Archives of Microbiology

, Volume 201, Issue 8, pp 1053–1060 | Cite as

Neptunomonas marina sp. nov., isolated from seawater

  • Wen-Ming Chen
  • Tsai-Ying Hsieh
  • Shih-Yi SheuEmail author
Original Paper


Strain HPM-16T, isolated from seawater, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of an up-to-date bacterial core gene set (92 protein clusters) indicated that strain HPM-16T formed a phylogenetic lineage in the genus Neptunomonas. Strain HPM-16T was most closely related to Neptunomonas concharum LHW37T with 16S rRNA gene sequence similarity of 96.7%. Cells were Gram-stain negative, facultatively anaerobic, motile by means of a single polar flagellum, rod-shaped and formed white colonies. Optimal growth occurred at 30–35 °C, pH 6.5–8, and in the presence of 2–5% NaCl. C18:1ω7c and summed feature 3 (C16:1ω7c and/or C16:1ω6c) were the predominant fatty acids. The only isoprenoid quinone was Q-8. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and several uncharacterized lipids. The major polyamines were putrescine and spermidine. The draft genome was approximately 3.68 Mb in size with a G + C content of 50.5 mol%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain HPM-16T should be classified as a novel species of the genus Neptunomonas, for which the name Neptunomonas marina sp. nov. is presented. The type strain is HPM-16T (= BCRC 80980T = LMG 29560T = KCTC 52235T).


Neptunomonas marina sp. nov. Gammaproteobacteria Oceanospirillales Oceanospirillaceae Polyphasic taxonomy 



The authors received no specific grant from any funding agency.

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Conflict of interest

The authors declare that there are no conflicts of interest.

Supplementary material

203_2019_1671_MOESM1_ESM.pdf (474 kb)
Supplementary material 1 (PDF 473 kb)


  1. Anzai Y, Kudo Y, Oyaizu H (1997) The phylogeny of genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 47:249–251CrossRefPubMedGoogle Scholar
  2. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477CrossRefPubMedPubMedCentralGoogle Scholar
  3. Beveridge TJ, Lawrence JR, Murray RGE (2007) Sampling and staining for light microscopy. In: Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al (eds) Methods for general and molecular bacteriology, 3rd edn. American Society for Microbiology, Washington, DC, pp 19–33Google Scholar
  4. Bowman JP (2000) Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50:1861–1868CrossRefPubMedGoogle Scholar
  5. Busse HJ, Auling G (1988) Polyamine pattern as chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11:1–8CrossRefGoogle Scholar
  6. Busse HJ, Bunka S, Hensel A, Lubitz W (1997) Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 47:698–708CrossRefGoogle Scholar
  7. Chang SC, Wang JT, Vandamme P, Hwang JH, Chang PS, Chen WM (2004) Chitinimonas taiwanensis gen. nov., sp. nov., a novel chitinolytic bacterium isolated from a freshwater pond for shrimp culture. Syst Appl Microbiol 27:43–49CrossRefPubMedGoogle Scholar
  8. Chen WM, Laevens S, Lee TM, Coenye T, de Vos P, Mergeay M, Vandamme P (2001) Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Microbiol 51:1729–1735CrossRefPubMedGoogle Scholar
  9. Collins MD (1994) Isoprenoid quinones. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 265–309Google Scholar
  10. Dittmer JCF, Lester RL (1964) A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 5:126–127PubMedGoogle Scholar
  11. Embley TM, Wait R (1994) Structural lipids of eubacteria. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 121–161Google Scholar
  12. Ewels P, Magnusson M, Lundin S, Käller M (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32:3047–3048CrossRefPubMedPubMedCentralGoogle Scholar
  13. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefPubMedPubMedCentralGoogle Scholar
  14. Felsenstein J (1993) PHYLIP (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USAGoogle Scholar
  15. Frommlet J, Guimarães B, Sousa L, Serôdio J, Alves A (2015) Neptunomonas phycophila sp. nov. isolated from a culture of Symbiodinium sp., a dinoflagellate symbiont of the sea anemone Aiptasia tagetes. Int J Syst Evol Microbiol 65:915–919CrossRefPubMedGoogle Scholar
  16. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91CrossRefPubMedGoogle Scholar
  17. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  18. Hedlund BP, Geiselbrecht AD, Bair TJ, Staley JT (1999) Polycyclic aromatic hydrocarbon degradation by a new marine bacterium, Neptunomonas naphthovorans gen. nov., sp. nov. Appl Environ Microbiol 65:251–259PubMedPubMedCentralGoogle Scholar
  19. Hosoya S, Adachi K, Kasai H (2009) Thalassomonas actiniarum sp. nov. and Thalassomonas haliotis sp. nov., isolated from marine animals. Int J Syst Evol Microbiol 59:686–690CrossRefPubMedGoogle Scholar
  20. Kämpfer P, Rossellό-Mora R, Hermansson M, Persson F, Huber B, Falsen E, Busse HJ (2007) Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 57:1510–1515CrossRefPubMedGoogle Scholar
  21. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  22. Kluge AG, Farris FS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32CrossRefGoogle Scholar
  23. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
  24. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A et al (2007) Clustal W and Clustal × version 2.0. Bioinformatics 23:2947–2948CrossRefPubMedGoogle Scholar
  25. Lee HW, Shin NR, Lee J, Roh SW, Whon TW, Bae JW (2012) Neptunomonas concharum sp. nov., isolated from a dead ark clam, and emended description of the genus Neptunomonas. Int J Syst Evol Microbiol 62:2657–2661CrossRefPubMedGoogle Scholar
  26. Lee I, Ouk Kim Y, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103CrossRefGoogle Scholar
  27. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60CrossRefGoogle Scholar
  28. Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J (2018) UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:280–285CrossRefPubMedGoogle Scholar
  29. Nokhal TH, Schlegel HG (1983) Taxonomic study of Paracoccus denitrificans. Int J Syst Bacteriol 33:26–37CrossRefGoogle Scholar
  30. Parte AC (2018) LPSN-list of prokaryotic names with standing in nomenclature (, 20 years on. Int J Syst Evol Microbiol 68:1825–1829CrossRefPubMedGoogle Scholar
  31. Powers EM (1995) Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 61:3756–3758PubMedPubMedCentralGoogle Scholar
  32. Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131CrossRefPubMedGoogle Scholar
  33. Rzhetsky A, Nei M (1993) Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 10:1073–1095PubMedGoogle Scholar
  34. Saitou N, Nei M (1987) The neighbor-joining method: a new method for constructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
  35. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Inc, NewarkGoogle Scholar
  36. Schlegel HG, Lafferty R, Krauss I (1970) The isolation of mutants not accumulating poly-β-hydroxybutyric acid. Arch Mikrobiol 71:283–294CrossRefPubMedGoogle Scholar
  37. Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069CrossRefGoogle Scholar
  38. Spiekermann P, Rehm BHA, Kalscheuer R, Baumeister D, Steinbüchel A (1999) A sensitive, viable-colony staining method using nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Arch Microbiol 171:73–80CrossRefGoogle Scholar
  39. Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al (eds) Methods for General and Molecular Bacteriology, 3rd. American Society for Microbiology, Washington, DC, pp 330–393Google Scholar
  40. Weisburg WG, Burns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703CrossRefPubMedPubMedCentralGoogle Scholar
  41. Wen CM, Tseng CS, Cheng CY, Li YK (2002) Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 35:213–219CrossRefPubMedGoogle Scholar
  42. Yang SH, Seo HS, Lee JH, Kim SJ, Kwon KK (2014) Neptunomonas acidivorans sp. nov., isolated from sediment, and emended description of the genus Neptunomonas. Int J Syst Evol Microbiol 64:3650–3654CrossRefPubMedGoogle Scholar
  43. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Laboratory of Microbiology, Department of Seafood ScienceNational Kaohsiung University of Science and TechnologyKaohsiung CityTaiwan
  2. 2.Department of Marine BiotechnologyNational Kaohsiung University of Science and TechnologyKaohsiung CityTaiwan

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