1887

Abstract

A taxonomic study was carried out on strain CIC4N-9, which was isolated from deep-sea water of the Indian Ocean. The bacterium was Gram-stain-negative, catalase- and oxidase-positive, rod-shaped and non-motile. Growth was observed at salinities of 0–9% and at temperatures of 4–41 °C. The isolate was able to degrade gelatin but not aesculin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CIC4N-9 belonged to the genus Pararhodobacter , with the highest sequence similarity to the only recognized species, Pararhodobacter aggregans D1-19 (96.9 %). The average nucleotide identity and estimated DNA–DNA hybridization values between strain CIC4N-9 and P. aggregans D1-19 were 80.4 and 23.0 %, respectively. The principal fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0, C18 : 1ω7c 11-methyl, C18 : 0 and C17 : 0. The G+C content of the chromosomal DNA was 66.8 mol%. The sole respiratory quinone was determined to be Q-10. Phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, two unknown phospholipids, four unknown aminolipids and one unknown polar lipid were present. The combined genotypic and phenotypic data show that strain CIC4N-9 represents a novel species within the genus Pararhodobacter , for which the name Pararhodobacter marinus sp. nov. is proposed. The type strain is CIC4N-9 (=MCCC 1A01225=KCTC 52336).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003219
2019-01-04
2019-10-23
Loading full text...

Full text loading...

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 [CrossRef][PubMed]
    [Google Scholar]
  2. Lai Q, Yuan J, Gu L, Shao Z. Marispirillum indicum gen. nov., sp. nov., isolated from a deep-sea environment. Int J Syst Evol Microbiol 2009;59:1278–1281 [CrossRef][PubMed]
    [Google Scholar]
  3. 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]
  4. 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 [CrossRef][PubMed]
    [Google Scholar]
  5. 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 [CrossRef][PubMed]
    [Google Scholar]
  6. 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 [CrossRef][PubMed]
    [Google Scholar]
  7. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28:2731–2739 [CrossRef][PubMed]
    [Google Scholar]
  8. 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]
  9. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  10. 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 [CrossRef][PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. 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 [CrossRef][PubMed]
    [Google Scholar]
  14. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef][PubMed]
    [Google Scholar]
  15. 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 [CrossRef][PubMed]
    [Google Scholar]
  16. 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 [CrossRef][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 [CrossRef][PubMed]
    [Google Scholar]
  18. 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 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  24. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:199–202 [CrossRef]
    [Google Scholar]
  25. Kates M. Lipid extraction procedures. Techniques of Lipidology Amsterdam: Elsevier; 1986; pp.100–111
    [Google Scholar]
  26. Lv XL, Xie BS, Cai M, Tang YQ, Wang YN et al. Halodurantibacterium flavum gen. nov., sp. nov., a non-phototrophic bacterium isolated from an oil production mixture. Curr Microbiol 2015;70:141–148 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003219
Loading
/content/journal/ijsem/10.1099/ijsem.0.003219
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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