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Abstract

A Gram-stain-positive, spore-forming actinomycete strain (HKI0641) was isolated from a soil sample collected in the Black Forest, Germany. During screening for antimicrobial natural products this bacterium was identified as a producer of the antibiotic telomycin. Morphological characteristics and chemotaxonomic data indicated that the strain belonged to the genus . The peptidoglycan of strain HKI0641 contained -diaminopimelic acid, and the fatty acid profile consisted predominantly of anteiso-C, iso-C, iso-C and C. MK-10(H), MK-10(H) and MK-10 were identified as the major menaquinones. To determine the taxonomic positioning of strain HKI0641, we computed a binary tanglegram of two rooted phylogenetic trees that were based upon 16S rRNA and gene sequences. The comparative analysis of the two common classification methods strongly supported the phylogenetic affiliation with the genus , but it also revealed discrepancies in the assignment at the level of the genomic species. 16S rRNA gene sequence analysis identified DSM 45161 (99.1 % sequence similarity) and DSM 45555 (99.0 %) as the nearest taxonomic neighbours, whereas the sequence of strain HKI0641 indicated a closer relationship to DSM 43813 (95.1 %). By means of DNA–DNA hybridization experiments, it was possible to resolve this issue and to clearly differentiate strain HKI0641 from other species of the genus . The type strains of the aforementioned species of the genus could be further distinguished from strain HKI0641 by several phenotypic properties, such as colony colour, NaCl tolerance and the utilization of carbon sources. The isolate was therefore assigned to a novel species of the genus , for which the name sp. nov. is proposed. The type strain is HKI0641 ( = DSM 45708 = CIP 110415).

Funding
This study was supported by the:
  • Deutsche Forschungsgemeinschaft (DFG)
  • Jena School for Microbial Communication (JSMC)
  • German Academic Exchange Service (DAAD) (Award A1071666)
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2013-10-01
2024-11-10
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References

  1. Alonso-Vega P., Normand P., Bacigalupe R., Pujic P., Lajus A., Vallenet D., Carro L., Coll P., Trujillo M. E. ( 2012 ). Genome sequence of Micromonospora lupini Lupac 08, isolated from root nodules of Lupinus angustifolius . . J Bacteriol 194, 4135. [View Article] [PubMed]
    [Google Scholar]
  2. Bérdy J. ( 2005 ). Bioactive microbial metabolites. . J Antibiot (Tokyo) 58, 126. [View Article] [PubMed]
    [Google Scholar]
  3. Böcker S., Hüffner F., Truss A., Wahlström M. ( 2009 ). A faster fixed-parameter approach to drawing binary tanglegrams. . Lect Notes Comput Sci 5917, 3849. [View Article]
    [Google Scholar]
  4. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. ( 1978 ). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . . Proc Natl Acad Sci U S A 75, 48014805. [View Article] [PubMed]
    [Google Scholar]
  5. Carro L., Spröer C., Alonso P., Trujillo M. E. ( 2012 ). Diversity of Micromonospora strains isolated from nitrogen fixing nodules and rhizosphere of Pisum sativum analyzed by multilocus sequence analysis. . Syst Appl Microbiol 35, 7380. [View Article] [PubMed]
    [Google Scholar]
  6. Cashion P., Holder-Franklin M. A., McCully J., Franklin M. ( 1977 ). A rapid method for the base ratio determination of bacterial DNA. . Anal Biochem 81, 461466. [View Article] [PubMed]
    [Google Scholar]
  7. Collins M. D., Jones D. ( 1980 ). Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2,4-diaminobutyric acid. . J Appl Bacteriol 48, 459470. [View Article]
    [Google Scholar]
  8. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. ( 1977 ). Distribution of menaquinones in actinomycetes and corynebacteria. . J Gen Microbiol 100, 221230. [View Article] [PubMed]
    [Google Scholar]
  9. Cundliffe E., Demain A. L. ( 2010 ). Avoidance of suicide in antibiotic-producing microbes. . J Ind Microbiol Biotechnol 37, 643672. [View Article] [PubMed]
    [Google Scholar]
  10. De Ley J., Cattoir H., Reynaerts A. ( 1970 ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12, 133142. [View Article] [PubMed]
    [Google Scholar]
  11. Dimkpa C. O., Merten D., Svatoš A., Büchel G., Kothe E. ( 2009 ). Metal-induced oxidative stress impacting plant growth in contaminated soil is alleviated by microbial siderophores. . Soil Biol Biochem 41, 154162. [View Article]
    [Google Scholar]
  12. Euzéby J. P. ( 2012 ). List of prokaryotic names with standing in nomenclature (LPSN). Société de Bactériologie Systématique et Vétérinaire (SBSV). . http://www.bacterio.cict.fr
    [Google Scholar]
  13. Garcia L. C., Martínez-Molina E., Trujillo M. E. ( 2010 ). Micromonospora pisi sp. nov., isolated from root nodules of Pisum sativum . . Int J Syst Evol Microbiol 60, 331337. [View Article] [PubMed]
    [Google Scholar]
  14. Genilloud O. ( 2012 ). Genus I. Micromonospora Ørskov 1923, 156AL . . In: Bergey's Manual of Systematic Bacteriology, , 2nd edn., vol. 5, pp. 10391057. Edited by Goodfellow M., Kämpfer P., Busse H.-J., Trujillo M. E., Suzuki K., Ludwig W., Whitman W. B. . New York:: Springer;.
    [Google Scholar]
  15. Goodfellow M., Stanton L. J., Simpson K. E., Minnikin D. E. ( 1990 ). Numerical and chemical classification of Actinoplanes and some related actinomycetes. . J Gen Microbiol 136, 1936. [View Article]
    [Google Scholar]
  16. Griebel T., Brinkmeyer M., Böcker S. ( 2008 ). EPoS: a modular software framework for phylogenetic analysis. . Bioinformatics 24, 23992400. [View Article] [PubMed]
    [Google Scholar]
  17. Groth I., Schumann P., Weiss N., Martin K., Rainey F. A. ( 1996 ). Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. . Int J Syst Bacteriol 46, 234239. [View Article] [PubMed]
    [Google Scholar]
  18. Hayakawa M., Nonomura H. ( 1987 ). Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. . J Ferment Technol 65, 501509. [View Article]
    [Google Scholar]
  19. Hirsch A. M., Valdés M. ( 2010 ). Micromonospora: an important microbe for biomedicine and potentially for biocontrol and biofuels. . Soil Biol Biochem 42, 536542. [View Article]
    [Google Scholar]
  20. Hotta K., Okami Y. ( 1996 ). Diversity in aminoglycoside antibiotic resistance of actinomycetes and its exploitation in the search for novel antibiotics. . J Ind Microbiol 17, 352358. [View Article]
    [Google Scholar]
  21. Huss V. A. R., Festl H., Schleifer K. H. ( 1983 ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. . Syst Appl Microbiol 4, 184192. [View Article] [PubMed]
    [Google Scholar]
  22. Kasai H., Tamura T., Harayama S. ( 2000 ). Intrageneric relationships among Micromonospora species deduced from gyrB-based phylogeny and DNA relatedness. . Int J Syst Evol Microbiol 50, 127134. [View Article] [PubMed]
    [Google Scholar]
  23. Koch C., Kroppenstedt R. M., Rainey F. A., Stackebrandt E. ( 1996 ). 16S Ribosomal DNA analysis of the genera Micromonospora, Actinoplanes, Catellatospora, Catenuloplanes, Couchioplanes, Dactylosporangium, and Pilimelia and emendation of the family Micromonosporaceae . . Int J Syst Bacteriol 46, 765768. [View Article] [PubMed]
    [Google Scholar]
  24. Kumar N. G., Urry D. W. ( 1973 ). Proton magnetic resonance assignments of the polypeptide antibiotic telomycin. . Biochemistry 12, 38113817. [View Article] [PubMed]
    [Google Scholar]
  25. Luedemann G. M., Brodsky B. C. ( 1963 ). Taxonomy of gentamicin-producing Micromonospora . . Antimicrob Agents Chemother (Bethesda) 161, 116124.[PubMed]
    [Google Scholar]
  26. Minnikin D. E., Alshamaony L., Goodfellow M. ( 1975 ). Differentiation of Mycobacterium, Nocardia, and related taxa by thin-layer chromatographic analysis of whole-organism methanolysates. . J Gen Microbiol 88, 200204. [View Article] [PubMed]
    [Google Scholar]
  27. Minnikin D. E., Collins M. D., Goodfellow M. ( 1979 ). Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. . J Appl Bacteriol 47, 8795. [View Article]
    [Google Scholar]
  28. Nett M., Hertweck C. ( 2011 ). Farinamycin, a quinazoline from Streptomyces griseus . . J Nat Prod 74, 22652268. [View Article] [PubMed]
    [Google Scholar]
  29. Nett M., Ikeda H., Moore B. S. ( 2009 ). Genomic basis for natural product biosynthetic diversity in the actinomycetes. . Nat Prod Rep 26, 13621384. [View Article] [PubMed]
    [Google Scholar]
  30. Paradis E., Claude J., Strimmer K. ( 2004 ). APE: analyses of phylogenetics and evolution in R language. . Bioinformatics 20, 289290. [View Article] [PubMed]
    [Google Scholar]
  31. Raaijmakers J. M., Mazzola M. ( 2012 ). Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. . Annu Rev Phytopathol 50, 403424. [View Article] [PubMed]
    [Google Scholar]
  32. Schleifer K. H., Kandler O. ( 1972 ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. . Bacteriol Rev 36, 407477.[PubMed]
    [Google Scholar]
  33. Schumann P. ( 2011 ). Peptidoglycan Structure. . Methods Microbiol 38, 101129. [View Article]
    [Google Scholar]
  34. Sheehan J. C., Mania D., Nakamura S., Stock J. A., Maeda K. ( 1968 ). The structure of telomycin. . J Am Chem Soc 90, 462470. [View Article] [PubMed]
    [Google Scholar]
  35. Shirling E. B., Gottlieb D. ( 1966 ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16, 313340. [View Article]
    [Google Scholar]
  36. Stackebrandt E., Rainey F. A., Ward-Rainey N. L. ( 1997 ). Proposal for a new hierarchic classification system, Actinobacteria classis nov.. Int J Syst Bacteriol 47, 479491. [View Article]
    [Google Scholar]
  37. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. & other authors ( 1987 ). International Committee on Systematic Bacteriology. R eport of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463464. [View Article]
    [Google Scholar]
  38. Zhi X.-Y., Li W.-J., Stackebrandt E. ( 2009 ). 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 59, 589608. [View Article] [PubMed]
    [Google Scholar]
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