1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 7

sp. nov., a marine bacterium isolated from salt flat sediment Free

Abstract

A Gram-stain-negative, aerobic, pale yellow-coloured, rod-shaped marine bacterium designated strain YJ-S2-02 was isolated from salt flat sediment sampled in Yongyu-do, Republic of Korea. Strain YJ-S2-02 grew at pH 6.0–9.0 (optimum, pH 7.0), 10–40 °C (optimum, 30 °C) and with optimum 1 % (w/v) NaCl. The 16S rRNA gene sequence analysis indicated that strain YJ-S2-02 was closely related to NBRC 102051 (97.8 %) followed by SM117 (97.5 %), H25 (97.3 %), US6-1 (96.8 %), STM-14 (96.6 %), EGI60015 (96.5 %), D39 (96.5 %) and MUSC 273 (95.9 %). The average nucleotide identity and estimated DNA–DNA hybridization values between YJ-S2-02 and related type strains were 77.0–77.9 % and 19.1–24.0 %. Strain YJ-S2-02 was characterized as having Q-10 as the predominant respiratory quinone and the principal fatty acids (>10 %) were summed feature 8 (C cω7, 20.7 %), C 6 (16.3 %) and C 6 (11.8 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingolipids and two unidentified lipids. The DNA G+C content of strain YJ-S2-02 was 65.6 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, YJ-S2-02 should be classified as representing a novel species within the genus , for which name is proposed, with the type strain YJ-S2-02 (=KACC 21677 =KCTC 72891=JCM 33996).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): marine bacteria , Novosphingobium , salt flat and Sphingomonadaceae
Funding
This study was supported by the:
  • korea university grant
    • Principle Award Recipient: YeonjaeYoo
  • ministry of oceans and fisheries (Award 20170318 and 20170325)
    • Principle Award Recipient: YeonjaeYoo
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004930
2021-07-30
2024-09-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/71/7/ijsem004930.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004930&mimeType=html&fmt=ahah

References

  1. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb, nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 1990; 34:99–119 [View Article] [PubMed]
     [Google Scholar]
  2. Takeuchi M, Hamana K, Hiraishi A. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 2001; 51:1405–1417 [View Article] [PubMed]
     [Google Scholar]
  3. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold L-M et al. Analysis of 1000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria. Front Microbiol 2020; 11:468 [PubMed]
     [Google Scholar]
  4. Kumar R, Kumari S, Anil Kumar P, Lal R. Novosphingobium. In Bergey's Manual of Systematics of Archaea and Bacteria 2015 pp 1–24
     [Google Scholar]
  5. Lee L-H, Azman A-S, Zainal N, Eng S-K, Fang C-M et al. Novosphingobium malaysiense sp. nov. isolated from mangrove sediment. Int J Syst Evol Microbiol 2014; 64:1194–1201 [PubMed]
     [Google Scholar]
  6. Kämpfer P, Young C-C, Busse H-J, Lin S-Y, Rekha P et al. Novosphingobium soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011; 61:259–263 [PubMed]
     [Google Scholar]
  7. Hyeon JW, Kim K, Son AR, Choi E, Lee SK et al. Novosphingobium humi sp. nov., isolated from soil of a military shooting range. Int J Syst Evol Microbiol 2017; 67:3083–3088 [View Article] [PubMed]
     [Google Scholar]
  8. Li H-F, Zou Z-T, Li B-Z, Wang X, Yang J-S et al. Novosphingobium sediminis sp. nov., isolated from the sediment of a eutrophic lake. J Gen Appl Microbiol 2012; 58:357–362 [PubMed]
     [Google Scholar]
  9. Huo Y-Y, You H, Li ZY, Wang C-S, Xu XW. Novosphingobium marinum sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2015; 65:676–680 [PubMed]
     [Google Scholar]
  10. Baek S-H, Lim JH, Jin L, Lee H-G, Lee S-T. Novosphingobium sediminicola sp. nov. isolated from freshwater sediment. Int J Syst Evol Microbiol 2011; 61:2464–2468 [PubMed]
     [Google Scholar]
  11. Ngo HTT, Trinh H, Kim J-H, Yang J-E, Won K-H et al. Novosphingobium lotistagni sp. nov., isolated from a lotus pond. Int J Syst Evol Microbiol 2016; 66:4729–4734 [View Article] [PubMed]
     [Google Scholar]
  12. Tiirola MA, Busse H-J, Kämpfer P, Männistö MK. Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process. Int J Syst Evol Microbiol 2005; 55:583–588 [PubMed]
     [Google Scholar]
  13. Liu Z-P, Wang B-J, Liu Y-H, Liu SJ. Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China. Int J Syst Evol Microbiol 2005; 55:1229–1232 [PubMed]
     [Google Scholar]
  14. Suzuki S, Hiraishi A. Novosphingobium naphthalenivorans sp. nov., a naphthalene-degrading bacterium isolated from polychlorinated-dioxin-contaminated environments. J Gen Appl Microbiol 2007; 53:221–228 [View Article] [PubMed]
     [Google Scholar]
  15. Gupta SK, Lal D, Lal R. Novosphingobium panipatense sp. nov. and Novosphingobium mathurense sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 2009; 59:156–161 [View Article] [PubMed]
     [Google Scholar]
  16. Niharika N, Moskalikova H, Kaur J, Sedlackova M, Hampl A et al. Novosphingobium barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 2013; 63:667–672 [View Article] [PubMed]
     [Google Scholar]
  17. Gao S, Zhang Y, Jiang N, Luo L, Li QX et al. Novosphingobium fluoreni sp. nov., isolated from rice seeds. Int J Syst Evol Microbiol 2015; 65:1409–1414 [View Article] [PubMed]
     [Google Scholar]
  18. Takizawa M, Colwell RR, Hill RT. Isolation and diversity of actinomycetes in the Chesapeake Bay. Appl Environ Microbiol 1993; 59:997–1002 [View Article] [PubMed]
     [Google Scholar]
  19. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [PubMed]
     [Google Scholar]
  20. 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]
  21. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  22. 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 [PubMed]
     [Google Scholar]
  23. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC bioinformatics 2013; 14:60 [PubMed]
     [Google Scholar]
  24. Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [PubMed]
     [Google Scholar]
  25. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:1–10
     [Google Scholar]
  26. Yoo Y, Lee DW, Lee H, Kwon B-O, Khim JS et al. Gemmobacter lutimaris sp. nov., a marine bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2019; 69:1676–1681 [View Article] [PubMed]
     [Google Scholar]
  27. Yoo Y, Lee H, Kwon B-O, Khim JS, Baek S et al. Marinobacter halodurans sp. nov., a halophilic bacterium isolated from sediment of a salt flat. Int J Syst Evol Microbiol 2020; 70:6294–6300 [View Article] [PubMed]
     [Google Scholar]
  28. Li Y-Q, Li L, Chen W, Duan Y-Q, Nimaichand S et al. Novosphingobium endophyticum sp. nov. isolated from roots of Glycyrrhiza uralensis. Arch Microbiol 2015; 197:911–918 [View Article] [PubMed]
     [Google Scholar]
  29. Chaudhary DK, Kim J. Novosphingobium naphthae sp. nov., from oil-contaminated soil. Int J Syst Evol Microbiol 2016; 66:3170–3176 [View Article] [PubMed]
     [Google Scholar]
  30. Sheu SY, Liu LP, Young CC, Chen WM. Novosphingobium fontis sp. nov., isolated from a spring. Int J Syst Evol Microbiol 2017; 67:2423–2429 [View Article] [PubMed]
     [Google Scholar]
  31. Yuan J, Lai Q, Zheng T, Shao Z. Novosphingobium indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment. Int J Syst Evol Microbiol 2009; 59:2084–2088 [View Article] [PubMed]
     [Google Scholar]
  32. Sohn JH, Kwon KK, Kang JH, Jung HB, Kim SJ. Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int J Syst Evol Microbiol 2004; 54:1483–1487 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004930
Loading
Novosphingobium aureum sp. nov., a marine bacterium isolated from salt flat sediment
Int J Syst Evol Microbiol 71, 004930 (2021); https://doi.org/10.1099/ijsem.0.004930
/content/journal/ijsem/10.1099/ijsem.0.004930
/content/journal/ijsem/10.1099/ijsem.0.004930
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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