Skip to content
1887

Abstract

Two Gram-stain-negative, facultatively anaerobic, non-motile and rod-shaped bacterial strains, designated 2201CG32-9 and 2304DJ12-6, were isolated from marine sponges collected in the Republic of Korea. Both strains exhibited catalase and oxidase activities but tested negative for nitrate reduction and indole production. Strain 2201CG32-9 showed optimal growth at 30 °C and pH 7.0–8.0 in the presence of 3% (w/v) NaCl, whereas strain 2304DJ12-6 grew optimally at 25 °C, pH 8.0 and 3% (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene and phylogenomic analysis of genome sequences indicated that strains 2201CG32-9 and 2304DJ12-6 represented novel species within the genus . Based on whole-genome phylogenomic analysis, the two strains were most closely related to OS29 and ATCC 700307, respectively. The average nucleotide identity values of these strains were found to be <75.9%, and their digital DNA–DNA hybridization values were <22.5%. The DNA G+C contents of strains 2201CG32-9 and 2304DJ12-6 were 56.5 and 53.5 mol%, respectively. In both strains, ubiquinone-8 was identified as the predominant respiratory quinone, and the major cellular fatty acids (>5.0%) were C, iso-C 3-OH, iso-C, iso-C, summed feature 8 and summed feature 9. As for polar lipids, both strains comprised phosphatidylglycerol, phosphatidylethanolamine and phosphoglycolipid as common major polar lipids. Strains 2201CG32-9 and 2304DJ12-6 are classified as two novel species of the genus based on a polyphasic taxonomic approach, for which the names sp. nov. (2201CG32-9=KACC 23829=JCM 37223) and sp. nov. (2304DJ12-6=KACC 23832=MCCC 1K09533) are proposed, respectively.

Funding
This study was supported by the:
  • National Institute for International Education (Award 2021R1I1A3046479)
    • Principal Award Recipient: Jin-SookPark
  • National Marine Biodiversity Institute of Korea
    • Principal Award Recipient: Jin-SookPark
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006980
2025-11-27
2025-12-15

Metrics

Loading full text...

Full text loading...

References

  1. González JM, Mayer F, Moran MA, Hodson RE, Whitman WB. Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community. Int J Syst Bacteriol 1997; 47:369–376 [View Article] [PubMed]
    [Google Scholar]
  2. Romanenko L, Kurilenko V, Otstavnykh N, Velansky P, Isaeva M et al. Microbulbifer okhotskensis sp. nov., isolated from a deep bottom sediment of the Okhotsk sea. Arch Microbiol 2022; 204:548 [View Article] [PubMed]
    [Google Scholar]
  3. Fu Y-H, Wu Z-C, Kong Y-H, Xu X-W, Sun C et al. Microbulbifer zhoushanensis sp. nov., Microbulbifer sediminum sp. nov. and Microbulbifer guangxiensis sp. nov., three marine bacteria isolated from a tidal flat. Int J Syst Evol Microbiol 2023; 73:5842 [View Article]
    [Google Scholar]
  4. Xiong Q, Wang D, Dong X, Liu D, Liu Y et al. Microbulbifer flavimaris sp. nov., a halophilic Gammaproteobacteria isolated from marine sediment of the Yellow Sea, China. Int J Syst Evol Microbiol 2019; 69:1135–1141 [View Article] [PubMed]
    [Google Scholar]
  5. Nishijima M, Takadera T, Imamura N, Kasai H, An K-D et al. Microbulbifer variabilis sp. nov. and Microbulbifer epialgicus sp. nov., isolated from Pacific marine algae, possess a rod-coccus cell cycle in association with the growth phase. Int J Syst Evol Microbiol 2009; 59:1696–1707 [View Article] [PubMed]
    [Google Scholar]
  6. Lee J-Y, Kim PS, Hyun D-W, Kim HS, Shin N-R et al. Microbulbifer echini sp. nov., isolated from the gastrointestinal tract of a purple sea urchin, Heliocidaris crassispina. Int J Syst Evol Microbiol 2017; 67:998–1004 [View Article]
    [Google Scholar]
  7. Ishaq N, Zhang M, Gao L, Ilan M, Li Z. Microbulbifer spongiae sp. nov., isolated from marine sponge Diacarnus erythraeanus. Int J Syst Evol Microbiol 2024; 74:6521 [View Article]
    [Google Scholar]
  8. Huang H, Mo K, Hu Y, Liu M, Zhu J et al. Microbulbifer harenosus sp. nov., an alginate-degrading bacterium isolated from coastal sand. Int J Syst Evol Microbiol 2020; 70:1639–1643 [View Article]
    [Google Scholar]
  9. Kämpfer P, Arun AB, Young C-C, Rekha PD, Martin K et al. Microbulbifer taiwanensis sp. nov., isolated from coastal soil. Int J Syst Evol Microbiol 2012; 62:2485–2489 [View Article]
    [Google Scholar]
  10. Yoon J-H, Jung S-Y, Kang S-J, Oh T-K. Microbulbifer celer sp. nov., isolated from a marine solar saltern of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2007; 57:2365–2369 [View Article]
    [Google Scholar]
  11. Yoon J-H, Kim I-G, Shin D-Y, Kang KH, Park Y-H. Microbulbifer salipaludis sp. nov., a moderate halophile isolated from a Korean salt marsh. Int J Syst Evol Microbiol 2003; 53:53–57 [View Article]
    [Google Scholar]
  12. Long M, Chen D, Fan H, Tang S, Gan Z et al. Microbulbifer bruguierae sp. nov., isolated from sediment of mangrove plant Bruguiera sexangula, and comparative genomic analyses of the genus Microbulbifer. Int J Syst Evol Microbiol 2024; 74:6209 [View Article]
    [Google Scholar]
  13. Camacho M, Redondo-Gómez S, Rodríguez-Llorente I, Rohde M, Spröer C et al. Labrenzia salina sp. nov., isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum. Int J Syst Evol Microbiol 2016; 66:5173–5180 [View Article] [PubMed]
    [Google Scholar]
  14. Hentschel U, Usher KM, Taylor MW. Marine sponges as microbial fermenters. FEMS Microbiol Ecol 2006; 55:167–177 [View Article] [PubMed]
    [Google Scholar]
  15. Thomas T, Rusch D, DeMaere MZ, Yung PY, Lewis M et al. Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis. ISME J 2010; 4:1557–1567 [View Article]
    [Google Scholar]
  16. Taylor MW, Radax R, Steger D, Wagner M. Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 2007; 71:295–347 [View Article] [PubMed]
    [Google Scholar]
  17. Moon YL, Kim KH, Park JS. Muricauda myxillae sp. nov., isolated from a marine sponge (Myxilla rosacea), and reclassification of Flagellimonas hymeniacidonis as Muricauda symbiotica nom. nov. Int J Syst Evol Microbiol 2023; 73:6040 [View Article]
    [Google Scholar]
  18. 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]
  19. 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]
  20. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article] [PubMed]
    [Google Scholar]
  21. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
    [Google Scholar]
  22. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
    [Google Scholar]
  23. 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]
  24. 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]
  25. Kim J, Na S-I, Kim D, Chun J. UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 2021; 59:609–615 [View Article] [PubMed]
    [Google Scholar]
  26. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article]
    [Google Scholar]
  27. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article]
    [Google Scholar]
  28. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  29. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [View Article] [PubMed]
    [Google Scholar]
  30. Tang S-K, Wang Y, Cai M, Lou K, Mao P-H et al. Microbulbifer halophilus sp. nov., a moderately halophilic bacterium from north-west China. Int J Syst Evol Microbiol 2008; 58:2036–2040 [View Article] [PubMed]
    [Google Scholar]
  31. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019; 47:D309–D314 [View Article] [PubMed]
    [Google Scholar]
  32. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007; 35:W182–5 [View Article] [PubMed]
    [Google Scholar]
  33. Kumar G, Kumar D, Jagadeeshwari U, Sreya PK, Shabbir A et al. Crateriforma spongiae sp. nov., isolated from a marine sponge and emended description of the genus “Crateriforma”. Antonie Van Leeuwenhoek 2021; 114:341–353 [View Article] [PubMed]
    [Google Scholar]
  34. Blin K, Shaw S, Vader L, Szenei J, Reitz ZL et al. antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation. Nucleic Acids Res 2025; 53:W32–W38 [View Article] [PubMed]
    [Google Scholar]
  35. Steiner LX, Wiese J, Rahn T, Borchert E, Slaby BM et al. Maribacter halichondriae sp. nov., isolated from the marine sponge Halichondria panicea, displays features of a sponge-associated life style. Antonie Van Leeuwenhoek 2024; 117:56 [View Article] [PubMed]
    [Google Scholar]
  36. Engelberts JP, Robbins SJ, de Goeij JM, Aranda M, Bell SC et al. Characterization of a sponge microbiome using an integrative genome-centric approach. ISME J 2020; 14:1100–1110 [View Article] [PubMed]
    [Google Scholar]
  37. Almeida JF, Marques M, Oliveira V, Egas C, Mil-Homens D et al. Marine sponge and octocoral-associated bacteria show versatile secondary metabolite biosynthesis potential and antimicrobial activities against human pathogens. Mar Drugs 2022; 21:34 [View Article] [PubMed]
    [Google Scholar]
  38. Johnston I, Osborn LJ, Markley RL, McManus EA, Kadam A et al. Identification of essential genes for Escherichia coli aryl polyene biosynthesis and function in biofilm formation. NPJ Biofilms Microbiomes 2021; 7:56 [View Article] [PubMed]
    [Google Scholar]
  39. Kim S-B, Kim KH, Park J-S. Paracoccus spongiarum sp. nov., isolated from the marine sponge, Phakellia elegans. Int J Syst Evol Microbiol 2024; 74:006566 [View Article]
    [Google Scholar]
  40. ZoBell CE, Claude E. Studies on marine bacteria, i: the cultural requirements of heterotrophic aerobes. J mar Res 1941; 4:42–75
    [Google Scholar]
  41. Smibert RM, Krieg NR. Phenotypic Characterization. In Gerhardt P. eds Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  42. Lányí B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1987; 19:1–67
    [Google Scholar]
  43. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  44. Moon Y-L, Kim KH, Park J-S. Chengkuizengella axinellae sp. nov., a symbiotic bacterium isolated from a marine sponge of the genus Axinella. Antonie Van Leeuwenhoek 2024; 117:106 [View Article] [PubMed]
    [Google Scholar]
  45. 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]
  46. 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]
/content/journal/ijsem/10.1099/ijsem.0.006980
Loading
/content/journal/ijsem/10.1099/ijsem.0.006980
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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