1887

Abstract

An isolate, 13K206, with typical morphological characteristics of the genus was obtained during a study searching for novel actinobacteria with biosynthetic potential from the Karakum Desert. A polyphasic approach was adopted to determine taxonomic affiliation of the strain. The strain showed chemotaxonomical properties consistent with its classification in the genus such as - and 3-OH-Apm in the cell-wall peptidoglycan, xylose in whole-cell hydrolysate and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as major polar lipids. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain was closely related to ‘’ S3-1, DSM 43818 and DS3186 with sequence similarities of 98.6, 98.5 and 98.4 %, respectively. Digital DNA–DNA hybridization and average nucleotide identity analyses in addition to gene analysis confirmed the assignment of the strain to a novel species within the genus for which the name sp. nov. is proposed. The type strain is 13K206 (=JCM 32583=DSM 107532). The DNA G+C content of the type strain is 72.4 mol%.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003752
2019-10-09
2019-10-22
Loading full text...

Full text loading...

References

  1. Krasil’nikov N. Ray Fungi and Related Organisms–Actinomycetales Moscow: Akademii Nauk SSSR (in Russian); 1938
    [Google Scholar]
  2. Zhi X-Y, Li W-J, Stackebrandt E. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. Int J Syst Evol Microbiol 2009;59: 589– 608 [CrossRef]
    [Google Scholar]
  3. Ørskov J. Investigations into the Morphology of the Ray Fungi Copenhagen, Denmark: Levin and Munksgaard; 1923
    [Google Scholar]
  4. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985; pp 173– 199
    [Google Scholar]
  5. Gao R, Liu C, Zhao J, Jia F, Yu C et al. Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora. Antonie van Leeuwenhoek 2014;105: 307– 315 [CrossRef]
    [Google Scholar]
  6. Koch C, Kroppenstedt RM, Stackebrandt E. Intrageneric relationships of the actinomycete genus Micromonospora. Int J Syst Bacteriol 1996;46: 383– 387 [CrossRef]
    [Google Scholar]
  7. Kasai H, Tamura T, Harayama S. Intrageneric relationships among Micromonospora species deduced from gyrB-based phylogeny and DNA relatedness. Int J Syst Evol Microbiol 2000;50: 127– 134 [CrossRef]
    [Google Scholar]
  8. Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME et al. Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Sci Rep 2018;8: 525 [CrossRef]
    [Google Scholar]
  9. Nouioui I, Carro L, García-López M, Meier-Kolthoff J, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2007;2018: 9
    [Google Scholar]
  10. Sangal V, Goodfellow M, Jones AL, Schwalbe EC, Blom J et al. Next-generation systematics: an innovative approach to resolve the structure of complex prokaryotic taxa. Sci Rep 2016;6: 38392 [CrossRef]
    [Google Scholar]
  11. Tang B, Xie F, Zhao W, Wang J, Dai S et al. A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus. Synth Syst Biotechnol 2016;1: 169– 186 [CrossRef]
    [Google Scholar]
  12. Riesco R, Carro L, Román-Ponce B, Prieto C, Blom J et al. Defining the species Micromonospora saelicesensis and Micromonospora noduli under the framework of genomics. Front Microbiol 2018;9: 1360 [CrossRef]
    [Google Scholar]
  13. 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]
  14. 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]
  15. Hu D, Chen Y, Sun C, Jin T, Fan G et al. Genome guided investigation of antibiotics producing Actinomycetales strain isolated from a Macau mangrove ecosystem. Sci Rep 2018;8: 14271 [CrossRef]
    [Google Scholar]
  16. Genilloud O, Genus I. Micromonospora Ørskov 1923, 156AL In Goodfellow M, Kämpfer P, Busse HJ, Trujillo ME, Suzuki KI. (editors) Bergey’s Manual of Systematic Bacteriology5, 2nd edn. New York: Springer; 2012; pp 1039– 1057
    [Google Scholar]
  17. Trujillo ME, Bacigalupe R, Pujic P, Igarashi Y, Benito P et al. Genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style?. PLoS One 2014;9: e108522 [CrossRef]
    [Google Scholar]
  18. Carro L, Veyisoglu A, Cetin D, Igual JM, Klenk H-P et al. A study of three bacteria isolated from marine sediment and description of Micromonospora globispora sp. nov. Syst Appl Microbiol 2019;42: 190– 197 [CrossRef]
    [Google Scholar]
  19. Trujillo ME, Kroppenstedt RM, Fernandez-Molinero C, Schumann P, Martínez-Molina E. Micromonospora lupini sp. nov. and Micromonospora saelicesensis sp. nov., isolated from root nodules of Lupinus angustifolius. Int J Syst Evol Microbiol 2007;57: 2799– 2804 [CrossRef]
    [Google Scholar]
  20. Carro L, Riesco R, Spröer C, Trujillo ME. Micromonospora luteifusca sp. nov. isolated from cultivated Pisum sativum. Syst Appl Microbiol 2016;39: 237– 242 [CrossRef]
    [Google Scholar]
  21. Hirsch P, Mevs U, Kroppenstedt RM, Schumann P, Stackebrandt E. Cryptoendolithic actinomycetes from Antarctic sandstone rock samples: Micromonospora endolithica sp. nov. and two isolates related to Micromonospora coerulea Jensen 1932. Syst Appl Microbiol 2004;27: 166– 174 [CrossRef]
    [Google Scholar]
  22. Carro L, Razmilic V, Nouioui I, Richardson L, Pan C et al. Hunting for cultivable Micromonospora strains in soils of the Atacama Desert. Antonie van Leeuwenhoek 2018;111: 1375– 1387 [CrossRef]
    [Google Scholar]
  23. Jiang Y, Li Q, Chen X, Jiang C. Isolation and cultivation methods of Actinobactera In Dhanasekaran D, Jiang Y. (editors) Actinobacteria–Basics and Biotechnological Application London: IntechOpen; 2016; pp 39– 57 pp
    [Google Scholar]
  24. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16: 313– 340 [CrossRef]
    [Google Scholar]
  25. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949;57: 141– 145
    [Google Scholar]
  26. Waksman SA. The Actinomycetes A summary of Current Knowledge New York: Ronald Press; 1967
    [Google Scholar]
  27. Waksman SA. The Actinomycetes Classification, Identification and Descriptions of Genera and Species vol. II Baltimore: Williams & Wilkins; 1961
    [Google Scholar]
  28. Kelly KL. Color-Name Charts Illustrated with Centroid Colors Chicago (Published in USA): Inter-Society Color Council-National Bureau of Standards; 1964
    [Google Scholar]
  29. Nash P, Krent M. Culture media In Ballows AHW, Herrmann KL, Isenberg HD, Shadomy HJ. (editors) Manual of Clinical Microbiology, 5th ed. Washington, DC: American Society for Microbiology; 1991; pp 1268– 1270
    [Google Scholar]
  30. 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]
  31. Goodfellow M. Numerical taxonomy of some Nocardioform bacteria. J Gen Microbiol 1971;69: 33– 80 [CrossRef]
    [Google Scholar]
  32. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974;24: 54– 63 [CrossRef]
    [Google Scholar]
  33. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974;28: 226– 231
    [Google Scholar]
  34. 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]
  35. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982;16: 584– 586
    [Google Scholar]
  36. Kuykendall LD, Roy MA, O'NEILL JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988;38: 358– 361 [CrossRef]
    [Google Scholar]
  37. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark: Microbial ID, Inc; 1990
  38. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990;13: 128– 130 [CrossRef]
    [Google Scholar]
  39. 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]
  40. Trujillo ME, Hong K, Genilloud O et al. The family Micromonosporaceae In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F et al. (editors) The Prokaryotes, 4th ed. Heidelberg: Springer Berlin; 2014; pp 499– 570
    [Google Scholar]
  41. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 1995;45: 240– 245 [CrossRef]
    [Google Scholar]
  42. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991;173: 697– 703 [CrossRef]
    [Google Scholar]
  43. 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 [CrossRef]
    [Google Scholar]
  44. 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]
    [Google Scholar]
  45. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4: 406– 425
    [Google Scholar]
  46. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17: 368– 376 [CrossRef]
    [Google Scholar]
  47. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39: 783– 791 [CrossRef]
    [Google Scholar]
  48. 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]
  49. Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ et al. antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification. Nucleic Acids Res 2017;45: W36– W41 [CrossRef]
    [Google Scholar]
  50. 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]
  51. Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 2010;5: e9490 [CrossRef]
    [Google Scholar]
  52. 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 [CrossRef]
    [Google Scholar]
  53. 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]
  54. Carro L, Pukall R, Spröer C, Kroppenstedt RM, Trujillo ME. Micromonospora halotolerans sp. nov., isolated from the rhizosphere of a Pisum sativum plant. Antonie van Leeuwenhoek 2013;103: 1245– 1254 [CrossRef]
    [Google Scholar]
  55. Carro L, Riesco R, Spröer C, Trujillo ME. Micromonospora ureilytica sp. nov., Micromonospora noduli sp. nov. and Micromonospora vinacea sp. nov., isolated from Pisum sativum nodules. Int J Syst Evol Microbiol 2016;66: 3509– 3514 [CrossRef]
    [Google Scholar]
  56. Fang B, Liu C, Guan X, Song J, Zhao J et al. Two new species of the genus Micromonospora: Micromonospora palomenae sp. nov. and Micromonospora harpali sp. nov. isolated from the insects. Antonie van Leeuwenhoek 2015;108: 141– 150 [CrossRef]
    [Google Scholar]
  57. Kim M, Oh H-S, Park S-C, 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]
  58. Maldonado LA et al. Salinispora arenicola gen. nov., sp. nov. and Salinispora tropica sp. nov., obligate marine actinomycetes belonging to the family Micromonosporaceae. Int J Syst Evol Microbiol 2005;55: 1759– 1766 [CrossRef]
    [Google Scholar]
  59. Rheims H, Schumann P, Rohde M, Stackebrandt E. Verrucosispora gifhornensis gen. nov., sp. nov., a new member of the actinobacterial family Micromonosporaceae. Int J Syst Bacteriol 1998;48 Pt 4: 1119– 1127 [CrossRef]
    [Google Scholar]
  60. Wang X, Jia F, Liu C, Zhao J, Wang L et al. Xiangella phaseoli gen. nov., sp. nov., a member of the family Micromonosporaceae. Int J Syst Evol Microbiol 2013;63: 2138– 2145 [CrossRef]
    [Google Scholar]
  61. 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]
  62. Disz T, Akhter S, Cuevas D, Olson R, Overbeek R et al. Accessing the seed genome databases via web services API: tools for programmers. BMC Bioinformatics 2010;11: 319 [CrossRef]
    [Google Scholar]
  63. Rosselló-Móra R, Trujillo ME, Sutcliffe IC. Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria. Antonie van Leeuwenhoek 2017;110: 455– 456 [CrossRef]
    [Google Scholar]
  64. Supong K, Suriyachadkun C, Pittayakhajonwut P, Suwanborirux K, Thawai C. Micromonospora spongicola sp. nov., an actinomycete isolated from a marine sponge in the gulf of Thailand. J Antibiot 2013;66: 505– 509 [CrossRef]
    [Google Scholar]
  65. Thawai C et al. Micromonospora eburnea sp. nov., isolated from a Thai peat swamp forest. Int J Syst Evol Microbiol 2005;55: 417– 422 [CrossRef]
    [Google Scholar]
  66. Jukes TH, Cantor CR. Evolution of protein molecules In Munro HN. editor Mammalian Protein Metabolism New York: Academic Press; 1969; pp 21– 132
    [Google Scholar]
  67. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 1978;75: 4801– 4805 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003752
Loading
/content/journal/ijsem/10.1099/ijsem.0.003752
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