1887

Abstract

A halophilic archaeon, strain H22, was isolated from a subterranean salt deposit sampled at Yunnan salt mine, PR China. Colonies of strain H22 were light pink-pigmented. Cells were coccus, non-motile, Gram-stain-negative, and did not lyse in distilled water. The strain was aerobic and grew at 20–55 °C (optimum, 37 °C), in the presence of 10–30 % (w/v) NaCl (20 %) and at pH 6.5–9.0 (pH 7.0). Mg was required for growth (optimum, 0.005 M). Major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and sulfated mannosyl-glucosyl-glycerol diether-1. Sequence similarity search based on the multiple 16S rRNA genes (rrnA, rrnB and rrnC) of strain H22 revealed that it was most closely related to species of the genera Haloarchaeobius , Haladaptatus , Halorussus and Halorubellus with relative low sequence similarities (91.9–93.7 %). The strain, however, shared highest rpoB′ gene sequence identities with Halorussus rarus TBN4 (90.8 % rpoB′ gene sequence similarity). Phylogenetic trees based on 16S rRNA and rpoB′ gene sequences revealed a robust lineage of the strain H22 with members of related genera of the family Halobacteriaceae . The DNA G+C content of strain H22 was 62.9 mol%. Genome-based analysis of average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) between strains H22 and its closest relative were equal or lower than 77.7 and 22.4 %, respectively, which were far below the threshold for delineation of a new species. Based on ANI values, in silico DDH, and distinct morphological and physiological differences from the previously described taxa, we suggest that strain H22 represents a novel species of a new genus within the family Halobacteriaceae , for which the name Halomicrococcus hydrotolerans gen. nov., sp. nov. is proposed. The type strain is H22 (=CGMCC 1.16291=NBRC 113231).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003534
2019-06-17
2019-08-22
Loading full text...

Full text loading...

References

  1. Andrei , Banciu HL, Oren A. Living with salt: metabolic and phylogenetic diversity of archaea inhabiting saline ecosystems. FEMS Microbiol Lett 2012;330: 1– 9 [CrossRef] [PubMed]
    [Google Scholar]
  2. Schubert BA, Lowenstein TK, Timofeeff MN, Parker MA. Halophilic Archaea cultured from ancient halite, Death Valley, California. Environ Microbiol 2010;12: 440– 454 [CrossRef] [PubMed]
    [Google Scholar]
  3. Xiao W, Wang ZG, Wang YX, Schneegurt MA, Li ZY et al. Comparative molecular analysis of the prokaryotic diversity of two salt mine soils in southwest China. J Basic Microbiol 2013;53: 942– 952 [CrossRef] [PubMed]
    [Google Scholar]
  4. Chen S, Liu HC, Zhou J, Xiang H. Haloparvum sedimenti gen. nov., sp. nov., a member of the family Haloferacaceae. Int J Syst Evol Microbiol 2016;66: 2327– 2334 [CrossRef] [PubMed]
    [Google Scholar]
  5. 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 [CrossRef]
    [Google Scholar]
  6. Dussault HP. An improved technique for staining red halophilic bacteria. J Bacteriol 1955;70: 484– 485 [PubMed]
    [Google Scholar]
  7. Hartmann R, Sickinger HD, Oesterhelt D. Anaerobic growth of halobacteria. Proc Natl Acad Sci USA 1980;77: 3821– 3825 [CrossRef] [PubMed]
    [Google Scholar]
  8. Cui HL, Lin ZY, Dong Y, Zhou PJ, Liu SJ et al. Halorubrum litoreum sp. nov., an extremely halophilic archaeon from a solar saltern. Int J Syst Evol Microbiol 2007;57: 2204– 2206 [CrossRef] [PubMed]
    [Google Scholar]
  9. 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]
  10. Chen S, Liu HC, Zhou J, Xiang H. Halorubrum pallidum sp. nov., an extremely halophilic archaeon isolated from a subterranean rock salt. Int J Syst Evol Microbiol 2016;66: 2980– 2986 [CrossRef] [PubMed]
    [Google Scholar]
  11. Kharroub K, Quesada T, Ferrer R, Fuentes S, Aguilera M et al. Halorubrum ezzemoulense sp. nov., a halophilic archaeon isolated from Ezzemoul sabkha, Algeria. Int J Syst Evol Microbiol 2006;56: 1583– 1588 [CrossRef] [PubMed]
    [Google Scholar]
  12. 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 [CrossRef] [PubMed]
    [Google Scholar]
  13. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017;67: 1613– 1617 [CrossRef] [PubMed]
    [Google Scholar]
  14. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999;41: 95– 98
    [Google Scholar]
  15. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28: 2731– 2739 [CrossRef] [PubMed]
    [Google Scholar]
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  17. Cui HL, Gao X, Yang X, Xu XW. Halorussus rarus gen. nov., sp. nov., a new member of the family Halobacteriaceae isolated from a marine solar saltern. Extremophiles 2010;14: 493– 499 [CrossRef] [PubMed]
    [Google Scholar]
  18. Makhdoumi-Kakhki A, Amoozegar MA, Bagheri M, Ramezani M, Ventosa A. Haloarchaeobius iranensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from a saline lake. Int J Syst Evol Microbiol 2012;62: 1021– 1026 [CrossRef] [PubMed]
    [Google Scholar]
  19. Sun DL, Jiang X, Wu QL, Zhou NY. Intragenomic heterogeneity of 16S rRNA genes causes overestimation of prokaryotic diversity. Appl Environ Microbiol 2013;79: 5962– 5969 [CrossRef] [PubMed]
    [Google Scholar]
  20. 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]
  21. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961;3: 208– IN1 [CrossRef]
    [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 [CrossRef] [PubMed]
    [Google Scholar]
  23. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987;37: 463– 464 [CrossRef]
    [Google Scholar]
  24. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017;110: 1281– 1286 [CrossRef] [PubMed]
    [Google Scholar]
  25. 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]
  26. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010;2: 117– 134 [CrossRef] [PubMed]
    [Google Scholar]
  27. 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 [CrossRef] [PubMed]
    [Google Scholar]
  28. Kates M. Techniques of Lipidology: Isolation, Analysis, and Identification of Lipids, 3 ed. Ottawa, Canada: NewportSomerville; 2010
    [Google Scholar]
  29. Oren A, Arahal DR, Ventosa A. Emended descriptions of genera of the family Halobacteriaceae. Int J Syst Evol Microbiol 2009;59: 637– 642 [CrossRef] [PubMed]
    [Google Scholar]
  30. Cui HL, Mou YZ, Yang X, Zhou YG, Liu HC et al. Halorubellus salinus gen. nov., sp. nov. and Halorubellus litoreus sp. nov., novel halophilic archaea isolated from a marine solar saltern. Syst Appl Microbiol 2012;35: 30– 34 [CrossRef] [PubMed]
    [Google Scholar]
  31. Savage KN, Krumholz LR, Oren A, Elshahed MS. Haladaptatus paucihalophilus gen. nov., sp. nov., a halophilic archaeon isolated from a low-salt, sulfide-rich spring. Int J Syst Evol Microbiol 2007;57: 19– 24 [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003534
Loading
/content/journal/ijsem/10.1099/ijsem.0.003534
Loading

Data & Media loading...

Supplementary File 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