1887

Abstract

A mannan-degrading halophilic archaeal strain, MD130-1, was isolated from a commercial salt sample. Cells were motile, rod-shaped, and stained Gram-negative. Colonies were pink pigmented. Strain MD130-1 was able to grow at 1.5–4.6 M NaCl (optimum, 3.6 M) at pH 6.0–8.0 (optimum, pH 7.0) and at 25–50 °C (optimum, 40 °C). The DNA G+C content was 62.1 mol% (genome). The orthologous 16S rRNA gene sequence showed the highest similarity (99.4 %) to those of JCM 7785 and JCM 8911. The values of genome relatedness between strain MD130-1 and species were 84.33–85.96 % in ANIb and 30.4–32.9 % using GGDC formula 2. The polar lipids of strain MD130-1 were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and triglycosyl diether-2. Based on the results of phenotypic and phylogenetic analyses, the strain represents a new species of the genus , for which the name sp. nov. is proposed. The type strain is MD130-1 (=JCM 33835=KCTC 4287) isolated from commercial salt made in Ishikawa prefecture, Japan.

Funding
This study was supported by the:
  • The Salt Science Research Foundation (Award No. 1445)
    • Principle Award Recipient: Hiroaki Minegishi
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004535
2020-10-23
2024-12-02
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/12/6331.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004535&mimeType=html&fmt=ahah

References

  1. Gupta RS, Naushad S, Fabros R, Adeolu M. 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 2016; 109:565–587 [View Article][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 [View Article]
    [Google Scholar]
  3. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
    [Google Scholar]
  4. Ventosa A, de la Haba RR, Sánchez-Porro C. Haloarcula. Bergey’s Manual of Systematics of Archaea and Bacteria JohnWiley & Sons, Ltd; 2015
    [Google Scholar]
  5. Barreteau H, Vandervennet M, Guédon L, Point V, Canaan S et al. Haloarcula sebkhae sp. nov., an extremely halophilic archaeon from Algerian hypersaline environment. Int J Syst Evol Microbiol 2019; 69:732–738 [View Article][PubMed]
    [Google Scholar]
  6. Oren A, Arahal DR, Ventosa A. Emended descriptions of genera of the family Halobacteriaceae . Int J Syst Evol Microbiol 2009; 59:637–642 [View Article][PubMed]
    [Google Scholar]
  7. Mylvaganam S, Dennis PP. Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui . Genetics 1992; 130:399–410[PubMed]
    [Google Scholar]
  8. Dennis PP, Ziesche S, Mylvaganam S. Transcription analysis of two disparate rRNA operons in the halophilic archaeon Haloarcula marismortui . J Bacteriol 1998; 180:4804–4813 [View Article][PubMed]
    [Google Scholar]
  9. Cui HL, Zhou PJ, Oren A, Liu SJ. Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium . Extremophiles 2009; 13:31–37 [View Article][PubMed]
    [Google Scholar]
  10. Minegishi H, Kamekura M, Kitajima-Ihara T, Nakasone K, Echigo A et al. Gene orders in the upstream of 16S rRNA genes divide genera of the family Halobacteriaceae into two groups. Int J Syst Evol Microbiol 2012; 62:188–195 [View Article][PubMed]
    [Google Scholar]
  11. Oren A, Ventosa A, Grant WD. Proposed minimal standards for description of new taxa in the order Halobacteriales. Int J Syst Bacteriol 1997; 47:233–238 [View Article]
    [Google Scholar]
  12. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. clustal W and clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article][PubMed]
    [Google Scholar]
  13. 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]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  15. Silvestro D, Michalak I. raxmlGUI: a graphical front-end for RAxML. Org Divers Evol 2012; 12:335–337 [View Article]
    [Google Scholar]
  16. Stamatakis A, Ludwig T, Meier H. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 2005; 21:456–463 [View Article][PubMed]
    [Google Scholar]
  17. 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]
  18. 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]
  19. Minegishi H, Kamekura M, Itoh T, Echigo A, Usami R et al. Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene. Int J Syst Evol Microbiol 2010; 60:2398–2408 [View Article][PubMed]
    [Google Scholar]
  20. Cline SW, Schalkwyk LC, Doolittle WF. Transformation of the archaebacterium Halobacterium volcanii with genomic DNA. J Bacteriol 1989; 171:4987–4991 [View Article][PubMed]
    [Google Scholar]
  21. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article][PubMed]
    [Google Scholar]
  22. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  23. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018; 34:1037–1039 [View Article][PubMed]
    [Google Scholar]
  24. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
    [Google Scholar]
  25. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  26. Minegishi H, Echigo A, Nagaoka S, Kamekura M, Usami R et al. Halarchaeum acidiphilum gen. nov., sp. nov., a moderately acidophilic haloarchaeon isolated from commercial solar salt. Int J Syst Evol Microbiol 2010; 60:2513–2516 [View Article][PubMed]
    [Google Scholar]
  27. Dussault HP. An improved technique for staining red halophilic bacteria. J Bacteriol 1955; 70:484–485 [View Article][PubMed]
    [Google Scholar]
  28. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article][PubMed]
    [Google Scholar]
  29. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  30. Kamekura M. Lipids of extreme halophiles. In Vreeland RH, Hochstein LI. (editors) The Biology of Halophilic Bacteria Boca Raton, FL: CRC Press; 1993 pp 135–161
    [Google Scholar]
  31. Ryu EK, MacCoss M. Modification of the Dittmer-Lester reagent for the detection of phospholipid derivatives on thin-layer chromatograms. J Lipid Res 1979; 20:561–563[PubMed]
    [Google Scholar]
  32. Echigo A, Minegishi H, Shimane Y, Kamekura M, Itoh T et al. Halomicroarcula pellucida gen. nov., sp. nov., a non-pigmented, transparent-colony-forming, halophilic archaeon isolated from solar salt. Int J Syst Evol Microbiol 2013; 63:3556–3562 [View Article][PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004535
Loading
/content/journal/ijsem/10.1099/ijsem.0.004535
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error