1887

Abstract

We investigated the taxonomic relationships among subsp. , subsp. , and . The 16S rRNA gene sequence similarity between subsp. and subsp. was 97.7 %, whereas subsp. , and showed 100 % nucleotide sequence identity. In addition, subsp. diastaticus and formed a single clade in the phylogenetic tree. Digital DNA–DNA relatedness between subsp. and subsp. was only 22.8%, indicative of different species. In comparison, DNA–DNA relatedness values for subsp. , and ranged from 95.8 to 97.2 %, suggesting the three taxa belong to the same genomospecies. Previously reported phenotypic data also supported synonymy. Therefore, we propose that subsp. should be classified as an independent species, sp. nov. The type strain is NBRC 13412 (=ATCC 3315=CBS 713.72=DSM 40496=ISP 5496=JCM 4745=NBRC 3714=NRRL B-1241=RIA 1373). Our data also suggests that and should be reclassified as later heterotypic synonyms of .

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004287
2020-07-09
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/7/4291.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004287&mimeType=html&fmt=ahah

References

  1. Krainsky A. Die Aktinomyceten und ihren Bedeutung in der Natur. Zentralblatt fur Bakteriologie, Parasitenkunde, Infektionskrankheiten und Hygiene . Abteilung II 1914; 41:649–688
    [Google Scholar]
  2. Baldacci E, Grein A, Spalla C. Studio di una "Serie" di specie di attinomiceti: A. diastaticus . Giornale di Microbiologia 1955; 1:127–143
    [Google Scholar]
  3. Waksman SA, Henrici AT, Family III. Streptomycetaceae Waksman and Henrici. In Breed RS, Murray EGD, Hitchens AP. (editors) Bergey's Manual of Determinative Bacteriology, 6th ed. Baltimore: The Williams & Wilkins Co; 1948 pp 929–980
    [Google Scholar]
  4. Pridham TG, Hesseltine CW, Benedict RG. A guide for the classification of streptomycetes according to selected groups; placement of strains in morphological sections. Appl Microbiol 1958; 6:52–79 [View Article][PubMed]
    [Google Scholar]
  5. Waksman SA, Curtis RE. The Actinomyces of the soil. Soil Sci 1916; 1:99–134 [View Article]
    [Google Scholar]
  6. Duché L. Les Actinomyces Du Groupe albus. Encyclopédie Mycologique 1934; 6:1–375
    [Google Scholar]
  7. Hu L, Chen X, Han L, Zhao L, Miao C et al. Two new phenazine metabolites with antimicrobial activities from soil-derived Streptomyces species. J Antibiot 2019; 72:574–577 [View Article][PubMed]
    [Google Scholar]
  8. Li Y, Han L, Rong H, Li L, Zhao L et al. Diastaphenazine, a new dimeric phenazine from an endophytic Streptomyces diastaticus subsp. ardesiacus . J Antibiot 2015; 68:210–212 [View Article][PubMed]
    [Google Scholar]
  9. Pérez-Zúñiga FJ, Seco EM, Cuesta T, Degenhardt F, Rohr J et al. CE-108, a new macrolide tetraene antibiotic. J Antibiot 2004; 57:197–204 [View Article][PubMed]
    [Google Scholar]
  10. Komaki H, Sakurai K, Hosoyama A, Kimura A, Igarashi Y et al. Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters among taxonomically close Streptomyces strains. Sci Rep 2018; 8:6888 [View Article][PubMed]
    [Google Scholar]
  11. Singh SP, Gaur R. Evaluation of antagonistic and plant growth promoting activities of chitinolytic endophytic actinomycetes associated with medicinal plants against Sclerotium rolfsii in chickpea. J Appl Microbiol 2016; 121:506–518 [View Article][PubMed]
    [Google Scholar]
  12. Tajana E, Fiechter A, Zimmermann W. Purification and characterization of two alpha-L-arabinofuranosidases from Streptomyces diastaticus . Appl Environ Microbiol 1992; 58:1447–1450 [View Article][PubMed]
    [Google Scholar]
  13. Hamedi J, Vaez Fakhri A, Mahdavi S. Biobleaching of mechanical paper pulp using Streptomyces rutgersensis UTMC 2445 isolated from a lignocellulose-rich soil. J Appl Microbiol 2020; 128:161–170 [View Article][PubMed]
    [Google Scholar]
  14. Su P, Wang D-X, Ding S-X, Zhao J. Isolation and diversity of natural product biosynthetic genes of cultivable bacteria associated with marine sponge Mycale sp. from the coast of Fujian, China. Can J Microbiol 2014; 60:217–225 [View Article][PubMed]
    [Google Scholar]
  15. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article][PubMed]
    [Google Scholar]
  16. 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][PubMed]
    [Google Scholar]
  17. Komaki H, Tamura T. Reclassification of Streptomyces rimosus subsp. paromomycinus as Streptomyces paromomycinus sp. nov. Int J Syst Evol Microbiol 2019; 69:2577–2583 [View Article][PubMed]
    [Google Scholar]
  18. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  19. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  20. 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]
  21. 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]
  22. 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 [View Article]
    [Google Scholar]
  23. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  24. Kämpfer P, Genus I et al. Streptomyces Waksman and Henrici 1943, 399AL emend. Witt and Stackbrandt 1990, 370 emend. Wellington, Stackebrandt, Sanders, Wolstrup and Jorgensen 1992, 159. In Whitman WB, Parte A, Goodfellow M, Kämpfer P, Busse H et al. (editors) Bergey's Manual of Systematic Bacteriology: The Actinobacteria, Part B New York: Springer; 2012 pp 1455–1781
    [Google Scholar]
  25. Shirling EB, Gottlieb D. Cooperative description of type strains of Streptomyces: V. additional descriptions. Int J Syst Bacteriol 1972; 22:265–394 [View Article]
    [Google Scholar]
  26. 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]
  27. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  28. Takahashi K, Nei M. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 2000; 17:1251–1258 [View Article][PubMed]
    [Google Scholar]
  29. Takasaka N, Kaweewan I, Ohnishi-Kameyama M, Kodani S. Isolation of a new antibacterial peptide actinokineosin from Actinokineospora spheciospongiae based on genome mining. Lett Appl Microbiol 2017; 64:150–157 [View Article][PubMed]
    [Google Scholar]
  30. Wang L, Zhu M, Zhang Q, Zhang X, Yang P et al. Diisonitrile natural product SF2768 functions as a chalkophore that mediates copper acquisition in Streptomyces thioluteus . ACS Chem Biol 2017; 12:3067–3075 [View Article][PubMed]
    [Google Scholar]
  31. Chen S, Huang X, Zhou X, Bai L, He J et al. Organizational and mutational analysis of a complete FR-008/candicidin gene cluster encoding a structurally related polyene complex. Chem Biol 2003; 10:1065–1076 [View Article][PubMed]
    [Google Scholar]
  32. Luo Y, Huang H, Liang J, Wang M, Lu L et al. Activation and characterization of a cryptic polycyclic tetramate macrolactam biosynthetic gene cluster. Nat Commun 2013; 4:2894 [View Article][PubMed]
    [Google Scholar]
  33. Xu F, Nazari B, Moon K, Bushin LB, Seyedsayamdost MR. Discovery of a cryptic antifungal compound from Streptomyces albus J1074 using high-throughput elicitor screens. J Am Chem Soc 2017; 139:9203–9212 [View Article][PubMed]
    [Google Scholar]
  34. Praseuth AP, Wang CCC, Watanabe K, Hotta K, Oguri H et al. Complete sequence of biosynthetic gene cluster responsible for producing triostin A and evaluation of quinomycin-type antibiotics from Streptomyces triostinicus . Biotechnol Prog 2008; 24:1226–1231 [View Article][PubMed]
    [Google Scholar]
  35. 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]
  36. Shirling EB, Gottlieb D. Cooperative description of type cultures of Streptomyces.: II. species descriptions from first study. Int J Syst Bacteriol 1968; 18:69–189 [View Article]
    [Google Scholar]
  37. Shirling EB, Gottlieb D. Cooperative description of type cultures of Streptomyces. IV. Species descriptions from the second, third and fourth studies. Int J Syst Bacteriol 1969; 19:391–512 [View Article]
    [Google Scholar]
  38. He L, Li W, Huang Y, Wang L, Liu Z et al. Streptomyces jietaisiensis sp. nov., isolated from soil in northern China. Int J Syst Evol Microbiol 2005; 55:1939–1944 [View Article][PubMed]
    [Google Scholar]
  39. Yu C, Liu C, Wang X, Zhao J, Yang L et al. Streptomyces polyrhachii sp. nov., a novel actinomycete isolated from an edible Chinese black ant (Polyrhachis vicina Roger). Antonie van Leeuwenhoek 2013; 104:1013–1019 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004287
Loading
/content/journal/ijsem/10.1099/ijsem.0.004287
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error