Skip to content
1887

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

Volume 73, Issue 5

sp. nov., isolated from marine sediment No Access

Abstract

A novel actinobacterium strain (M4I6) was isolated from marine sediment collected in Megas Gialos, Syros, Greece. On the basis of 16S rRNA gene sequence analysis, strain M4I6 was indicated as belonging to the genus , with high similarity to ‘’ LAM7112 (97.9 %), IFO 15555 (97.6 %), LIPI11-2-Ac042 (97.2 %) and LIPI11-2-Ac043 (97.2 %). Phylogenetic analysis of the 16S rRNA gene sequence of strain M4I6 showed that the strain formed a stable subclade with ‘’ LAM7112. The cell wall of the novel isolate contained -diaminopimelic acid and the whole-cell sugars were xylose, glucose and ribose. The predominant menaquinones were MK-9(H), MK-9(H) and MK-9(H). The phospholipid profile comprised phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannosides and an unknown phospholipid. The major fatty acids (>5 %) were anteiso-C, iso-C, 10-methyl-C, C, iso-C and C. Genome sequencing showed a DNA G+C content of 70.9 mol%. However, the low average nucleotide identity value, digital DNA–DNA hybridization and average amino acid identity values demonstrated that strain M4I6 could be readily distinguished from its closest related species. Based on data from this polyphasic study, strain M4I6 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is M4I6 (=DSM 101017=CGMCC 4.7854).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA , Actinoplanes maris sp. nov. , marine sediment and polyphasic taxonomy
Funding
This study was supported by the:
  • China Agriculture Research System of MOF and MARA (Award CARS-21)
    • Principle Award Recipient: You-XingZhao
  • Financial Fund of the Ministry of Agriculture and Rural Affairs, P. R. of China (Award NFZX2021)
    • Principle Award Recipient: You-XingZhao
  • Natural Science Foundation of Hainan Province (Award 821RC643)
    • Principle Award Recipient: Qing-YiXie
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005911
2023-05-30
2025-01-18
Loading full text...

Full text loading...

References

  1. Couch JN. Actinoplanes, a new genus of the Actinomycetales. J Elisha Mitchell Sci Soc 1950; 66:87–92
     [Google Scholar]
  2. Goodfellow M, Stanton LJ, Simpson KE, Minnikin DE. Numerical and chemical classification of actinoplanes and some related actinomycetes. J Gen Microbiol 1990; 136:19–36 [View Article]
     [Google Scholar]
  3. Tamura T, Hatano K. Phylogenetic analysis of the genus Actinoplanes and transfer of Actinoplanes minutisporangius Ruan et al. 1986 and “Actinoplanes aurantiacus” to Cryptosporangium minutisporangium comb. nov. and Cryptosporangium aurantiacum sp. nov. Int J Syst Evol Microbiol 2001; 51:2119–2125 [View Article] [PubMed]
     [Google Scholar]
  4. Zhang Y, Zhang J, Fan L, Pang H, Xin Y et al. Actinoplanes atraurantiacus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2012; 62:2533–2537 [View Article] [PubMed]
     [Google Scholar]
  5. Ma Q, Zhang Q, Jiang X, Kong D, Han X et al. Actinoplanes solisilvae sp. nov., isolated from Birch forest soil. Curr Microbiol 2020; 77:3799–3806 [View Article] [PubMed]
     [Google Scholar]
  6. Song J, Sun X, Luo X, He C, Huang Z et al. Actinoplanes aureus sp. nov., a novel protease-producing actinobacterium isolated from soil. Antonie van Leeuwenhoek 2021; 114:1517–1527 [View Article] [PubMed]
     [Google Scholar]
  7. Qu Z, Bao X-D, Xie Q-Y, Zhao Y-X, Yan B et al. Actinoplanes sediminis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2018; 68:71–75 [View Article] [PubMed]
     [Google Scholar]
  8. Xie Q, Lin H, Li L, Brown R, Goodfellow M et al. Verrucosispora wenchangensis sp. nov., isolated from mangrove soil. Antonie van Leeuwenhoek 2012; 102:1–7 [View Article] [PubMed]
     [Google Scholar]
  9. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int Jf Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  10. Raper KB, Fennell DI. The Genus Aspergillus Baltimore: Williams and Wilkins; 1965 p 686
     [Google Scholar]
  11. Ochi K. Metabolic initiation of differentiation and secondary metabolism by Streptomyces griseus: significance of the stringent response (ppGpp) and GTP content in relation to a factor. J Bacteriol 1987; 169:3608–3616 [View Article] [PubMed]
     [Google Scholar]
  12. Castiglione F, Lazzarini A, Carrano L, Corti E, Ciciliato I et al. Determining the structure and mode of action of microbisporicin, a potent lantibiotic active against multiresistant pathogens. Chem Biol 2008; 15:22–31 [View Article] [PubMed]
     [Google Scholar]
  13. Kelly KL. Inter-Society Color Council-National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  14. Matsumoto A, Takahashi Y, Kudo T, Seino A, Iwai Y et al. Actinoplanes capillaceus sp. nov., a new species of the genus Actinoplanes. Antonie van Leeuwenhoek 2000; 78:107–115
     [Google Scholar]
  15. Gregersen T. Rapid method for distinction of Gram-negative from Gram-positive bacteria. European J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
     [Google Scholar]
  16. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article] [PubMed]
     [Google Scholar]
  17. Arai T. Culture Media for Actinomycetes Tokyo: The Society for Actinomycetes Japan; 1975
     [Google Scholar]
  18. Williams ST, Cross T. Actinomycetes. In Booth C. eds Methods in Microbiology vol 4 London: Academic Press; 1971 pp 295–334
     [Google Scholar]
  19. Tresner HD, Danga F. Hydrogen sulfide production by Streptomyces as a criterion for species differentiation. J Bacteriol 1958; 76:239–244 [View Article] [PubMed]
     [Google Scholar]
  20. Kämpfer P, Steiof M, Dott W. Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 1991; 21:227–251 [View Article] [PubMed]
     [Google Scholar]
  21. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer J. eds Actinomycete Taxonomy (Special Publication No.6) Arlington VA: Society for Industrial Microbiology; 1980 pp 227–291
     [Google Scholar]
  22. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 1980; 188:221–233 [View Article]
     [Google Scholar]
  23. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In Technical Note vol 101 Newark, DE: Microbial ID; 1990
     [Google Scholar]
  24. 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]
  25. Wang C, Xu X-X, Qu Z, Wang H-L, Lin H-P et al. Micromonospora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil. Int J Syst Evol Microbiol 2011; 61:320–324 [View Article] [PubMed]
     [Google Scholar]
  26. Nakajima Y, Kitpreechavanich V, Suzuki K, Kudo T. Microbispora corallina sp. nov., a new species of the genus Microbispora isolated from Thai soil. Int J Syst Bacteriol 1999; 49 Pt 4:1761–1767 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
     [Google Scholar]
  28. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
     [Google Scholar]
  29. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1 [View Article]
     [Google Scholar]
  30. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
  32. 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]
  33. 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]
     [Google Scholar]
  34. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  35. Pospiech A, Neumann B. A versatile quick-prep of genomic DNA from Gram-positive bacteria. Trends Gene 1995; 11:217–218 [View Article]
     [Google Scholar]
  36. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
     [Google Scholar]
  37. 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]
  38. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article]
     [Google Scholar]
  39. 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]
  40. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016; 4e1900v1 [View Article]
     [Google Scholar]
  41. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
     [Google Scholar]
  42. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article]
     [Google Scholar]
  43. Lechevalier MP, De Bievre C, Lechevalier H. Chemotaxonomy of aerobic Actinomycetes: phospholipid composition. Biochem Syst Ecol 1977; 5:249–260 [View Article]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005911
Loading
Actinoplanes maris sp. nov., isolated from marine sediment
Int J Syst Evol Microbiol 73, 005911 (2023); https://doi.org/10.1099/ijsem.0.005911
/content/journal/ijsem/10.1099/ijsem.0.005911
/content/journal/ijsem/10.1099/ijsem.0.005911
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