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Volume 70, Issue 5

sp. nov., a new species of the genus isolated from deep-sea sediment in Japan Free

Abstract

A novel marine actinomycete, designated strain KJ-029, was isolated from a marine sediment sample (water depth of 226 m) in Kagoshima, Japan. 16S rRNA gene sequence analysis revealed that the new isolate was most closely related to LHW 63014 (99.3 % similarity). Phylogenetic analyses of the genus based on 16S rRNA gene sequences showed that strain KJ-029 was clustered with LHW 63014 and 202201. However, digital DNA–DNA hybridization analyses presented low levels of relatedness in the range of 24.8–32.9 % between strain KJ-029 and the above closely related strains. The novel strain contained -diaminopimelic acid and 3-OH-diaminopimelic acid, -glutamic acid, glycine and -alanine in the cell-wall peptidoglycan. The acyl type of the peptidoglycan was glycolyl and mycolic acids were absent. The major menaquinone was MK-9(H). The whole-cell sugars consisted of glucose, mannose, xylose and ribose. Phosphatidylethanolamine was detected as the major phospholipid and corresponded to phospholipid type II. The predominant cellular fatty acid was iso-C. The DNA G+C content of the genomic DNA was 71.5 mol%. Based on the present polyphasic study, strain KJ-029 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is KJ-029 (=NBRC 113519=TBRC 9233).

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): deep-sea sediment and Micromonospora pelagivivens sp.nov
Funding
This study was supported by the:
  • Institute for Fermentation, Osaka
    • Principle Award Recipient: Bungonsiri Intra
© 2020 The Authors

Erratum

An erratum has been published for this content:
Corrigendum: sp. nov., a new species of the genus isolated from deep-sea sediment in Japan
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2020-03-30
2024-05-02
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References

  1. Kamjam M, Sivalingam P, Deng Z, Hong K. Deep sea actinomycetes and their secondary metabolites. Front Microbiol 2017; 8:760–768 [View Article][PubMed][PubMed]
     [Google Scholar]
  2. Zhang G, Li J, Zhu T, Gu Q, Li D. Advanced tools in marine natural drug discovery. Curr Opin Biotechnol 2016; 42:13–23 [View Article][PubMed][PubMed]
     [Google Scholar]
  3. Xi L, Ruan J, Huang Y. Diversity and biosynthetic potential of culturable actinomycetes associated with marine sponges in the China seas. Int J Mol Sci 2012; 13:5917–5932 [View Article][PubMed][PubMed]
     [Google Scholar]
  4. Veyisoglu A, Carro L, Cetin D, Guven K, Spröer C et al. Micromonospora profundi sp. nov., isolated from deep marine sediment. Int J Syst Evol Microbiol 2016; 66:4735–4743 [View Article][PubMed][PubMed]
     [Google Scholar]
  5. Mincer TJ, Jensen PR, Kauffman CA, Fenical W. Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments. Appl Environ Microbiol 2002; 68:5005–5011 [View Article][PubMed][PubMed]
     [Google Scholar]
  6. Krasil’nikov NA. Ray Fungi and Related Organisms–Actinomycetales Moscow: Akademii Nauk SSSR (in Russian); 1938
     [Google Scholar]
  7. 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]
  8. Koch C, Kroppenstedt RM, Rainey FA, Stackebrandt E. 16S ribosomal DNA analysis of the genera Micromonospora, Actinoplanes, Catellatospora, Catenuloplanes, Couchioplanes, Dactylosporangium, and Pilimelia and emendation of the family Micromonosporaceae . Int J Syst Bacteriol 1996; 46:765–768 [View Article][PubMed][PubMed]
     [Google Scholar]
  9. Stackebrandt E, Rainey FA, Ward-Rainey NL. Proposal for a new Hierarchic classification system, actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 [View Article]
     [Google Scholar]
  10. Zhi X-Y, Li W-J, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009; 59:589–608 [View Article][PubMed][PubMed]
     [Google Scholar]
  11. Genilloud O. Bergey’s manual of systematic bacteriology. In Goodfellow M. editor The Actinobacteria, Part B 5, 2nd ed. Springer; 2012 pp 1035–1038
     [Google Scholar]
  12. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018; 9:22 [View Article]
     [Google Scholar]
  13. Li L, Zhu H-R, Xu Q-H, Lin H-W, Lu Y-H. Micromonospora craniellae sp. nov., isolated from a marine sponge, and reclassification of Jishengella endophytica as Micromonospora endophytica comb. nov. Int J Syst Evol Microbiol 2019; 69:715–720 [View Article][PubMed][PubMed]
     [Google Scholar]
  14. Trujillo ME, Hong K, Genilloud O. The family Micromonosporaceae . In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F. (editors) The Prokaryotes, 4th ed. Heidelberg: Springer Berlin; 2014 pp 499–570
     [Google Scholar]
  15. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  16. Jacobson E, Grauville WC, Fogs CE. Colour Harmony Manual, 4th ed. IL: Container Corporation of America; 1958
     [Google Scholar]
  17. Intra B, Matsumoto A, Inahashi Y, Omura S, Takahashi Y et al. Actinokineospora bangkokensis sp. nov., isolated from rhizospheric soil. Int J Syst Evol Microbiol 2013; 63:2655–2660 [View Article][PubMed][PubMed]
     [Google Scholar]
  18. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL. In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology 4 Baltimore: Williams & Wilkins; 1989 pp 2452–2492
     [Google Scholar]
  19. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  20. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [View Article][PubMed][PubMed]
     [Google Scholar]
  21. Také A, Nakashima T, Inahashi Y, Shiomi K, Takahashi Y et al. Analyses of the cell-wall peptidoglycan structures in three genera Micromonospora, Catenuloplanes, and Couchioplanes belonging to the family Micromonosporaceae by derivatization with FDLA and PMP using LC/MS. J Gen Appl Microbiol 2016; 62:199–205 [View Article][PubMed][PubMed]
     [Google Scholar]
  22. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  23. Nozawa Y, Sakai N, Arai K, Kawasaki Y, Harada K-ichi. Reliable and sensitive analysis of amino acids in the peptidoglycan of actinomycetes using the advanced Marfey's method. J Microbiol Methods 2007; 70:306–311 [View Article][PubMed][PubMed]
     [Google Scholar]
  24. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article][PubMed][PubMed]
     [Google Scholar]
  25. Uchida K, Aida KÔ. Acyl type of bacterial cell wall: its simple identification by colorimetric method. J Gen Appl Microbiol 1977; 23:249–260 [View Article]
     [Google Scholar]
  26. Tomiyasu I. Mycolic acid composition and thermally adaptative changes in Nocardia asteroides . J Bacteriol 1982; 151:828–837 [View Article][PubMed][PubMed]
     [Google Scholar]
  27. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed][PubMed]
     [Google Scholar]
  28. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
     [Google Scholar]
  29. Lechevalier MP, De Biévre C, Lechevalier H. Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 1977; 5:249–260 [View Article]
     [Google Scholar]
  30. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press;; 1985. pp 173–199
     [Google Scholar]
  31. Saito H, Miura KI. Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963; 72:619–629 [View Article][PubMed][PubMed]
     [Google Scholar]
  32. Lee I, Ouk Kim Y, Park S-C, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed][PubMed]
     [Google Scholar]
  33. 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; 14:60–78 [View Article][PubMed][PubMed]
     [Google Scholar]
  34. 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][PubMed]
     [Google Scholar]
  35. Také A, Matsumoto A, Ōmura S, Takahashi Y. Streptomyces lactacystinicus sp. nov. and Streptomyces cyslabdanicus sp. nov., producing lactacystin and cyslabdan, respectively. J Antibiot 2015; 68:322–327 [View Article][PubMed][PubMed]
     [Google Scholar]
  36. Takahashi Y, Matsumoto A, Seino A, Ueno J, Iwai Y et al. Streptomyces avermectinius sp. nov., an avermectin-producing strain. Int J Syst Evol Microbiol 2002; 52:2163–2168 [View Article][PubMed][PubMed]
     [Google Scholar]
  37. Matsumoto A, Yamada M, Ōmura S, Takahashi Y. Microterricola viridarii gen. nov., sp. nov., a new member of the family Microbacteriaceae . Int J Syst Evol Microbiol 2008; 58:1019–1023 [View Article][PubMed][PubMed]
     [Google Scholar]
  38. 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][PubMed]
     [Google Scholar]
  39. 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][PubMed]
     [Google Scholar]
  40. 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][PubMed]
     [Google Scholar]
  41. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  42. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed][PubMed]
     [Google Scholar]
  43. 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][PubMed]
     [Google Scholar]
  44. 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][PubMed]
     [Google Scholar]
  45. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed][PubMed]
     [Google Scholar]
  46. Li L, Zhu H, Xu Q, Lin H, Lu Y. Micromonospora craniellae sp. nov., isolated from a marine sponge, and reclassification of Jishengella endophytica as Micromonospora endophytica comb. nov. Int J Syst Evol Microbiol 2019
     [Google Scholar]
  47. Xie Q-Y, Wang C, Wang R, Qu Z, Lin H-P et al. Jishengella endophytica gen. nov., sp. nov., a new member of the family Micromonosporaceae . Int J Syst Evol Microbiol 2011; 61:1153–1159 [View Article][PubMed][PubMed]
     [Google Scholar]
  48. Kawamoto I, Yamamoto M, Nara T. Micromonospora olivasterospora sp. nov. Int J Syst Evol Bacteriol 1983;33:107–112..
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Micromonospora pelagivivens sp. nov., a new species of the genus Micromonospora isolated from deep-sea sediment in Japan
Int J Syst Evol Microbiol 70, 3069 (2020); https://doi.org/10.1099/ijsem.0.004136
/content/journal/ijsem/10.1099/ijsem.0.004136
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