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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 67, Issue 12

sp. nov., a proteolytic streptomycete isolated from soil under cerrado (savanna) vegetation cover Free

Abstract

A novel streptomycete, strain 594, isolated from Brazilian soil collected under cerrado (savanna) vegetation cover is described. Strain 594 produced thermophilic chitinolytic proteases in assays containing feather meal and corn steep liquor as sole sources of carbon and nitrogen. The strain produced white to grey aerial mycelium and spiral chains of spiny-surfaced spores on the aerial mycelium and did not produce diffusible pigments. The -isomer of diaminopimelic acid was present in the cell wall and menaquinones were predominantly MK-9(H6) (52 %) and MK-9(H8) (30 %) with 6 % MK-9(H4) and slightly less than 1 % MK-9(H2). Polar lipids present were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown phospholipid. The major fatty acids were anteiso-C, anteiso-C, anteiso-C and anteiso-C. The G+C content of the genomic DNA was 70.4 mol%. Phylogenetic analysis of the nearly complete 16S rRNA gene sequence indicated that it differed from described species. Multilocus sequence analysis (MLSA) using five housekeeping genes (, , , and ) comparing type strains showed that the MLSA distance of strain 594 to the most closely related species was greater than the 0.007 threshold. The DNA–DNA relatedness between the genome sequence of strain 594 and that of the phylogenetically nearest species was well below the species level recommendation. There was thus multiple evidence justifying the description of this strain as representing a novel species, for which the name sp. nov. is proposed. The type strain is 594 (=IMPPG 594=DSM 41949=NRRL B-24891).

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Keyword(s): DDH , genome taxonomy , MLSA and streptomyces
© Microbiology Society
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2017-12-01
2024-04-18
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References

  1. Waksman SA, Henrici AT. The nomenclature and classification of the actinomycetes. J Bacteriol 1943; 46:337–348[PubMed]
     [Google Scholar]
  2. Dietera A, Hamm A, Fiedler HP, Goodfellow M, Müller WE et al. Pyrocoll, an antibiotic, antiparasitic and antitumor compound produced by a novel alkaliphilic Streptomyces strain. J Antibiot 2003; 56:639–646 [View Article][PubMed]
     [Google Scholar]
  3. Baur S, Niehaus J, Karagouni AD, Katsifas EA, Chalkou K et al. Fluostatins C-E, novel members of the fluostatin family produced by Streptomyces strain Acta 1383. J Antibiot 2006; 59:293–297 [View Article][PubMed]
     [Google Scholar]
  4. de Souza RF, Coelho RR, Macrae A, Soares RM, Nery DC et al. Streptomyces lunalinharesii sp. nov., a chitinolytic streptomycete isolated from cerrado soil in Brazil. Int J Syst Evol Microbiol 2008; 58:2774–2778 [View Article][PubMed]
     [Google Scholar]
  5. de Azeredo LA, Leite SG, Freire DM, Benchetrit LC, Coelho RR. Proteases from actinomycetes interfere in solid media plate assays of hyaluronidase activity. J Microbiol Methods 2001; 45:207–212 [View Article][PubMed]
     [Google Scholar]
  6. De Azeredo LA, De Lima MB, Coelho RR, Freire DM. Thermophilic protease production by Streptomyces sp. 594 in submerged and solid-state fermentations using feather meal. J Appl Microbiol 2006; 100:641–647 [View Article][PubMed]
     [Google Scholar]
  7. De Azeredo LA, De Lima MB, Coelho RR, Freire DM. A low-cost fermentation medium for thermophilic protease production by Streptomyces sp. 594 using feather meal and corn steep liquor. Curr Microbiol 2006; 53:335–339 [View Article][PubMed]
     [Google Scholar]
  8. 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]
  9. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  10. 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]
  11. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. (editors) Actinomycete Taxonomy Fairfax, VA: Society for Industrial Microbiology; 1980 pp. 227–291
     [Google Scholar]
  12. 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]
  13. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
     [Google Scholar]
  14. 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]
  15. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDITechnical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  16. 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]
  17. Kroppenstedt RM, Goodfellow M. The family Thermomonosporaceae: Actinocorallia, Actinomadura, Spirillispora and Thermomonospora . In Dworkin M, Falkow S, Schleifer KH, Stackebrandt E. (editors) The Prokaryotes, Archaea and Bacteria: Firmicutes, Actinomycetes, 3rd ed. vol. 3 New York: Springer; 2006 pp. 682–724
     [Google Scholar]
  18. 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]
  19. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  20. Rintala H, Nevalainen A, Rönkä E, Suutari M. PCR primers targeting the 16S rRNA gene for the specific detection of streptomycetes. Mol Cell Probes 2001; 15:337–347 [View Article][PubMed]
     [Google Scholar]
  21. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989; 17:7843–7853 [View Article][PubMed]
     [Google Scholar]
  22. 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 [View Article][PubMed]
     [Google Scholar]
  23. 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 [View Article][PubMed]
     [Google Scholar]
  24. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–532[PubMed]
     [Google Scholar]
  25. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
     [Google Scholar]
  26. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony Methods. Mol Biol Evol 2016; 33:1870–1874 [Crossref]
     [Google Scholar]
  27. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  28. Felsenstein J. Phylogeny Inference Package (Phylip) Version 3.5 University of Washington: Seattle; 1993
     [Google Scholar]
  29. 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 [View Article][PubMed]
     [Google Scholar]
  30. 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 [View Article][PubMed]
     [Google Scholar]
  31. 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 [View Article][PubMed]
     [Google Scholar]
  32. Labeda DP, Dunlap CA, Rong X, Huang Y, Doroghazi JR et al. Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis. Antonie van Leeuwenhoek 2017; 110:563–583 [View Article][PubMed]
     [Google Scholar]
  33. Jolley KA, Maiden MC. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010; 11:595 [View Article][PubMed]
     [Google Scholar]
  34. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article][PubMed]
     [Google Scholar]
  35. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article][PubMed]
     [Google Scholar]
  36. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
     [Google Scholar]
  37. Minh BQ, Nguyen MA, von Haeseler A. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol 2013; 30:1188–1195 [View Article][PubMed]
     [Google Scholar]
  38. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article][PubMed]
     [Google Scholar]
  39. 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 [View Article][PubMed]
     [Google Scholar]
  40. 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 [View Article][PubMed]
     [Google Scholar]
  41. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article][PubMed]
     [Google Scholar]
  42. Auch AF, von Jan M, Klenk HP, 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][PubMed]
     [Google Scholar]
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Streptomyces odonnellii sp. nov., a proteolytic streptomycete isolated from soil under cerrado (savanna) vegetation cover
Int J Syst Evol Microbiol 67, 5211 (2017); https://doi.org/10.1099/ijsem.0.002446
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