1887

Abstract

A taxonomic study was carried out on strain YPA3-1-1, which was isolated from deep-sea sediment of the Pacific Ocean. The bacterium was Gram-stain-positive, oxidase-positive, catalase-negative, rod-shaped and spore-forming. Growth was observed at salinities of 1.0–6.0 % and at temperatures of 10–40 °C. The isolate could degrade gelatin and aesculin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YPA3-1-1 belonged to the genus , with the highest sequence similarity to the only typespecies, J15A17 (98.5 %). The estimated average nucleotide identity and DNA–DNA hybridization values between strain YPA3-1-1 and J15A17 were 88.1 and 35.0 %, respectively. The cell wall of strain YPA3-1-1 contained -diaminopimelic acid. The principal fatty acids (>10 %) were iso-C (35.5 %) and anteiso-C (17.5 %). The G+C content of the chromosomal DNA was 33.1 mol%. The respiratory quinone was determined to be MK-7 (100 %). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, glycolipid and three unidentified phospholipids. The combined genotypic and phenotypic data show that strain YPA3-1-1 represents a novel species within the genus , for which the name sp. nov. is proposed, with the type strain YPA3-1-1 (=MCCC 1A14042=KCTC 43019).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003530
2019-08-01
2024-11-05
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/8/2522.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003530&mimeType=html&fmt=ahah

References

  1. Foesel BU, Drake HL, Schramm A. Defluviimonas denitrificans gen. nov., sp. nov., and Pararhodobacter aggregans gen. nov., sp. nov., non-phototrophic Rhodobacteraceae from the biofilter of a marine aquaculture. Syst Appl Microbiol 2011; 34:498–502 [View Article][PubMed]
    [Google Scholar]
  2. Ausubel F, Brent R, Kingston R, Moore D, Seidman J et al. Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Biology, 3rd ed. New York: Wiley; 1995
    [Google Scholar]
  3. Liu C, Shao Z. Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. Int J Syst Evol Microbiol 2005; 55:1181–1186 [View Article][PubMed]
    [Google Scholar]
  4. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  5. Chun J, Lee JH, Jung Y, Kim M, Kim S et al. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261 [View Article][PubMed]
    [Google Scholar]
  6. 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]
  7. 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]
  8. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  9. Rzhetsky A, Nei M. Statistical properties of the ordinary least-squares, generalized least-squares, and minimum-evolution methods of phylogenetic inference. J Mol Evol 1992; 35:367–375 [View Article][PubMed]
    [Google Scholar]
  10. 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 [View Article][PubMed]
    [Google Scholar]
  11. 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]
  12. 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 [View Article][PubMed]
    [Google Scholar]
  13. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  14. 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]
  15. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article][PubMed]
    [Google Scholar]
  16. 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 [View Article][PubMed]
    [Google Scholar]
  17. 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 [View Article]
    [Google Scholar]
  18. Logan NA, Berge O, Bishop AH, Busse HJ, de Vos P et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 2009; 59:2114–2121 [View Article][PubMed]
    [Google Scholar]
  19. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd ed. Baltimore: Williams & Wilkins; 1967
    [Google Scholar]
  20. Dong X-Z, Cai M-Y. Determinative Manual for Routine Bacteriology Beijing: Scientific Press (English translation); 2001
    [Google Scholar]
  21. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: A Laboratory Manual, 2nd ed. Cold Spring Harbor: NY: Cold Spring Harbor Laboratory; 1989
    [Google Scholar]
  22. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI; 1990
    [Google Scholar]
  23. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
    [Google Scholar]
  24. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  25. Kates M. Lipid extraction procedures. Techniques of Lipidology Amsterdam: Elsevier; 1986 pp. 100–111
    [Google Scholar]
  26. Kates M. Lipid Extraction Procedures Amsterdam: Techniques of lipidology Elsevier; 1986 pp. 100–111
    [Google Scholar]
  27. Cao WR, Guo LY, du ZJ, das A, Saren G et al. Chengkuizengella sediminis gen. nov. sp. nov., isolated from sediment. Int J Syst Evol Microbiol 2017; 67:2672–2678 [View Article][PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.003530
Loading
/content/journal/ijsem/10.1099/ijsem.0.003530
Loading

Data & Media loading...

Supplements

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