1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 11

sp. nov., isolated from a marine sponge (), and reclassification of as nom. nov. No Access

Abstract

A Gram-stain-negative, aerobic and non-motile rods strain, designated as strain 2012CJ39-3, was isolated from a marine sponge, , collected on Chuja Island, Republic of Korea. Optimal growth of strain 2012CJ39-3 was observed at 25 °C, pH 7.0 and in the presence of 2.0–3.0 % (w/v) NaCl. Strain 2012CJ39-3 contained menaquinone-6 as the respiratory quinone, iso-C G, iso-C, and iso-C 3-OH as the predominant fatty acids, and phosphatidylethanolamine, an unidentified phospholipid, an unidentified glycolipid, three unidentified aminolipids and nine unidentified lipids as major polar lipids. The genomic DNA G+C content was 38.4 mol%. Results of phylogenetic analyses based on the 16S rRNA gene and whole-genome sequences revealed that strain 2012CJ39-3 formed a distinct phyletic lineage in the genus . Strain 2012CJ39-3 was most closely related to 176CP5-101, 2012CJ35-5, AsT0115, DSM 22638 and SW169 with 96.5, 96.4, 96.3, 95.8 and 95.6 % 16S rRNA gene sequence similarity, respectively. The average nucleotide identity and digital DNA–DNA hybridization values between strain 2012CJ39-3 and 2012CJ35-5, 176CP5-101, AsT0115, DSM 22638 and SW169 were 75.6, 74.2, 78.6, 75.3 and 74.8 % and 27.4, 19.9, 36.3, 24.2 and 18.9 %, respectively. Based on these results, strain 2012CJ39-3 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 2012CJ39-3 (=KACC 22644= LMG 32582). In addition, is reclassified as nom. nov.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): marine sponge , Muricauda myxillae , Muricauda symbiotica , Myxilla rosacea and new taxa
Funding
This study was supported by the:
  • Ministry of Education (Award 2021R1I1A3046479)
    • Principle Award Recipient: Jin-SookPark
  • National Marine Biodiversity Institute of Korea
    • Principle Award Recipient: Jin-SookPark
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006040
2023-11-20
2024-05-08
Loading full text...

Full text loading...

References

  1. Hentschel U, Piel J, Degnan SM, Taylor MW. Genomic insights into the marine sponge microbiome. Nat Rev Microbiol 2012; 10:641–654 [View Article] [PubMed]
     [Google Scholar]
  2. Wang G. Diversity and biotechnological potential of the sponge-associated microbial consortia. J Ind Microbiol Biotechnol 2006; 33:545–551 [View Article] [PubMed]
     [Google Scholar]
  3. Osinga R, Armstrong E, Grant Burgess J, Hoffmann F, Reitner J et al. Sponge—microbe associations and their importance for sponge bioprocess engineering. Hydrobiologia 2001; 461:55–62 [View Article]
     [Google Scholar]
  4. Hentschel U, Hopke J, Horn M, Friedrich AB, Wagner M et al. Molecular evidence for a uniform microbial community in sponges from different oceans. Appl Environ Microbiol 2002; 68:4431–4440 [View Article] [PubMed]
     [Google Scholar]
  5. 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]
  6. 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; 10:2083 [View Article] [PubMed]
     [Google Scholar]
  7. Shin J-Y, Park J-S. Muricauda spongiicola sp. nov., isolated from the sponge Callyspongia elongata. Int J Syst Evol Microbiol 2023; 73:5702 [View Article]
     [Google Scholar]
  8. Shin T-G, Park J-S. Flagellimonas hymeniacidonis sp. nov., Isolated from the sponge Hymeniacidon sinapium. Curr Microbiol 2021; 78:1061–1067 [View Article] [PubMed]
     [Google Scholar]
  9. Yoon B-J, Oh D-C. 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] [PubMed]
     [Google Scholar]
  10. Kim J, Kim KH, Chun BH, Khan SA, Jeon CO. Flagellimonas algicola sp. nov., Isolated from a marine red alga, Asparagopsis taxiformis. Curr Microbiol 2020; 77:294–299 [View Article] [PubMed]
     [Google Scholar]
  11. Chen Y, Hu Z, Wang H. Muricauda amphidinii sp. nov., a novel marine bacterium isolated from the phycosphere of dinoflagellate Amphidinium carterae. Int J Syst Evol Microbiol 2019; 71:004764 [View Article] [PubMed]
     [Google Scholar]
  12. 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] [PubMed]
     [Google Scholar]
  13. Wang D, Wu Y, Liu Y, Liu B, Gao Y et al. Muricauda abyssi sp. nov., a marine bacterium isolated from deep seawater of the Mariana Trench. Int J Syst Evol Microbiol 2022; 72:5615 [View Article] [PubMed]
     [Google Scholar]
  14. Zhao S, Liu R, Lai Q, Shao Z. Muricauda aurea sp. nov. and Muricauda profundi sp. nov., two marine bacteria isolated from deep sea sediment of Pacific Ocean. Int J Syst Evol Microbiol 2022; 72:5217 [View Article]
     [Google Scholar]
  15. Yoon JH, Lee MH, Oh TK, Park YH. Muricauda flavescens sp. nov. and Muricauda aquimarina sp. nov., isolated from a salt lake near Hwajinpo Beach of the East Sea in Korea, and emended description of the genus Muricauda. Int J Syst Evol Microbiol 2005; 55:1015–1019 [View Article] [PubMed]
     [Google Scholar]
  16. Arun AB, Chen W-M, Lai W-A, Chao J-H, Rekha PD et al. Muricauda lutaonensis sp. nov., a moderate thermophile isolated from a coastal hot spring. Int J Syst Evol Microbiol 2009; 59:2738–2742 [View Article] [PubMed]
     [Google Scholar]
  17. Kim D, Yoo Y, Khim JS, Yang D, Pathiraja D et al. Muricauda ochracea sp. nov., isolated from a tidal flat in the Republic of Korea. Int J Syst Evol Microbiol 2020; 70:4555–4561 [View Article] [PubMed]
     [Google Scholar]
  18. 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] [PubMed]
     [Google Scholar]
  19. Liang J, Yin Q, Zheng X, Wang Y, Song ZM et al. Muricauda Onchidii sp. nov., isolated from a marine invertebrate from South China sea, and transfers of Flagellimonas Algicola, Flagellimonas Pacifica and Flagellimonas maritima to Muricauda algicola comb. nov., Muricauda parva nom. nov. and Muricauda aurantiaca nom. nov., respectively, and emended description of the genus Muricauda. Int J Syst Evol Microbiol 2021; 71:4982 [View Article] [PubMed]
     [Google Scholar]
  20. Su Y, Yang X, Wang Y, Liu Y, Ren Q et al. Muricauda marina sp. nov., isolated from marine snow of Yellow Sea. Int J Syst Evol Microbiol 2017; 67:2446–2451 [View Article] [PubMed]
     [Google Scholar]
  21. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp 115–148
     [Google Scholar]
  22. 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]
  23. Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 2013; 29:2933–2935 [View Article] [PubMed]
     [Google Scholar]
  24. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article]
     [Google Scholar]
  25. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. 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]
  28. 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]
  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. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  31. Zheng J, Ge Q, Yan Y, Zhang X, Huang L et al. dbCAN3: automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Res 2023; 51:W115–W121 [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–W185 [View Article] [PubMed]
     [Google Scholar]
  33. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  34. Pita L, Rix L, Slaby BM, Franke A, Hentschel U. The sponge holobiont in a changing ocean: from microbes to ecosystems. Microbiome 2018; 6:1–18 [View Article] [PubMed]
     [Google Scholar]
  35. Carrier TJ, Maldonado M, Schmittmann L, Pita L, Bosch TCG et al. Symbiont transmission in marine sponges: reproduction, development, and metamorphosis. BMC Biol 2022; 20:100 [View Article] [PubMed]
     [Google Scholar]
  36. ZoBell CE. Studies on marine bacteria, I: the cultural requirements of heterotrophic aerobes. J Mar Res 1941; 4:42–75
     [Google Scholar]
  37. Tindall BJ, Sikorski J, Smibert RM, Kreig NR. Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd. edn Washington, DC: American Society of Microbiology; 2007 pp 330–393 [View Article]
     [Google Scholar]
  38. 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]
  39. 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 Met 1984; 2:233–241 [View Article]
     [Google Scholar]
  40. Miller L, Berger T. Bacterial identification by gas chromatography of whole cell fatty acids. In Hewlett-Packard Application Note 1985 pp 228–241
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.006040
Loading
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 73, 006040 (2023); https://doi.org/10.1099/ijsem.0.006040
/content/journal/ijsem/10.1099/ijsem.0.006040
/content/journal/ijsem/10.1099/ijsem.0.006040
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

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