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Volume 73, Issue 2

sp. nov., isolated from the sponge No Access

Abstract

A novel Gram-stain-negative, thin-rod-shaped, aerobic, non-motile and yellow-pigmented marine bacterium (designated strain 2012CJ35-5) was isolated from a marine sponge sampled in Jeju-do, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 2012CJ35-5 belonged to the family , and was most closely related to KCCM 90075 (96.3 %), JCM 33425 (95.7 %), KCTC 22665 (95.6 %), KCTC 52351 (95.6 %) and KCTC 22266 (94.9 %). Average nucleotide identity, amino acid identities and digital DNA–DNA hybridization between strain 2012CJ35-5 and the closest related strain were 72.6, 73.6 and 17.3 % respectively, indicating that strain 2012CJ35-5 represents a novel species of the genus . The genome size of strain 2012CJ35-5 is 3.8 Mbp and the G+C content is 43.9 mol%. Strain 2012CJ35-5 contained menaquinone 6 as the major respiratory quinone and phosphatidylethanolamine, four unidentified aminophospholipids and five unidentified lipids as major polar lipids. The fatty acids were mainly (>15 %) defined as C iso (31.7 %), C iso G (29.2 %) and C iso 3OH (18.0 %). Strain 2012CJ35-5 could be distinguished from the other members of the genus by a number of chemotaxonomic and phenotypic characteristics. Based on the results of polyphasic taxonomic analysis, strain 2012CJ35-5 (=KACC 22643=LMG 32584) represents a novel species within the genus , for which the name sp. nov. is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene sequence , genome sequence , Muricauda spongiicola and polyphasic taxonomy
Funding
This study was supported by the:
  • National Research Foundation of Korea (Award 2021R1I1A3046479)
    • Principle Award Recipient: Jin-SookPark
  • National Marine Biodiversity Institute of Korea (Award 2022M01100)
    • Principle Award Recipient: Jin-SookPark
© 2023 The Authors
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2023-02-07
2024-04-25
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References

  1. Bruns A, Rohde M, Berthe-Corti L. Muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from German North Sea intertidal sediment. Int J Syst Evol Microbiol 2001; 51:1997–2006 [View Article] [PubMed]
     [Google Scholar]
  2. Yoon BJ, Oh DC. Spongiibacterium flavum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the marine sponge Halichondria oshoro, and emended descriptions of the genera Croceitalea and Flagellimonas. Int J Syst Evol Microbiol 2012; 62:1158–1164 [View Article]
     [Google Scholar]
  3. Gao X, Zhang Z, Dai X, Zhang XH. Spongiibacterium pacificum sp. nov., isolated from seawater of South Pacific Gyre and emended description of the genus Spongiibacterium. Int J Syst Evol Microbiol 2015; 65:154–158 [View Article]
     [Google Scholar]
  4. Bae SS, Kwon KK, Yang SH, Lee HS, Kim SJ et al. Flagellimonas eckloniae gen. nov., sp. nov., a mesophilic marine bacterium of the family Flavobacteriaceae, isolated from the rhizosphere of Ecklonia kurome. Int J Syst Evol Microbiol 2007; 57:1050–1054 [View Article]
     [Google Scholar]
  5. García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T et al. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes. Front Microbiol 2019; 10:10 [View Article]
     [Google Scholar]
  6. 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]
  7. Hwang CY, Kim MH, Bae GD, Zhang GI, Kim YH et al. Muricauda olearia sp. nov., isolated from crude-oil-contaminated seawater, and emended description of the genus Muricauda. Int J Syst Evol Microbiol 2009; 59:1856–1861 [View Article]
     [Google Scholar]
  8. Liu L, Yu M, Zhou S, Fu T, Sun W et al. Muricauda alvinocaridis sp. nov., isolated from shrimp gill from the Okinawa Trough. Int J Syst Evol Microbiol 2020; 70:1666–1671 [View Article]
     [Google Scholar]
  9. Choi S, Lee JH, Kang JW, Choe HN, Seong CN. Flagellimonas aquimarina sp. nov., and transfer of Spongiibacterium flavum Yoon and Oh 2012 and S. pacificum Gao et al. 2015 to the genus Flagellimonas Bae et al. 2007 as Flagellimonas flava comb. nov. and F. pacifica comb. nov., respectively. Int J Syst Evol Microbiol 2018; 68:3266–3272 [View Article]
     [Google Scholar]
  10. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article] [PubMed]
     [Google Scholar]
  11. Leifson E. Atlas of Bacterial Flagellation New York: Academic Press;1960; [View Article]
     [Google Scholar]
  12. Atlas RM. Handbook of Microbiological Media Boca Raton, FL: CRC Press; 1993
     [Google Scholar]
  13. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria Cambridge: Cambridge University Press; 1974
     [Google Scholar]
  14. Cappuccino JG, Sherman N. Microbiology: A Laboratory Manual, 6th edn. San Francisco: Pearson Education Inc; 2002 pp 15–224
     [Google Scholar]
  15. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  16. 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]
  17. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article] [PubMed]
     [Google Scholar]
  18. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
     [Google Scholar]
  19. 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]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  21. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  22. 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]
     [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  24. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983 [View Article]
     [Google Scholar]
  25. 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]
  26. 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]
  27. 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]
  28. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  29. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  30. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:73–84 [View Article]
     [Google Scholar]
  31. Auch AF, von Jan M, Klenk H-P, 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 [View Article] [PubMed]
     [Google Scholar]
  32. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [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. Sasser M. Technical Note 101: Identification of bacteria by gas chromatography of cellular fatty acids Microbial ID, Inc; 1990
     [Google Scholar]
  35. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
     [Google Scholar]
  36. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  37. 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]
  38. 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 [View Article] [PubMed]
     [Google Scholar]
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Muricauda spongiicola sp. nov., isolated from the sponge Callyspongia elongata
Int J Syst Evol Microbiol 73, 005702 (2023); https://doi.org/10.1099/ijsem.0.005702
/content/journal/ijsem/10.1099/ijsem.0.005702
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