1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 10

sp. nov., a bacterium isolated from marine sediment in the East China Sea and emended description of the genus Free

Abstract

A Gram-negative, rod-shaped, non-motile and strictly aerobic bacterium, designated ZQ420, was isolated from marine sediment sampled on Zhoushan Island located in the East China Sea. Strain ZQ420 was able to grow at 10–45 °C, 0–12.0 % (w/v) NaCl and pH 5.5–9.0. Catalase and oxidase activities, nitrate reduction, HS production, hydrolysis of starch, casein, Tween 20, 40 and 80 were positive. Indole, methyl red, Voges–Proskauer test, hydrolysis of gelatin and Tween 60 were negative. The major cellular fatty acids were C 7, C and 11-methyl Cω7. Ubiquinone-10 (Q-10) was the only detected respiratory quinone. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids, three unidentified glycolipids, two unidentified aminolipid and two unidentified lipids. The DNA G+C content was 64.8 mol%. According to 16S rRNA gene sequence similarities, strain ZQ420 shared 97.9, 96.3 and 96.3 % similarities to the following species with validated names D1-19, PAMC27389 and 4-T-34, respectively. While sharing lower sequence similarities (<96.0 %) to other type species. Phylogenetic analyses showed that strain ZQ420 and D1-19 formed an independent cluster in the phylogenetic trees. The average nucleotide identity value between strain ZQ420 and D1-19 was 79.1 %. The DNA–DNA hybridization analysis revealed that strain ZQ420 shared 21.5 % DNA relatedness with D1-19. On the basis of its phenotypic, chemotaxonomic and genotypic characteristics, strain ZQ420 is considered to represent a novel species in the genus , for which the name sp. nov. is proposed. The type strain is ZQ420 (=KCTC 62579=MCCC 1K03530).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): marine sediment , Pararhodobacter marinus and taxonomy
© 2019 IUMS

Erratum

An erratum has been published for this content:
Erratum: sp. nov., a bacterium isolated from marine sediment in the East China Sea and emended description of the genus
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003627
2019-10-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/10/3293.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003627&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. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology, 1st ed. Beijing: Scientific Press; 2001 pp. 353–364
     [Google Scholar]
  3. Zhu XF. Modern experimental technique of microbiology Zhejiang University Press, Hangzhou English translation; 2011
     [Google Scholar]
  4. 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 [View Article]
     [Google Scholar]
  5. Kates M, Lipidology T. Isolation, Analysis and Identification of Lipids, 2nd ed. Amsterdam: Elsevier; 1986
     [Google Scholar]
  6. Zhang XQ, Sun C, Wang CS, Zhang X, Zhou X et al. Sinimarinibacterium flocculans gen. nov., sp. nov., a gammaproteobacterium from offshore surface seawater. Int J Syst Evol Microbiol 2015; 65:3541–3546 [View Article][PubMed]
     [Google Scholar]
  7. Sun C, Wu C, Su Y, Wang RJ, Fu GY et al. Hyphococcus flavus gen. nov., sp. nov., a novel alphaproteobacterium isolated from deep seawater. Int J Syst Evol Microbiol 2017; 67:4024–4031 [View Article][PubMed]
     [Google Scholar]
  8. 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]
  9. 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]
  10. 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]
  11. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  13. 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 [View Article][PubMed]
     [Google Scholar]
  14. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
     [Google Scholar]
  15. 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 [View Article][PubMed]
     [Google Scholar]
  16. 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]
  17. 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]
  18. 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]
  19. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003627
Loading
Pararhodobacter marinus sp. nov., a bacterium isolated from marine sediment in the East China Sea and emended description of the genus Pararhodobacter
Int J Syst Evol Microbiol 69, 3293 (2019); https://doi.org/10.1099/ijsem.0.003627
/content/journal/ijsem/10.1099/ijsem.0.003627
/content/journal/ijsem/10.1099/ijsem.0.003627
Loading

Data & Media loading...

Supplements

Supplementary File 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