Skip to main content
Log in

Thalassobius aquimarinus sp. nov., isolated from the Sea of Japan seashore

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

Abstract

An aerobic, Gram-negative, non-pigmented non-motile bacterium designed КMM 8518T was isolated from a seawater sampled from the Sea of Japan seashore. Strain КMM 8518T grew at 7–42 °C and in the presence of 1–7% NaCl. The phylogenetic analyses based on 16S rRNA gene and whole-genome sequences placed the novel strain КMM 8518T into the genus Thalassobius as a separate lineage. Strain КMM 8518T shared the highest 16S rRNA gene sequence similarity of 98% to Thalassobius gelatinovorus KCTC 22092T and similarity values of ≤ 97% to other recognized Thalassobius species. The average nucleotide identity and digital DNADNA hybridization values between strain КMM 8518T and T. gelatinovorus KCTC 22092T were 79.6% and 23.5%, respectively. The major respiratory quinone was ubiquinone-10. The major fatty acid was C18:1ω7c followed by 11-methyl C18:1ω7c. Polar lipids comprised phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid, and three unidentified lipids. The DNA G+C content of 62.7% was calculated from genome sequence analysis. Based on the phylogenetic analyses and distinctive phenotypic characteristics, the marine bacterium КMM 8518T is concluded to represent a novel species of the genus Thalassobius for which the name Thalassobius aquimarinus sp. nov. is proposed. The type strain of the species is strain KMM 8518T (= KCTC 82576T).

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

Access this article

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

  • Arahal DR, Macian MC, Garay E, Pujalte MJ (2005) Thalassobius mediterraneus gen. nov., sp. nov., and reclassification of Ruegeria gelatinovorans as Thalassobius gelatinovorus comb. nov. Int J Syst Evol Microbiol 55:2371–2376

    Article  CAS  Google Scholar 

  • Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, Zhu Q, Bolzan M, Cumbo F, May U, Sanders JG, Zolfo M, Kopylova E, Pasolli E, Knight R, Mirarab S, Huttenhower C, Segata N (2020) Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun 11:1–10

    Article  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 Bioinform Comput Biol 19:455–477

    Article  CAS  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 15:2114–2120

    Article  Google Scholar 

  • Bruns A, Rohde M, Berthe-Corti L (2001) Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 51:1997–2006

    Article  CAS  Google Scholar 

  • Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, Da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–468

    Article  CAS  Google Scholar 

  • Collins MD, Shah HN (1984) Fatty acid, menaquinone and polar lipid composition of Rothia dentosacariosa. Arch Microbiol 137:247–249

    Article  CAS  Google Scholar 

  • Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC (1989) Isolation and direct complete nucleotide determination of entire genes: characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17:7843–7853

    Article  CAS  Google Scholar 

  • Folch J, Lees M, Sloane Stanley GH (1957) A simple method for the isolation and purification of total lipids from animal tissues. J Biol Chem 226:497–509

    Article  CAS  Google Scholar 

  • Garrity GM, Bell JA, Lilburn T (2005) Family I. Rhodobacteraceae fam. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology, vol 2, 2nd edn. Springer, New York, p 161

    Google Scholar 

  • Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) (1994) Methods for general and molecular bacteriology. American Society for Microbiology, Washington

    Google Scholar 

  • Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: Quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075

    Article  CAS  Google Scholar 

  • Hördt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M (2020) Analysis of 1,000 type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria. Front Microbiol 11:468

    Article  Google Scholar 

  • Iwaki H, Yasukawa N, Fujioka M, Takada K, Hasegawa Y (2013) Isolation and characterization of a marine cyclohexylacetate-degrading bacterium Lutimaribacter litoralis sp. nov., and reclassification of Oceanicola pacificus as Lutimaribacter pacificus comb. nov. Curr Microbiol 66:588–593

    Article  CAS  Google Scholar 

  • Jin HM, Lee HJ, Kim JM, Park MS, Lee K, Jeon CO (2011) Litorimicrobium taeanense gen. nov., sp. nov., isolated from a sandy beach. Int J Syst Evol Microbiol 61:1392–1396

    Article  CAS  Google Scholar 

  • Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351

    Article  CAS  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549

    Article  CAS  Google Scholar 

  • Lafay B, Ruimy R, Rausch de Traubenberg C, Breittmayer V, Gauthier MJ, Christen R (1995) Roseobacter algicola sp. nov., a new marine bacterium isolated from the phycosphere of the toxin-producing dinoflagellate Prorocentrum lima. Int J Syst Bacteriol 45:290–296

    Article  CAS  Google Scholar 

  • Meier-Kolthoff JP, Göker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 1:1–10

    Google Scholar 

  • Mitchell K, Fallon RJ (1990) The determination of ubiquinone profiles by reversed-phase high performance thin-layer chromatography as an aid to the speciation of Legionellaceae. J Gen Microbiol 136:2035–2041

    Article  CAS  Google Scholar 

  • Nogi Y, Mori K, Makita H, Hatada Y (2016) Thalassobius abyssi sp. nov., a marine bacterium isolated from cold-seep sediment. Int J Syst Evol Microbiol 66:574–579

    Article  CAS  Google Scholar 

  • Park S, Lee MH, Lee JS, Oh TK, Yoon JH (2012) Thalassobius maritimus sp. nov., isolated from seawater. Int J Syst Evol Microbiol 62:8–12

    Article  CAS  Google Scholar 

  • Park S, Jung YT, Won SM, Park JM, Yoon JH (2014) Thalassobius aquaeponti sp. nov., an alphaproteobacterium isolated from seawater. Antonie Van Leeuwenhoek 106:535–542

    Article  CAS  Google Scholar 

  • Park I, Cha IT, Seo MJ (2016) Thalassobius litorarius sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 66:1666–1672

    Article  CAS  Google Scholar 

  • Pujalte MJ, Lucena T, Rodrigo-Torres L, Arahal DR (2018) Comparative genomics of Thalassobius including the description of Thalassobius activus sp. nov., and Thalassobius autumnalis sp nov. Front Microbiol 8:2645

    Article  Google Scholar 

  • Richter M, Rosselló-Móra R, Glöckner FO, Peplies J (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931

    Article  CAS  Google Scholar 

  • Romanenko LA, Tanaka N, Svetashev VI, Kalinovskaya NI (2011) Pacificibacter maritimus gen. nov., sp. nov., isolated from shallow marine sediment. Int J Syst Evol Microbiol 61:1375–1381

    Article  CAS  Google Scholar 

  • Romanenko LA, Kurilenko VV, Guzev KV, Svetashev VI (2019) Characterization of Labrenzia polysiphoniae sp. nov. isolated from red alga Polysiphonia sp. Arch Microbiol 201:705–712

    Article  CAS  Google Scholar 

  • Rüger HJ, Höfle MG (1992) Marine star-shaped aggregate-forming bacteria: Agrobacterium atlanticum sp. nov.; Agrobacterium meteori sp. nov.; Agrobacterium ferrugineum sp. nov., nom. rev.; Agrobacterium gelatinovorum sp. nov., nom. rev.; and Agrobacterium stellulatum sp. nov., nom. Int J Syst Bacteriol 42:133–143

    Article  Google Scholar 

  • Sasser M (1990) Microbial identification by gas chromatographic analysis of fatty acid methyl esters (GC-FAME). Technical Note 101. Newark, DE: MIDI

  • Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 14:6614–6624

    Article  Google Scholar 

  • Wirth JS, Whitman WB (2018) Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 68:2393–2411

    Article  CAS  Google Scholar 

  • Yi H, Chun J (2006) Thalassobius aestuarii sp. nov., isolated from tidal flat sediment. J Microbiol 44:171–176

    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

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We would like to thank Professor Dr. Edward R.B. Moore, the CCUG Culture Collection, University of Göteborg, Sweden, for providing the type strain Thalassobius mediterraneus CCUG 49438T for comparative analyses.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Lyudmila A. Romanenko.

Ethics declarations

Conflict of interest

All the authors have declared no conflict 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.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 234 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kurilenko, V.V., Romanenko, L.A., Chernysheva, N.Y. et al. Thalassobius aquimarinus sp. nov., isolated from the Sea of Japan seashore. Arch Microbiol 203, 3201–3207 (2021). https://doi.org/10.1007/s00203-021-02285-8

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00203-021-02285-8

Keyword

Navigation