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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 71, Issue 1

sp. nov., isolated from deep sea water Free

Abstract

A novel Gram-stain-positive, motile, aerobic, non-spore-forming and slender rod-shaped actinobacterium, designated strain CTD02-10-2, was isolated from deep sea water of the Indian Ocean. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CTD02-10-2 was grouped into a separated branch with JCM 14730 (98.4 % nucleotide sequence identity). The respiratory quinones were menaquinones with 11, 12, 13 and 14 isoprene units and anteiso-C, iso-C, anteiso-C A and anteiso-C were the major fatty acids. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and three unknown glycolipids. The genome of strain CTD02-10-2 was 2.59 Mb, with a DNA G+C content of 69.6 mol% and contained genes involved in the biosynthesis of alkylresorcinol, ansamycin, and carotenoids. DNA–DNA hybridization and average nucleotide identity values for whole-genome sequence comparisons between strain CTD02-10-2 and JCM 14730 were clearly below the thresholds used for the delineation of a new species. Based on its morphological and chemotaxonomic characteristics, as well as genotypic data, strain CTD02-10-2 was classified as a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CTD02-10-2 (=JCM 33842=MCCC 1A16619).

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  • Accepted:
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Keyword(s): Chryseoglobus indicus sp. nov. , Indian Ocean and polyphasic taxonomy
Funding
This study was supported by the:
  • Scientific Research Foundation of the Third Institute of Oceanography, MNR (Award No. 2019011)
    • Principle Award Recipient: Gaiyun Zhang
  • China Ocean Mineral Resources R&D Association (Award DY135-B2-01)
    • Principle Award Recipient: Gaiyun Zhang
© 2021 The Authors
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2020-11-13
2025-01-24
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References

  1. Baik KS, Park SC, Kim HJ, Lee KH, Seong CN. Chryseoglobus frigidaquae gen. nov., sp. nov., a novel member of the family Microbacteriaceae . Int J Syst Evol Microbiol 2010; 60:1311–1316 [View Article][PubMed]
     [Google Scholar]
  2. Leifson E. Atlas of bacterial flagellation. Q Rev Biol 1960; 242:
     [Google Scholar]
  3. Murray PR, Baron EJ, Pfaller MA, Tenover FC, Yolken RH. Manual of Clinical Microbiology, 7th ed. Washington, DC: American Society for Microbiology; 1999
     [Google Scholar]
  4. Cerny G. Studies on the aminopeptidase test for the distinction of Gram-negative from Gram-positive bacteria. European J Appl Microbiol Biotechnol 1978; 5:113–122 [View Article]
     [Google Scholar]
  5. LH X, WJ L, Liu ZH, Jiang CL, Principles AS. Methods and Practice Beijing: Science Press; 2007
     [Google Scholar]
  6. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
     [Google Scholar]
  7. Kaiser P, Geyer R, Surmann P, Fuhrmann H. LC–MS method for screening unknown microbial carotenoids and isoprenoid quinones. J Microbiol Methods 2012; 88:28–34 [View Article][PubMed]
     [Google Scholar]
  8. Sasser M. Identification of bacteria through fatty acid analysis. In Klement Z, Rudolph K, Sands DC. (editors) Methods in Phytobacteriology Budapest: Akademiai Kaido; 1990 pp 199–204
     [Google Scholar]
  9. Schleifer K, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1973; 37:407–477 [View Article][PubMed]
     [Google Scholar]
  10. Schumann P. Peptidoglycan structure. Method Microbiol 2011; 38:101–129
     [Google Scholar]
  11. Gogichaeva NV, Alterman MA. Amino acid analysis by means of MALDI TOF mass spectrometry or MALDI TOF/TOF tandem mass spectrometry. Methods Mol Biol 2019; 2030:17–31 [View Article][PubMed]
     [Google Scholar]
  12. WJ L, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia . Int J Syst Evol Microbiolo 2007; 57:1424–1428
     [Google Scholar]
  13. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; pp 115–175
     [Google Scholar]
  14. 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]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:189–204 [View Article][PubMed]
     [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  17. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  19. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article][PubMed]
     [Google Scholar]
  20. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
     [Google Scholar]
  21. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [View Article][PubMed]
     [Google Scholar]
  22. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I, S-I N, S-m H et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article][PubMed]
     [Google Scholar]
  23. 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]
  24. 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]
  25. Shahidi F, Chandrasekara A. 17 - The use of antioxidants in the preservation of cereals and low-moisture foods. In Shahidi F. editor Handbook of Antioxidants for Food Preservation Woodhead Publishing; 2015 pp 413–432
     [Google Scholar]
  26. Wang J, Li W, Wang H, Lu C. Pentaketide ansamycin Microansamycins A-I from Micromonospora sp. reveal diverse Post-PKS modifications. Org Lett 2018; 20:1058–1061 [View Article][PubMed]
     [Google Scholar]
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Chryseoglobus indicus sp. nov., isolated from deep sea water
Int J Syst Evol Microbiol 71, 004564 (2020); https://doi.org/10.1099/ijsem.0.004564
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