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Volume 73, Issue 5

sp. nov., an actinobacterium isolated from hot spring soil No Access

Abstract

An actinobacterium strain, PPF5-17, was isolated from hot spring soil collected from Chiang Rai province, Thailand. The strain exhibited morphological and chemotaxonomic properties similar to those of members of the genus . Colonies of PPF5-17 were strong pinkish red and turned black after sporulation in ISP 2 agar medium. Cells formed single spores directly on the substrate mycelium. Growth was observed from 15 to 45 °C and at pH 5–8. Maximum NaCl concentration for growth was 3 % (w/v). PPF5-17 was found to have -diaminopimelic acid, xylose, mannose and glucose in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannosides were observed as the membrane phospholipids. MK-10(H), MK-9(H), MK-10(H) and MK-9(H) were the major menaquinones. The predominant cellular fatty acids were iso-C, iso-C, anteiso-C and iso-C. PPF5-17 shared the highest 16S rRNA gene sequence similarity with LMG 30467 (99.3 %). A genome-based taxonomic study revealed that PPF5-17 was closely related to DSM 44815 in the phylogenomic tree with an average nucleotide identity by (ANIb) of 87.7 % and a digital DNA–DNA hybridization (dDDH) value of, 36.1 % which were below the threshold values for delineation of a novel species. Moreover, PPF5-17 could be distinguished from its closest neighbours, LMG 30467 and DSM 44815, with respect to a broad range of phenotypic properties. Thus, PPF5-17 represents a novel species, for which the name sp. nov. is proposed. The type strain is PPF5-17 (= TBRC 8478 = NBRC 113441).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , Actinomycete , hot spring soil , Micromonospora and whole-genome sequence analysis
Funding
This study was supported by the:
  • The National Science, Research and Innovation Fund (NSRF) (Award RE-KRIS/FF65/23)
    • Principle Award Recipient: ChittiThawai
© 2023 The Authors
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2024-05-01
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References

  1. Genilloud O. Genus Micromonospora. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki K et al. eds Bergey’s Manual of Systematic BacteriologyThe Actinobacteria vol 2 vol 5 New York: Springer; 2012 pp 1039–1057
     [Google Scholar]
  2. Ørskov J. Investigations into the Morphology of the Ray Fungi. Copenhagen: Levin and Munksgaard; 1923
  3. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article]
     [Google Scholar]
  4. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci 2009; 106:19126–19131 [View Article]
     [Google Scholar]
  5. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article]
     [Google Scholar]
  6. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
     [Google Scholar]
  7. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article]
     [Google Scholar]
  8. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article] [PubMed]
     [Google Scholar]
  9. Teeling H, Meyerdierks A, Bauer M, Amann R, Glöckner FO. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol 2004; 6:938–947 [View Article] [PubMed]
     [Google Scholar]
  10. 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]
  11. Li L, Zhu HR, Xu QH, Lin HW, Lu YH. 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]
     [Google Scholar]
  12. Kuncharoen N, Kudo T, Yuki M, Okuma M, Pittayakhajonwut P et al. Micromonospora radicis sp. nov., isolated from roots of Azadirachta indica var. siamensis Valenton, and reclassification of Jishengella zingiberis as Micromonospora zingiberis comb. nov. Int J Syst Evol Microbiol 2019; 69:2884–2891 [View Article]
     [Google Scholar]
  13. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  14. Thawai C, Tanasupawat S, Kudo T. Micromonospora caldifontis sp. nov., isolated from hot spring soil. Int J Syst Evol Microbiol 2019; 69:1336–1342 [View Article] [PubMed]
     [Google Scholar]
  15. Zhang J, Zhang L. Improvement of an isolation medium for Actinomycetes. MAS 2011; 5:124–127 [View Article]
     [Google Scholar]
  16. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  17. Tamaoka J. Determination of DNA Base Composition. In Goodfellow M, O’Donnell AG. eds Chemical Methods in Prokaryotic Systematics Chichester: John Wiley and Sons; 1994 pp 463–470
     [Google Scholar]
  18. 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]
  19. 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]
  20. 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]
  21. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
     [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  23. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
     [Google Scholar]
  24. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  25. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article]
     [Google Scholar]
  26. 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]
  27. 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]
     [Google Scholar]
  28. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Magazine 2014; 9:111–118 [View Article]
     [Google Scholar]
  29. 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]
  30. 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]
  31. The UniProt Consortium UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res 2019; 47:D506–D515
     [Google Scholar]
  32. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article]
     [Google Scholar]
  33. Awakawa T, Fujita N, Hayakawa M, Ohnishi Y, Horinouchi S. Characterization of the biosynthesis gene cluster for alkyl-O-dihydrogeranyl-methoxyhydroquinones in Actinoplanes missouriensis. Chembiochem 2011; 12:439–448 [View Article]
     [Google Scholar]
  34. Otsuka M, Ichinose K, Fujii I, Ebizuka Y. Cloning, sequencing, and functional analysis of an iterative type I polyketide synthase gene cluster for biosynthesis of the antitumor chlorinated polyenone neocarzilin in “Streptomyces carzinostaticus.”. Antimicrob Agents Chemother 2004; 48:3468–3476 [View Article] [PubMed]
     [Google Scholar]
  35. Tsakos M, Clement LL, Schaffert ES, Olsen FN, Rupiani S et al. Total synthesis and biological evaluation of Rakicidin A and discovery of a simplified bioactive analogue. Angew Chem Int Ed Engl 2016; 55:1030–1035 [View Article]
     [Google Scholar]
  36. Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database 2020; 2020:baaa062 [View Article]
     [Google Scholar]
  37. Kelly KL. Inter-Society Color Council-National Bureau of Standard Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  38. 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]
  39. Arai T. Culture media for actinomycetes. Tokyo: The Society for Actinomycetes Japan; 1975 pp 1–131
  40. Williams ST, Cross T. Actinomycetes. In Booth C. eds Methods in Microbiology vol 4 London: Academic Press;1971; pp 295–334
     [Google Scholar]
  41. 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]
  42. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  43. Uchida K, Aida K. An improved method for the glycolate test for simple identification of the acyl type of bacterial cell walls. J Gen Appl Microbiol 1984; 30:131–134 [View Article]
     [Google Scholar]
  44. 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]
  45. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  46. 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]
     [Google Scholar]
  47. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark: Microbial ID, Inc; 1990
  48. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  49. Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M. Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatog A 1980; 188:221–233 [View Article]
     [Google Scholar]
  50. Lechevalier MP, Lechevalier HA. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
     [Google Scholar]
  51. Lechevalier MP, De Bievre C, Lechevalier H. Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 1977; 5:249–260 [View Article]
     [Google Scholar]
  52. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. eds Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 173–199
     [Google Scholar]
  53. 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]
     [Google Scholar]
  54. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
     [Google Scholar]
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Micromonospora solifontis sp. nov., an actinobacterium isolated from hot spring soil
Int J Syst Evol Microbiol 73, 005819 (2023); https://doi.org/10.1099/ijsem.0.005819
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