1887

Abstract

During a bioprospection of bacteria with antimicrobial activity, the actinomycete strain A38 was isolated from a sediment sample of the Carpintero river located in the Gran Piedra Mountains, Santiago de Cuba province (Cuba). This strain was identified as a member of the genus by means of a polyphasic taxonomy study. Strain A38 was an aerobic Gram-positive filamentous bacterium that produced single spores in a well-developed vegetative mycelium. An aerial mycelium was absent. The cell wall contained -diaminopimelic acid and the whole-cell sugars were glucose, mannose, ribose and xylose. The major cellular fatty acids were isoC, 10 methyl C, anteiso-C and iso-C. The predominant menaquinones were MK-10(H) and MK-10(H6). Phylogenetic analysis of 16S rRNA gene sequences revealed that this strain was closely related to DSM 45142 (99.5 %), DSM 43903 (99.4 %), DSM 45555 (99.4 %), DSM 45782 (99.3 %), DSM 45794 (99.3 %), DSM 43813 (99.2 %) and DSM 45246 (99.2 %). The results of OrthoANIu analysis showed the highest similarity to DSM 43026 (96.4 %). However, the 16S rRNA and gene sequence-based phylogeny and phenotypic characteristics provided support to distinguish strain A38 as a novel species. On the basis of the results presented here, we propose to classify strain A38 (=LMG 30467=CECT 30034) as the type strain of the novel species sp. nov.

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2020-11-11
2021-10-25
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References

  1. Ørskov J. Investigations into the Morphology of the Ray Fungi Copenhagen: Levin and Munksgaard; 1923
    [Google Scholar]
  2. Gao R, Liu C, Zhao J, Jia F, Yu C et al. Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora . Antonie van Leeuwenhoek 2014; 105:307–315 [View Article][PubMed]
    [Google Scholar]
  3. Genilloud O. Family I. Micromonosporaceae Krasil’nikov 1938, 272AL emend. Zhi Li and Stackebrandt 2009, 599. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd edn, vol. 5, The Actinobacteria, Part B New York: Springer; 2012a pp 1035–1038
    [Google Scholar]
  4. Genilloud O. Order XI. Micromonosporales ord. nov. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd edn, vol. 5, The Actinobacteria, Part B New York: Springer; 2012b p 1035
    [Google Scholar]
  5. Genilloud O. Genus I. Micromonospora Ørskov 1923, 156AL p.1039-1057. In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd edn, vol. 5, The Actinobacteria, Part B New York: Springer; 2012c pp 1039–1057
    [Google Scholar]
  6. Anandan R, Dharumadurai D, Manogaran GP. An introduction to Actinobacteria. In Dhanasekaran D, Jiang Y. (editors) Actinobacteria: Basics and Biotechnological Applications Intech: Rijeka; 2016 pp 3–37
    [Google Scholar]
  7. Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C et al. Taxonomy, physiology, and natural products of actinobacteria. Microbiol Mol Biol Rev 2016; 80:1–43 [View Article][PubMed]
    [Google Scholar]
  8. Lee H-J, Whang K-S. Micromonospora fulva sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:1746–1751 [View Article][PubMed]
    [Google Scholar]
  9. Phongsopitanun W, Kudo T, Ohkuma M, Pittayakhajonwut P, Suwanborirux K et al. Micromonospora sediminis sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2016; 66:3235–3240 [View Article][PubMed]
    [Google Scholar]
  10. 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]
    [Google Scholar]
  11. Kaewkla O, Thamchaipinet A, Franco CMM. Micromonospora terminaliae sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of the medicinal plant Terminalia mucronata . Int J Syst Evol Microbiol 2017; 67:225–230 [View Article][PubMed]
    [Google Scholar]
  12. Carro L, Riesco R, Spröer C, Trujillo ME. Micromonospora ureilytica sp. nov., Micromonospora noduli sp. nov. and Micromonospora vinacea sp. nov., isolated from Pisum sativum nodules. Int J Syst Evol Microbiol 2016; 66:3509–3514 [View Article][PubMed]
    [Google Scholar]
  13. Zhao S, Liu C, Zheng W, Ma Z, Cao T et al. Micromonospora parathelypteridis sp. nov., an endophytic actinomycete with antifungal activity isolated from the root of Parathelypteris beddomei (Bak.) Ching. Int J Syst Evol Microbiol 2017; 67:268–274 [View Article][PubMed]
    [Google Scholar]
  14. Jia F, Liu C, Zhou S, Li J, Shen Y et al. Micromonospora vulcania sp. nov., isolated from volcanic sediment. Antonie van Leeuwenhoek 2015; 108:1383–1390 [View Article][PubMed]
    [Google Scholar]
  15. Kasai H, Tamura T, Harayama S. Intrageneric relationships among Micromonospora species deduced from gyrB-based phylogeny and DNA relatedness. Int J Syst Evol Microbiol 2000; 50 Pt 1:127–134 [View Article][PubMed]
    [Google Scholar]
  16. 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][PubMed]
    [Google Scholar]
  17. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  18. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  19. Snauwaert I, Papalexandratou Z, De Vuyst L, Vandamme P. Characterization of strains of Weissella fabalis sp. nov. and Fructobacillus tropaeoli from spontaneous cocoa bean fermentations. Int J Syst Evol Microbiol 2013; 63:1709–1716 [View Article][PubMed]
    [Google Scholar]
  20. 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]
  21. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  22. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article][PubMed]
    [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][PubMed]
    [Google Scholar]
  24. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 2004; 101:11030–11035 p. [View Article][PubMed]
    [Google Scholar]
  25. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
    [Google Scholar]
  26. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  28. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  29. le Roes M, Goodwin CM, Meyers PR. Gordonia lacunae sp. nov., isolated from an estuary. Syst Appl Microbiol 2008; 31:17–23 [View Article][PubMed]
    [Google Scholar]
  30. Kirby BM, Meyers PR. Micromonospora tulbaghiae sp. nov., isolated from the leaves of wild garlic, Tulbaghia violacea . Int J Syst Evol Microbiol 2010; 60:1328–1333 [View Article][PubMed]
    [Google Scholar]
  31. Everest GJ, Meyers PR. The use of gyrB sequence analysis in the phylogeny of the genus Amycolatopsis . Antonie van Leeuwenhoek 2009; 95:1–11 [View Article][PubMed]
    [Google Scholar]
  32. Everest GJ, Meyers PR. Micromonospora equina sp. nov., isolated from soil from a racecourse. Int J Syst Evol Microbiol 2013; 63:879–885 [View Article][PubMed]
    [Google Scholar]
  33. 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][PubMed]
    [Google Scholar]
  34. 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]
    [Google Scholar]
  35. 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][PubMed]
    [Google Scholar]
  36. Riesco R, Carro L, Román-Ponce B, Prieto C, Blom J et al. Defining the species Micromonospora saelicesensis and Micromonospora noduli under the framework of genomics. Front Microbiol 2018; 9:1360 [View Article][PubMed]
    [Google Scholar]
  37. Kroppenstedt RM, Mayilraj S, Wink JM, Kallow W, Schumann P et al. Eight new species of the genus Micromonospora, Micromonospora citrea sp. nov., Micromonospora echinaurantiaca sp. nov., Micromonospora echinofusca sp. nov. Micromonospora fulviviridis sp. nov., Micromonospora inyonensis sp. nov., Micromonospora peucetia sp. nov., Micromonospora sagamiensis sp. nov., and Micromonospora viridifaciens sp. nov. Syst Appl Microbiol 2005; 28:328–339 [View Article][PubMed]
    [Google Scholar]
  38. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  39. Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T et al. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 2014; 42:D581–D591 [View Article][PubMed]
    [Google Scholar]
  40. Arai T. Culture Media for Actinomycetes Tokyo: The Society for Actinomycetes, Japan; 1975
    [Google Scholar]
  41. 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]
  42. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article][PubMed]
    [Google Scholar]
  43. Schumann P. Peptidoglycan structure. Meth Microbiol 2011; 38:101–129
    [Google Scholar]
  44. 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]
  45. Groth I, Schumann P, Weiss N, Martin K, Rainey FA. Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 1996; 46:234–239 [View Article][PubMed]
    [Google Scholar]
  46. 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]
  47. Miller L, Berger T. Bacterial identification by gas chromatography of whole-cell fatty acids. Hewlett Packard Application Note 1985 pp 228–241
    [Google Scholar]
  48. Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME et al. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci Rep 2018; 8:525 [View Article][PubMed]
    [Google Scholar]
  49. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article][PubMed]
    [Google Scholar]
  50. 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]
  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]
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