1887

Abstract

Five actinobacteria isolates, KC201, KC401, KC310, KC712 and 6K102, were recovered from the Karakum Desert during an investigation of novel actinobacteria with biotechnological potential. A polyphasic approach confirmed the affiliation of the strains to the genus . The strains showed chemotaxonomic and morphological properties consistent with their classification in the genus . Furthermore, these strains clearly distinguished and formed well supperted clades in phylogenetic and phylogenomic trees. Low ANI and dDDH values and distinguishing phenotypic properties between isolates KC201, KC310, KC712 and 6K102 showed that these strains belonged to novel species, the names proposed for these taxa are sp. nov., sp. nov., sp. nov. and sp. nov., with the type strains KC310 (=CGMCC 4.7331 =DSM 102919 =KCTC 39774), KC712 (=CGMCC 4.7334 =DSM 102925 =KCTC 39776), KC201 (=CGMCC 4.7339 =DSM 102917 =KCTC 39781) and 6K102 (=CGMCC 4.7541 =JCM 32916), respectively.

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2019-11-06
2019-11-17
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References

  1. Zhang Z, Wang Y, Ruan J. Reclassification of Thermomonospora and Microtetraspora. Int J Syst Bacteriol 1998;48: 411– 422 [CrossRef]
    [Google Scholar]
  2. Chiba S, Suzuki M, Ando K. Taxonomic re-evaluation of 'Nocardiopsis' sp. K-252T (= NRRL 15532T): a proposal to transfer this strain to the genus Nonomuraea as Nonomuraea longicatena sp. nov. Int J Syst Bacteriol 1999;49 Pt 4: 1623– 1630 [CrossRef]
    [Google Scholar]
  3. Cao P, Wang Y, Sun P, Li C, Zhao J et al. Nonomuraea lactucae sp. nov., a novel actinomycete isolated from rhizosphere soil of lettuce (Lactuca sativa). Int J Syst Evol Microbiol 2019;69: 316– 321 [CrossRef]
    [Google Scholar]
  4. Kämpfer P, Genus VI. Nonomuraea In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki K. (editors) Bergey's Manual of Systematic Bacteriology 2nd Edn, Vol 5, The Actinobacteria, Part A 2012; pp 1844– 1861
    [Google Scholar]
  5. Wang X, Zhao J, Liu C, Wang J, Shen Y et al. Nonomuraea solani sp. nov., an actinomycete isolated from eggplant root (Solanum melongena L.). Int J Syst Evol Microbiol 2013;63: 2418 2423 [CrossRef]
    [Google Scholar]
  6. Zheng W, Zhao J, Li D, Jiang H, Han L et al. Nonomuraea lycopersici sp. nov., isolated from the root of tomato plants (Solanum lycopersicum L.). Antonie van Leeuwenhoek 2018;111: 1095– 1103 [CrossRef]
    [Google Scholar]
  7. Goodfellow M, Quintana ET. The Family Streptosporangiaceae In Dworkin MFS, Rosenberg E, Schleifer KH, Stackebrandt E. (editors) The Prokaryotes3 Archaea Bacteria: Firmicutes, Actinomycetes; 2006; pp 725– 753
    [Google Scholar]
  8. Nazari B, Forneris CC, Gibson MI, Moon K, Schramma KR et al. Nonomuraea sp. ATCC 55076 harbours the largest actinomycete chromosome to date and the kistamicin biosynthetic gene cluster. Medchemcomm 2017;8: 780– 788 [CrossRef]
    [Google Scholar]
  9. Dalmastri C, Gastaldo L, Marcone GL, Binda E, Congiu T et al. Classification of Nonomuraea sp. ATCC 39727, an actinomycete that produces the glycopeptide antibiotic A40926, as Nonomuraea gerenzanensis sp. nov. Int J Syst Evol Microbiol 2016;66: 912– 921 [CrossRef]
    [Google Scholar]
  10. Fleck WF, Strauss DG, Meyer J, Porstendorfer G. Fermentation, isolation, and biological activity of maduramycin: a new antibiotic from Actinomadura rubra. Z Allg Mikrobiol 1978;18: 389– 398 [CrossRef]
    [Google Scholar]
  11. Naganawa H, Hashizume H, Kubota Y, Sawa R, Takahashi Y et al. Biosynthesis of the cyclitol moiety of pyralomicin 1a in Nonomuraea spiralis MI178-34F18. J Antibiot 2002;55: 578– 584 [CrossRef]
    [Google Scholar]
  12. Nakagawa M, Hayakawa Y, Imamura K, Seto H, Otake N. Microbial conversion of anthracyclinones to carminomycins by a blocked mutant of Actinomadura roseoviolacea. J Antibiot 1989;42: 1698– 1703 [CrossRef]
    [Google Scholar]
  13. Nakagawa M, Hayakawa Y, Kawaı H, Imamura K, Inoue H et al. A new anthracycline antibiotic N-formyl-13-dihydrocarminomycin. J Antibiot 1983;36: 457– 458 [CrossRef]
    [Google Scholar]
  14. Okazaki TaN A. Studies in actinomycetes isolated from Australian soils In GBSaGM Szabo. editor Biological, Biochemical and Biomedical Aspects of Actinomycetes Budapest: Akadémiai Kiadó; 1985; pp 739– 741
    [Google Scholar]
  15. Tamura A, Furuta R, Naruto S, Ishii H. Actinotiocin, a new sulfur-containing peptide antibiotic from Actinomadura pusilla. J Antibiot 1973;26: 343– 350 [CrossRef]
    [Google Scholar]
  16. Ara I, Kudo T, Matsumoto A, Takahashi Y, Omura S. Nonomuraea maheshkhaliensis sp. nov., a novel actinomycete isolated from mangrove rhizosphere mud. J Gen Appl Microbiol 2007;53: 159– 166 [CrossRef]
    [Google Scholar]
  17. Shen Y, Jia F, Liu C, Li J, Guo S et al. Nonomuraea zeae sp. nov., isolated from the rhizosphere of corn (Zea mays L.). Int J Syst Evol Microbiol 2016;66: 2259– 2264 [CrossRef]
    [Google Scholar]
  18. Qin S, Zhao GZ, Klenk HP, Li J, Zhu WY et al. Nonomuraea antimicrobica sp. nov., an endophytic actinomycete isolated from a leaf of Maytenus austroyunnanensis. Int J Syst Evol Microbiol 2009;59: 2747– 2751 [CrossRef]
    [Google Scholar]
  19. Fang BZ, Hua ZS, Han MX, Zhang ZT, Wang YH et al. Nonomuraea cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample. Int J Syst Evol Microbiol 2017;67: 4692– 4697 [CrossRef]
    [Google Scholar]
  20. Quadri SR, Tian X-P, Zhang J, Li J, Nie G-X et al. Nonomuraea indica sp. nov., novel actinomycetes isolated from lime-stone open pit mine, India. J Antibiot 2015;68: 491– 495 [CrossRef]
    [Google Scholar]
  21. Rachniyom H, Matsumoto A, Indananda C, Duangmal K, Takahashi Y et al. Nonomuraea syzygii sp. nov., an endophytic actinomycete isolated from the roots of a jambolan plum tree (Syzygium cumini L. Skeels). Int J Syst Evol Microbiol 2015;65: 1234– 1240 [CrossRef]
    [Google Scholar]
  22. Xi L, Zhang L, Ruan J, Huang Y. Nonomuraea maritima sp. nov., isolated from coastal sediment. Int J Syst Evol Microbiol 2011;61: 2740– 2744 [CrossRef]
    [Google Scholar]
  23. Suksaard P, Mingma R, Srisuk N, Matsumoto A, Takahashi Y et al. Nonomuraea purpurea sp. nov., an actinomycete isolated from mangrove sediment. Int J Syst Evol Microbiol 2016;66: 4987– 4992 [CrossRef]
    [Google Scholar]
  24. Wu H, Liu B. Nonomuraea thermotolerans sp. nov., a thermotolerant actinomycete isolated from mushroom compost. Int J Syst Evol Microbiol 2016;66: 894– 900 [CrossRef]
    [Google Scholar]
  25. Nakaew N, Sungthong R, Yokota A, Lumyong S. Nonomuraea monospora sp. nov., an actinomycete isolated from cave soil in Thailand, and emended description of the genus Nonomuraea. Int J Syst Evol Microbiol 2012;62: 3007– 3012 [CrossRef]
    [Google Scholar]
  26. Saricaoglu S, Nouioui I, Ay H, Saygin H, Bektas KI et al. Nonomuraea insulae sp. nov., isolated from forest soil. Antonie van Leeuwenhoek 2018;111: 2051– 2059 [CrossRef]
    [Google Scholar]
  27. Sripreechasak P, Phongsopitanun W, Supong K, Pittayakhajonwut P, Kudo T et al. Nonomuraea rhodomycinica sp. nov., isolated from peat swamp forest soil. Int J Syst Evol Microbiol 2017;67: 1683– 1687 [CrossRef]
    [Google Scholar]
  28. Camas M, Sazak A, Spröer C, Klenk HP, Cetin D et al. Nonomuraea jabiensis sp. nov., isolated from arid soil. Int J Syst Evol Microbiol 2013;63: 212– 218 [CrossRef]
    [Google Scholar]
  29. Li X, Zhang L, Ding Y, Gao Y, Ruan J et al. Nonomuraea jiangxiensis sp. nov., isolated from acidic soil. Int J Syst Evol Microbiol 2012;62: 1409– 1413 [CrossRef]
    [Google Scholar]
  30. Lipun K, Teo WFA, Tongpan J, Matsumoto A, Duangmal K. Nonomuraea suaedae sp. nov., isolated from rhizosphere soil of Suaeda maritima (L.) Dumort. J Antibiot 2019;72: 518 523 [CrossRef]
    [Google Scholar]
  31. Zhao GZ, Li J, Huang HY, Zhu WY, Xu LH et al. Nonomuraea rhizophila sp. nov., an actinomycete isolated from rhizosphere soil. Int J Syst Evol Microbiol 2011;61: 2141– 2145 [CrossRef]
    [Google Scholar]
  32. Zhao J, Mu S, Zhao Q, Jiang S, Cao P et al. Nonomuraea rhizosphaerae sp. nov., an actinomycete isolated from the rhizosphere soil of a rubber tree (Hevea brasiliensis Muell. Arg). Antonie van Leeuwenhoek 2018;111: 2009– 2016 [CrossRef]
    [Google Scholar]
  33. Huang H, Liu M, Zhong W, Mo K, Zhu J et al. Nonomuraea mangrovi sp. nov., an actinomycete isolated from mangrove soil. Int J Syst Evol Microbiol 2018;68: 3144– 3148 [CrossRef]
    [Google Scholar]
  34. Tan GYA, Ward AC, Goodfellow M. Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media. Syst Appl Microbiol 2006;29: 557– 569 [CrossRef]
    [Google Scholar]
  35. Hayakawa M, Nonomura H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. Journal of Fermentation Technology 1987;65: 501– 509 [CrossRef]
    [Google Scholar]
  36. ZoBell CE. Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. J Mar Res 1941;4: 41– 75
    [Google Scholar]
  37. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985;49: 1– 7
    [Google Scholar]
  38. Mincer TJ, Jensen PR, Kauffman CA, Fenical W. Widespread and persistent populations of a major new marine actinomycete taxon in ocean sediments. Appl Environ Microbiol 2002;68: 5005– 5011 [CrossRef]
    [Google Scholar]
  39. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16: 313– 340 [CrossRef]
    [Google Scholar]
  40. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991;173: 697– 703 [CrossRef]
    [Google Scholar]
  41. Yoon SH, Ha SM, 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 [CrossRef]
    [Google Scholar]
  42. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30: 2725– 2729 [CrossRef]
    [Google Scholar]
  43. 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 [CrossRef]
    [Google Scholar]
  44. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4: 406– 425 [CrossRef]
    [Google Scholar]
  45. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17: 368– 376 [CrossRef]
    [Google Scholar]
  46. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971;20: 406– 416 [CrossRef]
    [Google Scholar]
  47. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39: 783– 791 [CrossRef]
    [Google Scholar]
  48. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 2017;45: D535– D542 [CrossRef]
    [Google Scholar]
  49. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008;9: 75 [CrossRef]
    [Google Scholar]
  50. 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 [CrossRef]
    [Google Scholar]
  51. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast Distance-Based phylogeny inference program. Mol Biol Evol 2015;32: 2798– 2800 [CrossRef]
    [Google Scholar]
  52. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972;106: 645– 668 [CrossRef]
    [Google Scholar]
  53. Kreft L, Botzki A, Coppens F, Vandepoele K, Van Bel M. PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization. Bioinformatics 2017;33: 2946– 2947 [CrossRef]
    [Google Scholar]
  54. Liu Y, Lai Q, Göker M, Meier-Kolthoff JP, Wang M et al. Genomic insights into the taxonomic status of the Bacillus cereus group. Sci Rep 2015;5: 14082 [CrossRef]
    [Google Scholar]
  55. Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V et al. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 2014;9: 2 [CrossRef]
    [Google Scholar]
  56. 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]
    [Google Scholar]
  57. 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 [CrossRef]
    [Google Scholar]
  58. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019;47: W81– W87 [CrossRef]
    [Google Scholar]
  59. 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]
    [Google Scholar]
  60. 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 [CrossRef]
    [Google Scholar]
  61. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Environ Microbiol 1974;28: 226– 231
    [Google Scholar]
  62. 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]
  63. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996;42: 989– 1005 [CrossRef]
    [Google Scholar]
  64. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: MIDI Inc; 1990
    [Google Scholar]
  65. 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]
  66. Collins M. Isoprenoid quinone analysis in bacterial classification and identification In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics Academic Press; 1985; pp 267– 285
    [Google Scholar]
  67. Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA et al. Numerical classification of Streptomyces and related genera. Microbiology 1983;129: 1743– 1813 [CrossRef]
    [Google Scholar]
  68. Waksman SA. The actinomycetes. A summary of current knowledge The Actinomycetes A summary of current knowledge 1967
    [Google Scholar]
  69. Waksman SA. The Actinomycetes Vol II Classification, identification and descriptions of genera and species 1961
    [Google Scholar]
  70. 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]
  71. Saygin H, Ay H, Guven K, Cetin D, Sahin N. Desertiactinospora gelatinilytica gen. nov., sp. nov., a new member of the family Streptosporangiaceae isolated from the Karakum Desert. Antonie van Leeuwenhoek 2019;112: 409– 423 [CrossRef]
    [Google Scholar]
  72. Nash P, Krent MM. Culture media In Balows AHW, Herrmann KL, Isenberg HD, Shadomy HJ. (editors) Manual of Clinical Microbiology Washington, DC: American Society for Microbiology; 1991; pp 1268– 1270
    [Google Scholar]
  73. Goodfellow M. Numerical taxonomy of some nocardioform bacteria. J Gen Microbiol 1971;69: 33– 80 [CrossRef]
    [Google Scholar]
  74. Gordon RE, Barnett DA, Handerhan JE, Pang CHN. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974;24: 54– 63 [CrossRef]
    [Google Scholar]
  75. Küster E, Williams S. Production of hydrogen sulfide by streptomycetes and methods for its detection. Appl Environ Microbiol 1964;12: 46– 52
    [Google Scholar]
  76. Goodfellow M, Nouioui I, Sanderson R, Xie F, Bull AT. Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama desert soils. Antonie van Leeuwenhoek 2018;111: 1315– 1332 [CrossRef]
    [Google Scholar]
  77. Jukes TH, Cantor CR. Evolution of protein molecules In HN M. editor Mammalian Protein Metabolism New York: Academic Press; 1969; pp 21– 132
    [Google Scholar]
  78. Roes Mle, Meyers PR. Nonomuraea candida sp. nov., a new species from South African soil. Antonie van Leeuwenhoek 2008;93: 133– 139 [CrossRef]
    [Google Scholar]
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