Skip to content
1887

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

Volume 70, Issue 8

sp. nov., isolated from the sea surface microlayer in the Southwestern Pacific Ocean, and emended description of the genus Free

Abstract

A Gram-stain-negative, non-motile, facultatively anaerobic and rod-shaped bacterial strain, designated PAMC 28131, was isolated from a sea surface microlayer sample in the open water of the Pacific Ocean. Phylogenetic analysis of the 16S rRNA gene sequence of strain PAMC 28131 revealed an affiliation to the genus with the closest species RB16-17 (sequence similarity of 98.2 %). Strain PAMC 28131 was able to grow optimally with 0.5–1.0 % NaCl and at pH 6.5–7.0 and 30 °C. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, an unidentified aminolipid, an unidentified glycolipid and an unidentified lipid. The major cellular fatty acids (>10 %) were C ω6 and/or C ω7 (42.6 %), C ω6 (19.3 %) and C ω6 and/or C ω7 (15.8 %), and the respiratory quinone was Q-10. The genomic DNA G+C content was 65.3 mol%. The phylogenetic, phenotypic and chemotaxonomic data showed that strain PAMC 28131 could be clearly distinguished from RB16-17. Thus, strain PAMC 28131 should be classified as representing a novel species in the genus , for which the name sp. nov. is proposed. The type strain is PAMC 28131 (=KCCM 43127=JCM 30734).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): new species , Pacific Ocean , Sandaracinobacter neustonicus and sea surface microlayer
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004333
2020-07-23
2026-03-11

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/8/4698.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004333&mimeType=html&fmt=ahah

References

  1. Yurkov V, Stackebrandt E, Buss O, Vermeglio A, Gorlenko V et al. Reorganization of the genus Erythromicrobium: description of "Erythromicrobium sibiricum" as Sandaracinobacter sibiricus gen. nov., sp. nov., and of "Erythromicrobium ursincola" as Erythromonas ursincola gen. nov., sp. nov. Int J Syst Bacteriol 1997; 47:1172–1178 [View Article]
     [Google Scholar]
  2. Yurkov V, Gorlenko V. Erythrobacter sibiricus sp. nov., a new freshwater aerobic bacterial species containing bacteriochlorophyll a . Microbiology 1990; 59:85–89
     [Google Scholar]
  3. Yurkov V, Lysenko A, Gorlenko V. Hybridization analysis of the classification of bacteriochlorophyll a-containing freshwater aerobic bacteria. Microbiology 1991; 60:362–366
     [Google Scholar]
  4. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
     [Google Scholar]
  5. Aller JY, Kuznetsova MR, Jahns CJ, Kemp PF. The sea surface microlayer as a source of viral and bacterial enrichment in marine aerosols. J Aerosol Sci 2005; 36:801–812 [View Article]
     [Google Scholar]
  6. Cho BC, Hwang CY. Prokaryotic abundance and 16S rRNA gene sequences detected in marine aerosols on the East Sea (Korea). FEMS Microbiol Ecol 2011; 76:327–341 [View Article][PubMed]
     [Google Scholar]
  7. Hwang CY, Lee I, Hwang YJ, Yoon SJ, Lee WS et al. Pseudoalteromonas neustonica sp. nov., isolated from the sea surface microlayer of the Ross Sea (Antarctica), and emended description of the genus Pseudoalteromonas . Int J Syst Evol Microbiol 2016; 66:3377–3382 [View Article][PubMed]
     [Google Scholar]
  8. Tindall BJ, Rosselló-Móra R, Busse H-J, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249–266 [View Article][PubMed]
     [Google Scholar]
  9. Hwang CY, Lee I, Cho Y, Lee YM, Jung Y-J et al. Sediminicola arcticus sp. nov., a psychrophilic bacterium isolated from deep-sea sediment, and emended description of the genus Sediminicola . Int J Syst Evol Microbiol 2015; 65:1567–1571 [View Article][PubMed]
     [Google Scholar]
  10. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article][PubMed]
     [Google Scholar]
  11. Yoon S-H, Ha S-M, 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]
  12. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM et al. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 2014; 42:D633–D642 [View Article][PubMed]
     [Google Scholar]
  13. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
     [Google Scholar]
  14. 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]
  15. 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]
  16. 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]
  17. Hillis DM, Moritz C, Mable BK, Olmstead RG. Molecular Systematics Sunderland, MA: Sinauer Associates; 1996 pp 407–514
     [Google Scholar]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  19. Stackebrandt E. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  20. Lee I, Chalita M, Ha S-M, Na S-I, Yoon S-H et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057 [View Article][PubMed]
     [Google Scholar]
  21. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article][PubMed]
     [Google Scholar]
  22. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article][PubMed]
     [Google Scholar]
  23. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 2017; 45:D535–D542 [View Article][PubMed]
     [Google Scholar]
  24. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2020; 36:1925–1927
     [Google Scholar]
  25. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  26. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  27. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd ed. Baltimore: Williams & Wilkins; 1967
     [Google Scholar]
  28. Scheutz F, Strockbine NA. Escherichia. Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Ltd; 2015
     [Google Scholar]
  29. Grimont PAD, Grimont F. Enterobacter. Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Ltd; 2015
     [Google Scholar]
  30. Frederiksen W. Citrobacter. Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Ltd; 2015
     [Google Scholar]
  31. Cappuccino JG, Sherman N. Microbiology: a laboratory manual San Francisco: Pearson/Benjamin Cummings; 2005
     [Google Scholar]
  32. Hansen GH, Sørheim R. Improved method for phenotypical characterization of marine bacteria. J Microbiol Methods 1991; 13:231–241 [View Article]
     [Google Scholar]
  33. 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]
  34. Komagata K, Suzuki K-I. Lipid and Cell-Wall Analysis in Bacterial Systematics. Method Microbiol 19 Elsevier; 1988 pp 161–207
     [Google Scholar]
  35. Collins MD. Analysis of Isoprenoid Quinones. Method Microbiol 18 Elsevier; 1985 pp 329–366
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.004333
Loading
Sandaracinobacter neustonicus sp. nov., isolated from the sea surface microlayer in the Southwestern Pacific Ocean, and emended description of the genus Sandaracinobacter
Int J Syst Evol Microbiol 70, 4698 (2020); https://doi.org/10.1099/ijsem.0.004333
/content/journal/ijsem/10.1099/ijsem.0.004333
/content/journal/ijsem/10.1099/ijsem.0.004333
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