1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 3

sp. nov., isolated from soil on Iheya Island, Japan No Access

Abstract

A novel actinomycete, designated strain OK19-0408, was isolated from soil collected on Iheya island, Okinawa prefecture, Japan. Using the polyphasic taxonomic approach, comparing 16S rRNA gene sequences, the new isolate was found to be most closely related to JCM12675 (98.71 %). Phylogenetic analyses using 16S rRNA sequences indicated that strain OK19-0408 was clustered with JCM15587. However, digital DNA–DNA hybridization analyses indicated a low relatedness, in the range of 33.9–34.7 %, between strain OK19-0408 and these closely related strains. Strain OK19-0408 contained -diaminopimelic acid and whole-cell sugars consisting of arabinose and galactose. The acyl type of the peptidoglycan was acetyl and mycolic acids were absent in strain OK19-0408. The major menaquinone was MK-9(H) and hydroxy-phosphatidylethanolamine was detected as the predominant phospholipid. The predominant cellular fatty acid was iso-C. The DNA G+C content of the genomic DNA was 71.5 mol%. Based on the polyphasic approach, strain OK19-0408 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain of the type species is OK19-0408 (=NBRC115671=TBRC16040).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Actinomycetes , Amycolatopsis iheyensis sp. nov and Family Pseudonocardiaceae
© 2023 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005757
2023-03-23
2024-04-27
Loading full text...

Full text loading...

References

  1. Lechevalier MP, Prauser H, Labeda DP, Ruan J-S. Two new genera of nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int JSyst Bacteriol 1986; 36:29–37 [View Article]
     [Google Scholar]
  2. Lee SD. Amycolatopsis ultiminotia sp. nov., isolated from rhizosphere soil, and emended description of the genus Amycolatopsis. Int J Syst Evol Microbiol 2009; 59:1401–1404 [View Article]
     [Google Scholar]
  3. Tang S-K, Wang Y, Guan T-W, Lee J-C, Kim C-J et al. Amycolatopsis halophila sp. nov., a halophilic actinomycete isolated from a salt lake. Int J Syst Evol Microbiol 2010; 60:1073–1078 [View Article]
     [Google Scholar]
  4. Gillis M, Vandamme P, DeVos P, Swings J, Kersters K. Polyphasic Taxonomy. In Brenner DJ, Krieg NR, Staley JT, Garrity GM. eds Bergey’s Manual® of Systematic Bacteriology, 2nd edn. Boston, MA: Springer; 2005 [View Article]
     [Google Scholar]
  5. 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; 9:2007 [View Article]
     [Google Scholar]
  6. Tedsree N, Tanasupawat S, Sritularak B, Kuncharoen N, Likhitwitayawuid K et al. Amycolatopsis dendrobii sp. nov., an endophytic actinomycetes isolated from Dendrobium heterocarpum Lindl. Int J Syst Evol Microbiol 2019; 69:715–720
     [Google Scholar]
  7. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
     [Google Scholar]
  8. Embley MT, Smida J, Stackebrandt E. The phylogeny of mycolate-less wall chemotype IV actinomycetes and description of Pseudonocardiaceae fam. nov. Syst Appl Microbiol 1988; 11:44–52 [View Article]
     [Google Scholar]
  9. Tan GYA, Goodfellow M. Genus V. Amycolatopsis Lechevalier, Prauser, Labeda and Ruan 1986, 34VP emend. Lee 2009,1403. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki K. eds Bergey’s of Systematic Bacteriology, 2nd edn. vol 5 New York: Springer; 2012 pp 1334–1358
     [Google Scholar]
  10. Camas M, Sahin N, Sazak A, Spröer C, Klenk H-P. Amycolatopsis magusensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2013; 63:1254–1260 [View Article]
     [Google Scholar]
  11. Tatar D, Sazak A, Guven K, Cetin D, Sahin N. Amycolatopsis cihanbeyliensis sp. nov., a halotolerant actinomycete isolated from a salt mine. Int J Syst Evol Microbiol 2013; 63:3739–3743 [View Article]
     [Google Scholar]
  12. Klykleung N, Tanasupawat S, Pittayakhajonwut P, Ohkuma M, Kudo T. Amycolatopsis stemonae sp. nov., isolated from a Thai medicinal plant. Int J Syst Evol Microbiol 2015; 65:3894–3899 [View Article]
     [Google Scholar]
  13. Zhang G, Wang L, Li J, Zhou Y. Amycolatopsis albispora sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2016; 66:3860–3864 [View Article]
     [Google Scholar]
  14. Bian J, Li Y, Wang J, Song F-H, Liu M et al. Amycolatopsis marina sp. nov., an actinomycete isolated from an ocean sediment. Int J Syst Evol Microbiol 2009; 59:477–481 [View Article]
     [Google Scholar]
  15. Zhang G, Wang L, Li J, Zhou Y. Amycolatopsis albispora sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2016; 66:3860–3864 [View Article]
     [Google Scholar]
  16. Dasari VRRK, Muthyala MKK, Nikku MY, Donthireddy SRR. Novel pyridinium compound from marine actinomycete, Amycolatopsis alba var. nov. DVR D4 showing antimicrobial and cytotoxic activities in vitro. Microbiol Res 2012; 167:346–351 [View Article]
     [Google Scholar]
  17. Song Z, Xu T, Wang J, Hou Y, Liu C et al. Secondary metabolites of the genus Amycolatopsis: structures, bioactivities and biosynthesis. Molecules 2021; 26:1884 [View Article]
     [Google Scholar]
  18. Sensi P, Greco AM, Ballotta R. Rifomycin. I. isolation and properties of rifomycin B and rifomycin complex. Antibiot Annu 1959; 7:262–270
     [Google Scholar]
  19. Barna JC, Williams DH. The structure and mode of action of glycopeptide antibiotics of the vancomycin group. Annu Rev Microbiol 1984; 38:339–357 [View Article]
     [Google Scholar]
  20. Saito H, Miura KI. Preparation transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 1963; 72:619–629 [View Article]
     [Google Scholar]
  21. Matsumoto A, Yamada M, Omura 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]
     [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]
     [Google Scholar]
  23. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  24. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  26. 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]
     [Google Scholar]
  27. 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]
     [Google Scholar]
  28. Matsumoto A, Yamada M, Omura 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]
     [Google Scholar]
  29. Wink JM, Kroppenstedt RM, Ganguli BN, Nadkarni SR, Schumann P et al. Three new antibiotic producing species of the genus Amycolatopsis, Amycolatopsis balhimycina sp. nov., A. tolypomycina sp. nov., A. vancoresmycina sp. nov., and description of Amycolatopsis keratiniphila subsp. keratiniphila subsp. nov. and A. keratiniphila subsp. nogabecina subsp. nov. Syst Appl Microbiol 2003; 26:38–46 [View Article]
     [Google Scholar]
  30. Tan GYA, Robinson S, Lacey E, Goodfellow M. Amycolatopsis australiensis sp. nov., an actinomycete isolated from arid soils. Int J Syst Evol Microbiol 2006; 56:2297–2301 [View Article]
     [Google Scholar]
  31. 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]
  32. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article]
     [Google Scholar]
  33. Tomiyasu I. Mycolic acid composition and thermally adaptative changes in Nocardia asteroides. J Bacteriol 1982; 151:828–837 [View Article]
     [Google Scholar]
  34. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article]
     [Google Scholar]
  35. 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]
  36. Sasser M. Technical Note 101: Identificationof bacteria by gas chromatography of cellular fatty acids Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  37. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int JSyst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  38. Jacobson E, Grauville WC, Fogs CE. Colour Harmony Manual, 4th edn. Container Corporation of America; 1958
     [Google Scholar]
  39. Chaiya L, Matsumoto A, Wink J, Inahashi Y, Risdian C et al. Amycolatopsis eburnea sp. nov., an actinomycete associated with arbuscular mycorrhizal fungal spores. Int J Syst Evol Microbiol 2019; 69:3603–3608 [View Article]
     [Google Scholar]
  40. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL. In Williams ST, Sharpe ME, Holt JG. eds Bergey’s Manual of Systematic Bacteriology vol 4 Williams & Wilkins: Baltimore; 1989 pp 2452–2492
     [Google Scholar]
  41. Gordon RE, Barnett DA, Handerhan JE, Pang C-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  42. Mccarthy AJ, Cross T. A taxonomic study of Thermomonospora and other monosporic actinomycetes. Microbiology 1984; 130:5–25 [View Article]
     [Google Scholar]
  43. Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
     [Google Scholar]
  44. 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]
     [Google Scholar]
  45. 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]
     [Google Scholar]
  46. 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]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005757
Loading
Amycolatopsis iheyensis sp. nov., isolated from soil on Iheya Island, Japan
Int J Syst Evol Microbiol 73, 005757 (2023); https://doi.org/10.1099/ijsem.0.005757
/content/journal/ijsem/10.1099/ijsem.0.005757
/content/journal/ijsem/10.1099/ijsem.0.005757
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