1887

Abstract

A Gram-stain-positive, strictly aerobic, motile and rod-shaped bacterium, designated strain LJ137, was isolated from the sediment of Taihu Lake in China. A polyphasic approach was used to investigate its taxonomic position. Strain LJ137 grew optimally at pH 7.5, at 37 °C and with 2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LJ137 was most closely related to the genera Ornithinibacillus and Oceanobacillus. The closest phylogenetic neighbours were Ornithinibacillus halophilus KCTC 13822, Ornithinibacillus salinisoli LCB256 and Oceanobacillus limi KCTC 13823, with 95.2, 96.5 and 95.6 % 16S rRNA gene sequence similarity, respectively. The peptidoglycan amino acid type was A4α (l-Lys–d-Asp). The major respiratory quinone was menaquinone-7 (MK-7). The polar lipids of strain LJ137 contained diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, two aminophospholipids and one unidentified lipid. The G+C content of the genomic DNA was 40.4 mol%. The dominant cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. Based on the phenotypic, chemotaxonomic, phylogenetic and genome sequence characteristics of this strain, a novel species, Ornithinibacillus gellani sp. nov., is proposed. The type strain is LJ137 (=CGMCC 1.13678=NBRC 113552). An emended description of the genus Ornithinibacillus is presented.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003500
2019-06-11
2019-08-19
Loading full text...

Full text loading...

References

  1. Mayr R, Busse HJ, Worliczek HL, Ehling-Schulz M, Scherer S. Ornithinibacillus gen. nov., with the species Ornithinibacillus bavariensis sp. nov. and Ornithinibacillus californiensis sp. nov. Int J Syst Evol Microbiol 2006;56: 1383– 1389 [CrossRef] [PubMed]
    [Google Scholar]
  2. Kämpfer P, Falsen E, Lodders N, Langer S, Busse HJ et al. Ornithinibacillus contaminans sp. nov., an endospore-forming species. Int J Syst Evol Microbiol 2010;60: 2930– 2934 [CrossRef] [PubMed]
    [Google Scholar]
  3. Shin NR, Whon TW, Kim MS, Roh SW, Jung MJ et al. Ornithinibacillus scapharcae sp. nov., isolated from a dead ark clam. Antonie van Leeuwenhoek 2012;101: 147– 154 [CrossRef] [PubMed]
    [Google Scholar]
  4. Bagheri M, Amoozegar MA, Schumann P, Didari M, Mehrshad M et al. Ornithinibacillus halophilus sp. nov., a moderately halophilic, gram-stain-positive, endospore-forming bacterium from a hypersaline lake. Int J Syst Evol Microbiol 2013;63: 844– 848 [CrossRef] [PubMed]
    [Google Scholar]
  5. Wu C, Chang M, Yang G, Zhou S, Zhuang L. Ornithinibacillus heyuanensis sp. nov., isolated from South China. Antonie van Leeuwenhoek 2014;106: 235– 241 [CrossRef] [PubMed]
    [Google Scholar]
  6. Lu Q, Yang G, Ma C, Qin D, Li D et al. Ornithinibacillus halotolerans sp. nov., isolated from a saline soil. Int J Syst Evol Microbiol 2014;64: 1685– 1689 [CrossRef] [PubMed]
    [Google Scholar]
  7. Lu Q, Yuan H, Li J, Zhao Y, Zhou S. Ornithinibacillus composti sp. nov., isolated from sludge compost and emended description of the genus Ornithinibacillus. Antonie van Leeuwenhoek 2015;107: 813– 819 [CrossRef] [PubMed]
    [Google Scholar]
  8. Gan L, Zhang H, Long X, Tian J, Wang Z et al. Ornithinibacillus salinisoli sp. nov., a moderately halophilic bacterium isolated from a saline-alkali soil. Int J Syst Evol Microbiol 2018;68: 769– 775 [CrossRef] [PubMed]
    [Google Scholar]
  9. Schaeffer AB, Fulton MD. A simplified method of staining endospores. Science 1933;77: 194 [CrossRef] [PubMed]
    [Google Scholar]
  10. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
    [Google Scholar]
  11. Ventosa A, Quesada E, Rodriguez-Valera F, Ruiz-Berraquero F, Ramos-Cormenzana A. Numerical taxonomy of moderately halophilic gram-negative Rods. Microbiology 1982;128: 1959– 1968 [CrossRef]
    [Google Scholar]
  12. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966;45: 493– 496 [CrossRef] [PubMed]
    [Google Scholar]
  13. Moreno C, Romero J, Espejo RT. Polymorphism in repeated 16S rRNA genes is a common property of type strains and environmental isolates of the genus Vibrio. Microbiology 2002;148: 1233– 1239 [CrossRef] [PubMed]
    [Google Scholar]
  14. 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]
  15. 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]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4: 406– 425 [CrossRef] [PubMed]
    [Google Scholar]
  17. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992;9: 945– 967
    [Google Scholar]
  18. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993;10: 512– 526 [CrossRef] [PubMed]
    [Google Scholar]
  19. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for Bigger Datasets. Mol Biol Evol 2016;33: 1870– 1874 [CrossRef] [PubMed]
    [Google Scholar]
  20. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16: 111– 120 [CrossRef] [PubMed]
    [Google Scholar]
  21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  22. Pospiech A, Neumann B. A versatile quick-prep of genomic DNA from gram-positive bacteria. Trends Genet 1995;11: 217– 218 [CrossRef] [PubMed]
    [Google Scholar]
  23. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014;30: 2114– 2120 [CrossRef] [PubMed]
    [Google Scholar]
  24. 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]
  25. Massouras A, Hens K, Gubelmann C, Uplekar S, Decouttere F et al. Primer-initiated sequence synthesis to detect and assemble structural variants. Nat Methods 2010;7: 485– 486 [CrossRef] [PubMed]
    [Google Scholar]
  26. Stoesser G, Baker W, van den Broek AE, Camon E, Hingamp P et al. The EMBL nucleotide sequence database. nucleic acids res 2000;28:19-23. Updated article in this issue. Nucleic Acids Res 2001;29: 17– 21
    [Google Scholar]
  27. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983;29: 319– 322 [CrossRef]
    [Google Scholar]
  28. Schleifer KH. Analysis of the chemical composition and primary structure of murein. Method Microbiol 1985;18: 123– 156
    [Google Scholar]
  29. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972;36: 407– 477 [PubMed]
    [Google Scholar]
  30. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Method Microbiol 1987;19: 161– 207
    [Google Scholar]
  31. Tsubouchi T, Shimane Y, Usui K, Shimamura S, Mori K et al. Brevundimonas abyssalis sp. nov., a dimorphic prosthecate bacterium isolated from deep-subsea floor sediment. Int J Syst Evol Microbiol 2013;63: 1987– 1994 [CrossRef] [PubMed]
    [Google Scholar]
  32. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984;2: 233– 241 [CrossRef]
    [Google Scholar]
  33. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc 1990
    [Google Scholar]
  34. Bagheri M, Amoozegar MA, Schumann P, Didari M, Mehrshad M et al. Ornithinibacillus halophilus sp. nov., a moderately halophilic, Gram-stain-positive, endospore-forming bacterium from a hypersaline lake. Int J Syst Evol Microbiol 2013;63: 844– 848 [CrossRef] [PubMed]
    [Google Scholar]
  35. Amoozegar MA, Bagheri M, Didari M, Mehrshad M, Schumann P et al. Aquibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Virgibacillus koreensis as Aquibacillus koreensis comb. nov. and Virgibacillus albus as Aquibacillus albus comb. nov. Int J Syst Evol Microbiol 2014;64: 3616– 3623 [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003500
Loading
/content/journal/ijsem/10.1099/ijsem.0.003500
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