1887

Abstract

A novel actinomycete, strain 1_25, was isolated from soil under a black Gobi rock sample from Shuangta, PR China, and characterized using a polyphasic taxonomic approach. The results of comparative analysis of the 16S rRNA gene sequences indicated the 1_25 represented a member of the genus . Chemotaxonomic data revealed that 1_25 possessed MK-9(H) as the major menaquinone. The cell wall contained -diaminopimelic acid (-DAP) and the whole-cell sugar pattern consisted of ribose, glucose and galactose. Major fatty acid methyl esters were observed to be iso-C (23.6 %), and anteiso-C (10.4 %). The genomic DNA G+C content of 1_25 was 69 mol %. The results of phylogenetic analysis based on 16S rRNA gene sequence indicated that 1_25 had high sequence similarity with 172205 (98.1 %), TRM 66187 (98 %), and JCM4580 (98 %). In addition to the differences in phenotypic characters, the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between 1_25 and closely related species were below the recommended threshold values for assigning strains to the same species. The fermentation product of 1_25 in ISP2 had an inhibitory effect on . On the basis of these genotypic and phenotypic characteristics, strain 1_25 (=JCM 34936=GDMCC 4.216) represents a novel species of the genus , for which the name sp. nov. is proposed.

Funding
This study was supported by the:
  • the Scientific Project of Gansu Province, China (Award 20JR5RA548)
    • Principle Award Recipient: yingwen
  • the Scientific Project of Gansu Province, China (Award 18JR2TA019)
    • Principle Award Recipient: yingwen
  • the Scientific Project of Gansu Province, China (Award 20YF3WA007)
    • Principle Award Recipient: yingwen
  • the National Key R&D Program of China (Award 2019YFE0121100)
    • Principle Award Recipient: TuoChen
  • The National Natural Science Foundation of China (Award 31870479)
    • Principle Award Recipient: WeiZhang
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2022-03-23
2022-07-06
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References

  1. Waksman SA, Henrici AT. The nomenclature and classification of the actinomycetes. J Bacteriol 1943; 46:337–341 [View Article] [PubMed]
    [Google Scholar]
  2. Jiang S, Piao C, Yu Y, Cao P, Li C et al. Streptomyces capitiformicae sp. nov., a novel actinomycete producing angucyclinone antibiotics isolated from the head of Camponotus japonicus Mayr. Int J Syst Evol Microbiol 2018; 68:118–124 [View Article] [PubMed]
    [Google Scholar]
  3. Ma L, Zeng H, Xia Z, Luo X, Zhang L et al. Streptomyces lycii sp. nov., an endogenous actinomycete isolated from Lycium ruthenicum. Int J Syst Evol Microbiol 2020; 70:5197 [View Article] [PubMed]
    [Google Scholar]
  4. Zhou S, Li Z, Bai L, Yan K, Zhao J et al. Streptomyces castaneus sp. nov., a novel actinomycete isolated from the rhizosphere of Peucedanum praeruptorum Dunn. Arch Microbiol 2017; 199:45–50 [View Article] [PubMed]
    [Google Scholar]
  5. Saimee Y, Duangmal K. Streptomyces spirodelae sp. nov., isolated from duckweed. Int J Syst Evol Microbiol 2021; 71:005106 [View Article] [PubMed]
    [Google Scholar]
  6. Goodfellow M, Busarakam K, Idris H, Labeda DP, Nouioui I et al. Streptomyces asenjonii sp. nov., isolated from hyper-arid Atacama Desert soils and emended description of Streptomyces viridosporus Pridham et al. 1958. Antonie van Leeuwenhoek 2017; 110:1133–1148 [View Article] [PubMed]
    [Google Scholar]
  7. Santhanam R, Rong X, Huang Y, Andrews BA, Asenjo JA et al. Streptomyces bullii sp. nov., isolated from a hyper-arid Atacama Desert soil. Antonie van Leeuwenhoek 2013; 103:367–373 [View Article] [PubMed]
    [Google Scholar]
  8. Santhanam R, Okoro CK, Rong X, Huang Y, Bull AT et al. Streptomyces deserti sp. nov., isolated from hyper-arid Atacama Desert soil. Antonie van Leeuwenhoek 2012; 101:575–581 [View Article] [PubMed]
    [Google Scholar]
  9. Maiti PK, Das S, Sahoo P, Mandal S. Streptomyces sp SM01 isolated from Indian soil produces a novel antibiotic picolinamycin effective against multi drug resistant bacterial strains. Sci Rep 2020; 10:10092 [View Article] [PubMed]
    [Google Scholar]
  10. Li L, Wang J, Zhou YJ, Lin HW, Lu YH. Streptomyces reniochalinae sp. nov. and Streptomyces diacarni sp. nov., from marine sponges. Int J Syst Evol Microbiol 2019; 69:99–104 [View Article] [PubMed]
    [Google Scholar]
  11. Sujarit K, Kudo T, Ohkuma M, Pathom-Aree W, Lumyong S. Streptomyces palmae sp. nov., isolated from oil palm (Elaeis guineensis) rhizosphere soil. Int J Syst Evol Microbiol 2016; 66:3983–3988 [View Article] [PubMed]
    [Google Scholar]
  12. Lechevalier HA, Lechevalier MP, Gerber NN. Chemical composition as a criterion in the classification of actinomycetes. Adv Appl Microbiol 1971; 14:47–72 [View Article] [PubMed]
    [Google Scholar]
  13. Berdy J. Bioactive microbial metabolites - A personal view. J Antibiot 2005; 58:1–26
    [Google Scholar]
  14. Kim YH, Park BS, Bhatia SK, Seo H-M, Jeon J-M et al. Production of rapamycin in Streptomyces hygroscopicus from glycerol-based media optimized by systemic methodology. J Microbiol Biotechnol 2014; 24:1319–1326 [View Article] [PubMed]
    [Google Scholar]
  15. Vurukonda S, Giovanardi D, Stefani E. Plant growth promoting and biocontrol activity of Streptomyces spp. as endophytes. Int J Mol Sci 2018; 19:E952 [View Article] [PubMed]
    [Google Scholar]
  16. Tiwari K, Gupta RK. Rare actinomycetes: a potential storehouse for novel antibiotics. Crit Rev Biotechnol 2012; 32:108–132 [View Article] [PubMed]
    [Google Scholar]
  17. 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]
  18. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7 [View Article] [PubMed]
    [Google Scholar]
  19. Zhang B, Yang R, Zhang G, Liu Y, Zhang D et al. Characteristics of Planococcus antioxidans sp. nov., an antioxidant-producing strain isolated from the desert soil in the Qinghai-Tibetan Plateau. Microbiologyopen 2020; 9:1183–1196 [View Article] [PubMed]
    [Google Scholar]
  20. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  21. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018; 46:D851–D860 [View Article] [PubMed]
    [Google Scholar]
  22. Li W, O’Neill KR, Haft DH, DiCuccio M, Chetvernin V et al. RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. Nucleic Acids Res 2021; 49:D1020–D1028 [View Article] [PubMed]
    [Google Scholar]
  23. 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]
  24. 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]
  25. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  26. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
    [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. 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]
  29. Nei M, Kumar S. Molecular Evolution and Phylogenetics USA: Oxford University Press; 2000
    [Google Scholar]
  30. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  31. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article] [PubMed]
    [Google Scholar]
  32. 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]
  33. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J et al. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
    [Google Scholar]
  34. 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]
  35. 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] [PubMed]
    [Google Scholar]
  36. Kim M, Oh HS, Park SC, 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]
  37. Rodriguez-R LM, Gunturu S, Harvey WT, Rosselló-Mora R, Tiedje JM et al. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucleic Acids Res 2018; 46:W282–W288 [View Article] [PubMed]
    [Google Scholar]
  38. Guo YP, Zheng W, Rong XY, 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]
  39. 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]
  40. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  41. Monfort WF. Standard methods for the examination of water and sewage. Am J Public Health 1923; 13:498–499 [View Article]
    [Google Scholar]
  42. Thom C, Church MB, May OE. The Penicillia Baltimore: Williams & Wilkins; 1930
    [Google Scholar]
  43. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145 [View Article] [PubMed]
    [Google Scholar]
  44. Pridham TG, Gottlieb D. The utilization of carbon compounds by some actinomycetales as an aid for species determination. J Bacteriol 1948; 56:107–114 [View Article] [PubMed]
    [Google Scholar]
  45. 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]
  46. Gordon RE, Barnett DA, Handerhan JE, Pang C-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  47. 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]
  48. Sasser M. MIDI technical note 101. Identification of bacteria by gas chromatography of cellular fatty acids Newark. DE: MIDI; 1990 pp 1–7
    [Google Scholar]
  49. 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]
  50. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. Soc Appl Bacteriol Tech Ser 1985267–287
    [Google Scholar]
  51. 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]
  52. 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. Journal of Microbiological Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  53. Bertani G. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol 1951; 62:293–300 [View Article] [PubMed]
    [Google Scholar]
  54. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011; 39:W339–46 [View Article] [PubMed]
    [Google Scholar]
  55. Hu H, Lin HP, Xie QY, Li L, Xie XQ et al. Streptomyces qinglanensis sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2012; 62:596–600 [View Article] [PubMed]
    [Google Scholar]
  56. Cui Y, Baek S-H, Wang L, Lee H-G, Cui C et al. Streptomyces panacagri sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2012; 62:780–785 [View Article] [PubMed]
    [Google Scholar]
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