Skip to main content
SpringerLink
Log in

Neptunomonas marina sp. nov., isolated from seawater

  • Original Paper
  • Published:
Archives of Microbiology Aims and scope Submit manuscript

Abstract

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).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • 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 47:249–251

    Article  CAS  PubMed  Google Scholar 

  • 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 19:455–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 19–33

    Google Scholar 

  • 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 50:1861–1868

    Article  CAS  PubMed  Google Scholar 

  • Busse HJ, Auling G (1988) Polyamine pattern as chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11:1–8

    Article  CAS  Google Scholar 

  • Busse HJ, Bunka S, Hensel A, Lubitz W (1997) Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 47:698–708

    Article  CAS  Google Scholar 

  • 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 27:43–49

    Article  CAS  PubMed  Google Scholar 

  • 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 51:1729–1735

    Article  CAS  PubMed  Google Scholar 

  • Collins MD (1994) Isoprenoid quinones. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 265–309

    Google Scholar 

  • Dittmer JCF, Lester RL (1964) A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. J Lipid Res 5:126–127

    CAS  PubMed  Google Scholar 

  • Embley TM, Wait R (1994) Structural lipids of eubacteria. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 121–161

    Google Scholar 

  • Ewels P, Magnusson M, Lundin S, Käller M (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32:3047–3048

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (1993) PHYLIP (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA

  • 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 65:915–919

    Article  CAS  PubMed  Google Scholar 

  • 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 57:81–91

    Article  CAS  PubMed  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • 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 65:251–259

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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 59:686–690

    Article  CAS  PubMed  Google Scholar 

  • 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 57:1510–1515

    Article  CAS  PubMed  Google Scholar 

  • Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Kluge AG, Farris FS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32

    Article  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 23:2947–2948

    Article  CAS  PubMed  Google Scholar 

  • 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 62:2657–2661

    Article  CAS  PubMed  Google Scholar 

  • 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 66:1100–1103

    Article  CAS  PubMed  Google Scholar 

  • Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60

    Article  Google Scholar 

  • 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 56:280–285

    Article  CAS  PubMed  Google Scholar 

  • Nokhal TH, Schlegel HG (1983) Taxonomic study of Paracoccus denitrificans. Int J Syst Bacteriol 33:26–37

    Article  Google Scholar 

  • Parte AC (2018) LPSN-list of prokaryotic names with standing in nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 68:1825–1829

    Article  PubMed  Google Scholar 

  • 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 61:3756–3758

    CAS  PubMed  PubMed Central  Google Scholar 

  • Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131

    Article  PubMed  PubMed Central  Google Scholar 

  • Rzhetsky A, Nei M (1993) Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 10:1073–1095

    CAS  PubMed  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for constructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Inc, Newark

    Google Scholar 

  • Schlegel HG, Lafferty R, Krauss I (1970) The isolation of mutants not accumulating poly-β-hydroxybutyric acid. Arch Mikrobiol 71:283–294

    Article  CAS  PubMed  Google Scholar 

  • Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069

    Article  CAS  PubMed  Google Scholar 

  • 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 171:73–80

    Article  CAS  PubMed  Google Scholar 

  • 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 330–393

    Google Scholar 

  • Weisburg WG, Burns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wen CM, Tseng CS, Cheng CY, Li YK (2002) Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 35:213–219

    Article  CAS  PubMed  Google Scholar 

  • 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 64:3650–3654

    Article  CAS  PubMed  Google Scholar 

  • 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 67:1613–1617

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Funding

The authors received no specific grant from any funding agency.

Author information

Authors and Affiliations

  1. Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan

    Wen-Ming Chen & Tsai-Ying Hsieh

  2. Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan

    Shih-Yi Sheu

Authors
  1. Wen-Ming Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tsai-Ying Hsieh
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Shih-Yi Sheu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shih-Yi Sheu.

Ethics declarations

Conflict of interest

The authors declare that there are no conflicts of interest.

Additional information

Communicated by Erko Stackebrandt.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence and the draft genome of Neptunomonas marina strain HPM-16T are LT223128 and SACQ00000000. The Digital Protologue database Taxon Number for strain HPM-16T is TA00504.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 473 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chen, WM., Hsieh, TY. & Sheu, SY. Neptunomonas marina sp. nov., isolated from seawater. Arch Microbiol 201, 1053–1060 (2019). https://doi.org/10.1007/s00203-019-01671-7

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00203-019-01671-7

Keywords

Search

Navigation