1887

Abstract

A novel actinobacterium, designated strain 1AS2c, was isolated from the wheat rhizosphere collected from the Brazilian biome. A polyphasic approach, including phenotypic characterization and phylogenetic multilocus sequence analysis (MLSA), was used to determine the taxonomic position of this strain. Analysis of the 16S rRNA gene sequence indicated that the novel strain is closely related to NBRC 13026, NBRC 13465 and ASBV-1, sharing a similarity value of 98.2, 98.1 and 97.9 %, respectively. Additionally, MLSA of five housekeeping genes (, , , and ) showed evolutionary distances beyond the 0.007 threshold, as well as low DNA–DNA relatedness between strain 1AS2c and its closest phylogenetic neighbours ( NBRC 13026, NBRC 13465 and ASBV-1: 56, 62.5 and 63.0 %, respectively), indicating a new phylogenetic lineage. The phylogenetic, chemotaxonomic and phenotypic characteristics support the assignment of strain 1AS2c to the genus , representing a novel species. It is concluded that strain 1AS2c (=CMAA 1679=NRRL B-65479=DSM 105299) can be classified as the type strain of a novel species of the genus , for which the name sp. nov. is proposed.

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2019-08-01
2019-12-11
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References

  1. Waksman SA, Henrici AT. The nomenclature and classification of the actinomycetes. J Bacteriol 1943;46:337–341[PubMed]
    [Google Scholar]
  2. Bérdy J. Thoughts and facts about antibiotics: where we are now and where we are heading. J Antibiot 2012;65:385–395 [CrossRef][PubMed]
    [Google Scholar]
  3. Goodfellow M, Fiedler HP. A guide to successful bioprospecting: informed by actinobacterial systematics. Antonie van Leeuwenhoek 2010;98:119–142 [CrossRef][PubMed]
    [Google Scholar]
  4. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002;52:1043–1047 [CrossRef][PubMed]
    [Google Scholar]
  5. Goodfellow M, Kumar Y, Labeda DP, Sembiring L. The Streptomyces violaceusniger clade: a home for Streptomycetes with rugose ornamented spores. Antonie van Leeuwenhoek 2007;92:173–199 [CrossRef][PubMed]
    [Google Scholar]
  6. Guo Y, Zheng W, Rong X, Huang Y. A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. Int J Syst Evol Microbiol 2008;58:149–159 [CrossRef][PubMed]
    [Google Scholar]
  7. Rong X, Huang Y. Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA-DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species. Int J Syst Evol Microbiol 2010;60:696–703 [CrossRef][PubMed]
    [Google Scholar]
  8. Rong X, Huang Y. Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst Appl Microbiol 2012;35:7–18 [CrossRef][PubMed]
    [Google Scholar]
  9. Rong X, Huang Y. Multi-locus sequence analysis: taking prokaryotic systematics to the next level. Methods Microbiol 2014;41:221–251
    [Google Scholar]
  10. Kim BY, Zucchi TD, Fiedler HP, Goodfellow M. Streptomyces cocklensis sp. nov., a dioxamycin-producing actinomycete. Int J Syst Evol Microbiol 2012;62:279–283 [CrossRef][PubMed]
    [Google Scholar]
  11. Kim BY, Zucchi TD, Fiedler HP, Goodfellow M. Streptomyces staurosporininus sp. nov., a staurosporine-producing actinomycete. Int J Syst Evol Microbiol 2012;62:966–970 [CrossRef][PubMed]
    [Google Scholar]
  12. da Silva LJ, Taketani RG, de Melo IS, Goodfellow M, Zucchi TD et al. Streptomyces araujoniae sp. nov.: an actinomycete isolated from a potato tubercle. Antonie van Leeuwenhoek 2013;103:1235–1244 [CrossRef][PubMed]
    [Google Scholar]
  13. Silva FS, Souza DT, Zucchi TD, Pansa CC, De Figueiredo Vasconcellos RL et al. Streptomyces atlanticus sp. nov., a novel actinomycete isolated from marine sponge Aplysina fulva (Pallas, 1766). Antonie van Leeuwenhoek 2016;109:1467–1474 [CrossRef][PubMed]
    [Google Scholar]
  14. Gordon RE, Mihm JM. The type species of the genus Nocardia. J Gen Microbiol 1962;27:1–10 [CrossRef][PubMed]
    [Google Scholar]
  15. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16:313–340 [CrossRef]
    [Google Scholar]
  16. Lee I, Chalita M, Ha SM, Na SI, Yoon SH et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017;67:2053–2057 [CrossRef][PubMed]
    [Google Scholar]
  17. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells and metagenomes. Genome Res 2015;25:1043–1055 [CrossRef][PubMed]
    [Google Scholar]
  18. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  19. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012;62:716–721 [CrossRef][PubMed]
    [Google Scholar]
  20. Rong X, Guo Y, Huang Y. Proposal to reclassify the Streptomyces albidoflavus clade on the basis of multilocus sequence analysis and DNA-DNA hybridization, and taxonomic elucidation of Streptomyces griseus subsp. solvifaciens. Syst Appl Microbiol 2009;32:314–322 [CrossRef][PubMed]
    [Google Scholar]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425 [CrossRef][PubMed]
    [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef][PubMed]
    [Google Scholar]
  23. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20:406–416 [CrossRef]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. Felsenstein J. Phylogenies and the comparative method. Am Nat 1985;125:1–15 [CrossRef]
    [Google Scholar]
  26. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017;110:1281–1286 [CrossRef][PubMed]
    [Google Scholar]
  27. Gonzalez JM, Saiz-Jimenez C. A simple fluorimetric method for the estimation of DNA-DNA relatedness between closely related microorganisms by thermal denaturation temperatures. Extremophiles 2005;9:75–79 [CrossRef][PubMed]
    [Google Scholar]
  28. 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 [CrossRef][PubMed]
    [Google Scholar]
  29. Labeda DP, Rong X, Huang Y, Doroghazi JR, Ju KS et al. Taxonomic evaluation of species in the Streptomyces hirsutus clade using multi-locus sequence analysis and proposals to reclassify several species in this clade. Int J Syst Evol Microbiol 2016;66:2444–2450 [CrossRef][PubMed]
    [Google Scholar]
  30. 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 [CrossRef][PubMed]
    [Google Scholar]
  31. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987;37:463–464 [CrossRef]
    [Google Scholar]
  32. O'Donnell AG, Falconer C, Goodfellow M, Ward AC, Williams E. Biosystematics and diversity amongst novel carboxydotrophic actinomycetes. Antonie van Leeuwenhoek 1993;64:325–340 [CrossRef][PubMed]
    [Google Scholar]
  33. Kämpfer P. Genus I. Streptomyces. In Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K et al. (editors) Bergey’s Manual of Systematic Bacteriology, The Actinobacteria, 2nd ed. New York, NY: Springer; 2012; pp.1455–1462
    [Google Scholar]
  34. Cheng G, Huang Y, Yang H, Liu F. Streptomyces felleus YJ1: potential biocontrol agents against the Sclerotinia stem rot (Sclerotinia sclerotiorum) of oilseed rape. J Agric Sci 2014;6:91–98 [CrossRef]
    [Google Scholar]
  35. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974;28:226–231
    [Google Scholar]
  36. Uchida K, Kudo T, Suzuki KI, 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 [CrossRef][PubMed]
    [Google Scholar]
  37. 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 [CrossRef]
    [Google Scholar]
  38. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, Technical Note 101. Newark, DE: MIDI; 1990
    [Google Scholar]
  39. Gonzalez JM, Saiz-Jimenez C. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 2002;4:770–773[PubMed]
    [Google Scholar]
  40. Labeda DP, Goodfellow M, Brown R, Ward AC, Lanoot B et al. Phylogenetic study of the species within the family Streptomycetaceae. Antonie van Leeuwenhoek 2012;101:73–104 [CrossRef][PubMed]
    [Google Scholar]
  41. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970;20:435–443 [CrossRef]
    [Google Scholar]
  42. Han JH, Cho MH, Kim SB. Ribosomal and protein coding gene based multigene phylogeny on the family Streptomycetaceae. Syst Appl Microbiol 2012;35:1–6 [CrossRef][PubMed]
    [Google Scholar]
  43. Maciejewska M, Adam D, Martinet L, Naômé A, Całusińska M et al. A phenotypic and genotypic analysis of the antimicrobial potential of cultivable streptomyces isolated from cave moonmilk deposits. Front Microbiol 2016;7:1455 [CrossRef][PubMed]
    [Google Scholar]
  44. Labeda DP, Doroghazi JR, Ju KS, Metcalf WW. Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov. Int J Syst Evol Microbiol 2014;64:894–900 [CrossRef][PubMed]
    [Google Scholar]
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