]
    [Google Scholar]
  16. Hewitt E. J., Nicholas D. J. D..( 1964;). Enzymes of inorganic nitrogen metabolism. . In Modern Methods of Plant Analysis , pp. 167–172. Edited by Linskens H. F., Sanwal B. D., Tracey M. V.. Heidelberg:: Springer;.
    [Google Scholar]
  17. Holding A. J., Nicholas D. J. D..( 1971;). Routine biochemical tests. . Methods Microbiol 6: 1–32.[CrossRef]
    [Google Scholar]
  18. Huelsenbeck J. P., Ronquist F..( 2001;). MRBAYES: Bayesian inference of phylogenetic trees. . Bioinformatics 17: 754–755. [CrossRef] [PubMed]
    [Google Scholar]
  19. Kamagata Y., Mikami E..( 1991;). Isolation and characterization of a novel thermophilic methanosaeta strain. . Int J Syst Bacteriol 41: 191–196. [CrossRef]
    [Google Scholar]
  20. Kim K. K., Lee K. C., Lee J. S..( 2011;). Halogranum salarium sp. nov., a halophilic archaeon isolated from sea salt. . Syst Appl Microbiol 34: 576–580. [CrossRef] [PubMed]
    [Google Scholar]
  21. Koh H. W., Song H. S., Song U., Yim K. J., Roh S. W., Park S. J..( 2015;). Halolamina sediminis sp. nov., an extremely halophilic archaeon isolated from solar salt. . Int J Syst Evol Microbiol 65: 2479–2484. [CrossRef] [PubMed]
    [Google Scholar]
  22. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar B. A., Lai T., Steppi S. et al.( 2004;). arb: a software environment for sequence data. . Nucleic Acids Res 32: 1363–1371. [CrossRef] [PubMed]
    [Google Scholar]
  23. Makhdoumi-Kakhki A., Amoozegar M. A., Bagheri M., Ramezani M., Ventosa A..( 2012;). Haloarchaeobius iranensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from a saline lake. . Int J Syst Evol Microbiol 62: 1021–1026. [CrossRef] [PubMed]
    [Google Scholar]
  24. Minegishi H., Kamekura M., Itoh T., Echigo A., Usami R., Hashimoto T..( 2010;). Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B′ (rpoB′) gene. . Int J Syst Evol Microbiol 60: 2398–2408. [CrossRef] [PubMed]
    [Google Scholar]
  25. Mori K., Yamamoto H., Kamagata Y., Hatsu M., Takamizawa K..( 2000;). Methanocalculus pumilus sp. nov., a heavy-metal-tolerant methanogen isolated from a waste-disposal site. . Int J Syst Evol Microbiol 50: 1723–1729. [CrossRef] [PubMed]
    [Google Scholar]
  26. Mori K., Kim H., Kakegawa T., Hanada S..( 2003;). A novel lineage of sulfate-reducing microorganisms: Thermodesulfobiaceae fam. nov., Thermodesulfobium narugense, gen. nov., sp. nov., a new thermophilic isolate from a hot spring. . Extremophiles 7: 283–290. [CrossRef] [PubMed]
    [Google Scholar]
  27. Mori K., Maruyama A., Urabe T., Suzuki K., Hanada S..( 2008a;). Archaeoglobus infectus sp. nov., a novel thermophilic, chemolithoheterotrophic archaeon isolated from a deep-sea rock collected at Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean. . Int J Syst Evol Microbiol 58: 810–816. [CrossRef] [PubMed]
    [Google Scholar]
  28. Mori K., Sunamura M., Yanagawa K., Ishibashi J., Miyoshi Y., Iino T., Suzuki K., Urabe T..( 2008b;). First cultivation and ecological investigation of a bacterium affiliated with the candidate phylum OP5 from hot springs. . Appl Environ Microbiol 74: 6223–6229. [CrossRef] [PubMed]
    [Google Scholar]
  29. Mori K., Nurcahyanto D. A., Kawasaki H., Lisdiyanti P., Yopi Y., Suzuki K. I..( 2015;). Haloarchaeobius baliensis sp. nov., isolated from a solar saltern. . Int J Syst Evol Microbiol 66: 38–43. [CrossRef] [PubMed]
    [Google Scholar]
  30. Mou Y. Z., Qiu X. X., Zhao M. L., Cui H. L., Oh D., Dyall-Smith M. L..( 2012;). Halohasta litorea gen. nov. sp. nov., and Halohasta litchfieldiae sp. nov., isolated from the Daliang aquaculture farm, China and from Deep Lake, Antarctica, respectively. . Extremophiles 16: 895–901. [CrossRef] [PubMed]
    [Google Scholar]
  31. Nakagawa Y., Yamasato K..( 1993;). Phylogenetic diversity of the genus Cytophaga revealed by 16S rRNA sequencing and menaquinone analysis. . J Gen Microbiol 139: 1155–1161. [CrossRef] [PubMed]
    [Google Scholar]
  32. Oren A..( 2012;). Taxonomy of the family Halobacteriaceae: a paradigm for changing concepts in prokaryote systematics. . Int J Syst Evol Microbiol 62: 263–271. [CrossRef] [PubMed]
    [Google Scholar]
  33. Oren A..( 2014;). The family Halobacteriaceae. . In The Prokaryotes, pp. 41–121. Edited by Rosenberg E., DeLong E., Lory S., Stackebrandt E., Thompson F.. Berlin Heidelberg:: Springer;.
    [Google Scholar]
  34. Oren A., Gurevich P., Gemmell R. T., Teske A..( 1995;). Halobaculum gomorrense gen. nov., sp. nov., a novel extremely halophilic archaeon from the Dead Sea. . Int J Syst Bacteriol 45: 747–754. [CrossRef] [PubMed]
    [Google Scholar]
  35. Ronquist F., Huelsenbeck J. P..( 2003;). MrBayes 3: Bayesian phylogenetic inference under mixed models. . Bioinformatics 19: 1572–1574. [CrossRef] [PubMed]
    [Google Scholar]
  36. Saitou N., Nei M..( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4: 406–425.[PubMed]
    [Google Scholar]
  37. Shimoshige H., Yamada T., Minegishi H., Echigo A., Shimane Y., Kamekura M., Itoh T., Usami R..( 2013;). Halobaculum magnesiiphilum sp. nov., a magnesium-dependent haloarchaeon isolated from commercial salt. . Int J Syst Evol Microbiol 63: 861–866. [CrossRef] [PubMed]
    [Google Scholar]
  38. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G..( 1997;). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. . Nucleic Acids Res 25: 4876–4882. [CrossRef] [PubMed]
    [Google Scholar]
  39. Viver T., Cifuentes A., Díaz S., Rodríguez-Valdecantos G., González B., Antón J., Rosselló-Móra R..( 2015;). Diversity of extremely halophilic cultivable prokaryotes in Mediterranean, Atlantic and Pacific solar salterns: evidence that unexplored sites constitute sources of cultivable novelty. . Syst Appl Microbiol 38: 266–275. [CrossRef] [PubMed]
    [Google Scholar]
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