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Volume 72, Issue 5

sp. nov., isolated from a tropical peat swamp forest soil, and proposal for the reclassification of as a later heterotypic synonym of No Access

Abstract

A polyphasic approach was used to describe strain RB6PN24, a novel actinobacterium isolated from peat swamp forest soil collected from Rayong province, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus and showed the highest sequence similarities to IFO 15206 (98.7 %) and MMS16-CNU292 (98.5 %). Strain RB6PN24 contained major amounts of -diaminopimelic acid, galactose, mannose and ribose in the whole-cell hydrolysates. MK-9(H) and MK-9(H) were the predominant menaquinones of the micro-organism. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unidentified lipid, four unidentified aminolipids and six unidentified phospholipids. Mycolic acids were not present. The major fatty acids were iso-C, iso-C, anteiso-C, iso-C, anteiso-C and C. The draft genome size of strain RB6PN24 was 8.09 Mbp, with 72.1 mol% G+C content and predicted to contain at least 44 biosynthetic gene clusters encoding diverse secondary metabolites. Furthermore, the strain exhibited low average nucleotide identity and digital DNA–DNA hybridization values with MMS16-CNU292 (89.1 %, 42.4 %) and DSM 41654 (79.5 %, 25.5 %). The results of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses revealed that strain RB6PN24 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is RB6PN24 (=TBRC 14818=NBRC 115116). In addition, the comparison of the whole genome sequences and phenotypic features suggested that and belong to the same species. Therefore, it is proposed that is reclassified as a later heterotypic synonym of .

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Keyword(s): actinobacteria , Kitasatospora , peat swamp forest and polyphasic taxonomy
© 2022 The Authors
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2022-05-06
2024-04-24
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References

  1. 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] [PubMed]
     [Google Scholar]
  2. Omura S, Takahashi Y, Iwai Y, Tanaka H. Kitasatosporia, a new genus of the order Actinomycetales . J Antibiot (Tokyo) 1982; 35:1013–1019 [View Article] [PubMed]
     [Google Scholar]
  3. Kämpfer P. Genus I. Kitasatospora corrig. Omura, Takahashi, Iwai and Tanaka 1983, 672VP emend. Zhang, Wang and Ruan 1997, 1053. In Goodfellow M, Kämpfer P, Busse H-J, Trujillo M, Suzuki K. eds Bergey’s Manual of Systematics Bacteriology vol 5 New York: Springer; 2012 pp 1768–1777
     [Google Scholar]
  4. Takahashi Y. Genus Kitasatospora, taxonomic features and diversity of secondary metabolites. J Antibiot (Tokyo) 2017; 70:506–513 [View Article] [PubMed]
     [Google Scholar]
  5. Hayakawa M, Nonomura H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 1987; 65:501–509 [View Article]
     [Google Scholar]
  6. Himaman W, Suksaard P, Mingma R, Matsumoto A, Duangmal K. Cryptosporangium eucalypti sp. nov., an actinomycete isolated from Eucalyptus camaldulensis roots. Int J Syst Evol Microbiol 2017; 67:3077–3082 [View Article] [PubMed]
     [Google Scholar]
  7. Kieser T, Bibb MJ, Buttner MJ, Chater KF, Hopwood DA. Practical Streptomyces Genetics Norwich: John Innes Foundation Norwich; 2000
     [Google Scholar]
  8. Himaman W, Thamchaipenet A, Pathom-Aree W, Duangmal K. Actinomycetes from Eucalyptus and their biological activities for controlling Eucalyptus leaf and shoot blight. Microbiol Res 2016; 188–189:42–52 [View Article] [PubMed]
     [Google Scholar]
  9. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:096412 [View Article] [PubMed]
     [Google Scholar]
  10. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
     [Google Scholar]
  11. 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]
  12. 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]
  13. Tarlachkov SV, Starodumova IP. TaxonDC: calculating the similarity value of the 16S rRNA gene sequences of prokaryotes or ITS regions of fungi. J Bioinf Genom 2017; 3:1–4
     [Google Scholar]
  14. 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]
  15. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
     [Google Scholar]
  16. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  17. 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]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  19. 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]
  20. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article] [PubMed]
     [Google Scholar]
  21. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  22. 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] [PubMed]
     [Google Scholar]
  23. 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] [PubMed]
     [Google Scholar]
  24. 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]
     [Google Scholar]
  25. 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]
  26. Becker B, Lechevalier MP, Lechevalier HA. Chemical composition of cell-wall preparations from strains of various form-genera of aerobic actinomycetes. Appl Microbiol 1965; 13:236–243 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  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. Tomiyasu I. Mycolic acid composition and thermally adaptative changes in Nocardia asteroides . J Bacteriol 1982; 151:828–837 [View Article] [PubMed]
     [Google Scholar]
  30. Uchida K, Kudo T, Suzuki K-I, Nakase T. A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 1999; 45:49–56 [View Article] [PubMed]
     [Google Scholar]
  31. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI Inc: Newark; 1990
  32. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  33. Mundie D. The NBS/ISCC Color System Pittsburgh, PA: Polymath Systems; 1995
     [Google Scholar]
  34. Smith AC, Hussey MA. Gram stain protocols. ASM 2005; 1:14
     [Google Scholar]
  35. Williams S, Davies F, Mayfield C, Khan M. Studies on the ecology of actinomycetes in soil II. The pH requirements of streptomycetes from two acid soils. Soil Biol Biochem 1971; 3:187–195 [View Article]
     [Google Scholar]
  36. Gordon RE, Barnett DA, Handerhan JE, Pang CHN. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
     [Google Scholar]
  37. 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]
  38. Gordon RE, Mihm JM. A comparative study of some strains received as nocardiae. J Bacteriol 1957; 73:15–27 [View Article] [PubMed]
     [Google Scholar]
  39. Küster E, Williams ST. Production of hydrogen sulfide by streptomycetes and methods for its detection. Appl Microbiol 1964; 12:46–52 [View Article]
     [Google Scholar]
  40. Gerhardt P, Murray RGE, Krieg NR, Wood WA. Methods for General and Molecular Bacteriology American Society for Microbiology; 1994
     [Google Scholar]
  41. Duggar BM. Aureomycin: a product of the continuing search for new antibiotics. Ann N Y Acad Sci 1948; 51:177–181 [View Article] [PubMed]
     [Google Scholar]
  42. Virgilio A, Hengeller C. Produzione di Tetraciclina con Streptomyces psammoticus . Farm Ediz Scient 1960; 15:164–174
     [Google Scholar]
  43. Groth I, Schütze B, Boettcher T, Pullen CB, Rodriguez C et al. Kitasatospora putterlickiae sp. nov., isolated from rhizosphere soil, transfer of Streptomyces kifunensis to the genus Kitasatospora as Kitasatospora kifunensis comb. Int J Syst Evol Microbiol 2003; 53:2033–2040 [View Article] [PubMed]
     [Google Scholar]
  44. Sripreechasak P, Matsumoto A, Suwanborirux K, Inahashi Y, Shiomi K et al. Streptomyces siamensis sp. nov., and Streptomyces similanensis sp. nov., isolated from Thai soils. J Antibiot (Tokyo) 2013; 66:633–640 [View Article]
     [Google Scholar]
  45. Nguyen TM, Kim J. Streptomyces gilvifuscus sp. nov., an actinomycete that produces antibacterial compounds isolated from soil. Int J Syst Evol Microbiol 2015; 65:3493–3500 [View Article] [PubMed]
     [Google Scholar]
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Kitasatospora humi sp. nov., isolated from a tropical peat swamp forest soil, and proposal for the reclassification of Kitasatospora psammotica as a later heterotypic synonym of Kitasatospora aureofaciens
Int J Syst Evol Microbiol 72, 005356 (2022); https://doi.org/10.1099/ijsem.0.005356
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