Skip to content
1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 74, Issue 5

sp. nov., a novel member isolated from coastal mudflat sediment of Meishan Islandin the East China Sea No Access

Abstract

A Gram-negative, rod-shaped, non-motile and strictly aerobic strain, designated NBU2979, was isolated from a coastal mudflat located on Meishan Island in the East China Sea. Strain NBU2979 grew optimally at 32 °C, with 2.0 % NaCl (w/v) and at pH 7.0–7.5. The predominant fatty acid (>10 %) was iso-C. The major polar lipids included phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylcholine, an unidentified glycolipid, two unidentified aminophospholipids, an unidentified phospholipid and an unidentified lipid. The only respiratory quinone was ubiquinone-8. Comparative analysis of 16S rRNA gene sequences showed that strain NBU2979 exhibited highest similarity to F2 (98.0 %), S1101 (97.5 %), KMM 3900 (96.6 %), 3539 (95.5 %), sw153 (95.2 %) and S6413 (94.9 %). Phylogenetic analyses indicated that strain NBU2979 clustered with the genus and was closely related to strain F2. The average nucleotide identity and digital DNA–DNA hybridization values between strain NBU2979 and related species of genus were well below the threshold limit for prokaryotic species delineation. The DNA G+C content of strain NBU2979 was 51.6 mol%. Based on its phenotypic, chemotaxonomic and genotypic data, strain NBU2979 (=KCTC 82911=MCCC 1K06402) is considered to be a representative of a novel species in the genus , for which the name sp. nov. is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): coastal mudflat sediment , Marinicella and taxonomy
Funding
This study was supported by the:
  • Higher Education Discipline Innovation Project (Award D16013)
    • Principle Award Recipient: weiyanzhang
  • Scientific Research Foundation for Returned Scholars of Ministry of Education (Award IF2021087)
    • Principle Award Recipient: weiyanzhang
  • Science and Technology Development Center, Ministry of Education (Award 2021Z046)
    • Principle Award Recipient: weiyanzhang
  • Natural Science Foundation of Zhejiang Province (Award LGF22C010001)
    • Principle Award Recipient: weiyanzhang
  • National Natural Science Foundation of China (Award 32100001, 42176101)
    • Principle Award Recipient: weiyanzhang
© 2024 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006374
2024-05-24
2025-06-12
Loading full text...

Full text loading...

References

  1. Garrity GM, Bell JA, Lilburn T. Class III. Gammaproteobacteria class. nov. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. eds Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol 2 Springer; 2005 p 1
     [Google Scholar]
  2. Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV. Marinicella litoralis gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater. Int J Syst Evol Microbiol 2010; 60:1613–1619 [View Article] [PubMed]
     [Google Scholar]
  3. Wang Y, Liu Y, Zhang Z, Zheng Y, Zhang XH. Marinicella pacifica sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2016; 66:2313–2318 [View Article]
     [Google Scholar]
  4. Zhong YL, Sun XK, Hui JG, Teng HL, Du ZJ. Marinicella rhabdoformis sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2020; 70:3528–3533 [View Article] [PubMed]
     [Google Scholar]
  5. Wang XQ, Li CM, Dunlap CA, Rooney AP, Du ZJ. Marinicella sediminis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2018; 68:2335–2339 [View Article] [PubMed]
     [Google Scholar]
  6. Zhang J, Lian FB, Gao YZ, Du ZJ, Wang MY. Marinicella marina sp. nov. and Marinicella gelatinilytica sp. nov., isolated from coastal sediment, and genome analysis and habitat distribution of the genus Marinicella. Int J Syst Evol Microbiol 2023; 73:6130 [View Article] [PubMed]
     [Google Scholar]
  7. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology, 1st edn Beijing: Scientific Press; 2001 pp 353–364
     [Google Scholar]
  8. Zhu XF. Modern Experimental Technique of Microbiology Zhejiang University Press, Hangzhou English translation; 2011
     [Google Scholar]
  9. Zhang W, Zhu S, Cheng Y, Ding L, Li S et al. Rheinheimera mangrovi sp. nov., a bacterium isolated from mangrove sediment. Int J Syst Evol Microbiol 2020; 70:6188–6194 [View Article] [PubMed]
     [Google Scholar]
  10. Qi J, Wang B, Hao BI. Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J Mol Evol 2004; 58:1–11 [View Article] [PubMed]
     [Google Scholar]
  11. 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]
  12. Kates M. Techniques of Lipidology. Isolation, Analysis and Identification of Lipids, 2nd ed Amsterdam: Elsevier; 1986
     [Google Scholar]
  13. Zhang X-Q, Sun C, Wang C-S, Zhang X, Zhou X et al. Sinimarinibacterium flocculans gen. nov., sp. nov., a gammaproteobacterium from offshore surface seawater. Int J Syst Evol Microbiol 2015; 65:3541–3546 [View Article] [PubMed]
     [Google Scholar]
  14. Sun C, Wu C, Su Y, Wang R-J, Fu G-Y et al. Hyphococcus flavus gen. nov., sp. nov., a novel alphaproteobacterium isolated from deep seawater. Int J Syst Evol Microbiol 2017; 67:4024–4031 [View Article] [PubMed]
     [Google Scholar]
  15. 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]
  16. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
     [Google Scholar]
  17. 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]
  18. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  20. 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]
  21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  22. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
     [Google Scholar]
  23. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
     [Google Scholar]
  24. Lowe TM, Chan PP. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 2016; 44:W54–W57 [View Article] [PubMed]
     [Google Scholar]
  25. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article] [PubMed]
     [Google Scholar]
  26. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B et al. The COG database: an updated version includes eukaryotes. BMC Bioinform 2003; 4:1–14 [View Article] [PubMed]
     [Google Scholar]
  27. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S et al. NCBI BLAST: a better web interface. Nucleic Acids Res 2008; 36:W5–W9 [View Article] [PubMed]
     [Google Scholar]
  28. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [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 HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  31. Zuo G. CVTree: a parallel alignment-free phylogeny and taxonomy tool based on composition Vectors of genomes. Genom Proteom Bioinform 2021; 19:662–667 [View Article] [PubMed]
     [Google Scholar]
  32. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  33. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006374
Loading
Marinicella meishanensis sp. nov., a novel Marinicella member isolated from coastal mudflat sediment of Meishan Islandin the East China Sea
Int J Syst Evol Microbiol 74, 006374 (2024); https://doi.org/10.1099/ijsem.0.006374
/content/journal/ijsem/10.1099/ijsem.0.006374
/content/journal/ijsem/10.1099/ijsem.0.006374
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