1887

Abstract

A filamentous, Gram-positive actinobacterium was isolated from acidic rocks in a medieval alum slate mine and was investigated by means of a polyphasic taxonomic approach. A 16S rRNA gene sequence similarity study indicated that strain HKI 0501 forms an individual line of descent and is related to certain members of the suborder , order (<95 % sequence similarity). Distance-matrix and neighbour-joining analyses set the branching point of the novel isolate between two clades, one being represented by members of the genus (family ‘’) and the other by members of the genera and (family and family , respectively). The organism had -diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan and xylose as the characteristic cell-wall sugar. The muramic acid in the peptidoglycan was found to be -acetylated. The major menaquinones were MK-9(H), MK-9(H) and MK-9(H) and the fatty acid profile was characterized by the predominance of iso-C, 10-methyl C, C 9 and 10-methyl iso-C. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol and several unknown phospholipids and glycolipids. Mycolic acids were absent. The DNA G+C content was 65 mol%. The distinct phylogenetic position and the phenotypic markers that clearly separate the novel organism from all other members of the suborder indicate that strain HKI 0501 represents a novel genus and species, for which the name gen. nov., sp. nov. is proposed. The type strain of is HKI 0501 (=DSM 19247 =JCM 14718).

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2008-07-01
2019-12-09
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References

  1. Ahrens, R. & Moll, G. ( 1970; ). Ein neues knospendes Bakterium aus der Ostsee. Arch Mikrobiol 70, 243–265 (in German).[CrossRef]
    [Google Scholar]
  2. Becker, B., Lechevalier, M. P. & Lechevalier, H. A. ( 1965; ). Chemical composition of cell-wall preparations from strains of various form-genera of aerobic actinomycetes. Appl Microbiol 13, 236–243.
    [Google Scholar]
  3. Becking, J. H. ( 1970; ). Frankiaceae fam. nov. (Actinomycetales) with one new combination and six new species of the genus Frankia Brunchorst 1887, 174. Int J Syst Bacteriol 20, 201–220.[CrossRef]
    [Google Scholar]
  4. Brunchorst, J. ( 1886; ). Über einige Wurzelanschwellungen besonders diejenigen von Alnus und den Elaeagnaceen. Bot Inst Tubingen 2, 151–177 (in German).
    [Google Scholar]
  5. Carlsohn, M. R., Groth, I., Tan, G. Y. A., Schütze, B., Saluz, H.-P., Munder, T., Yang, J., Wink, J. & Goodfellow, M. ( 2007; ). Amycolatopsis saalfeldensis sp. nov., a novel actinomycete isolated from a medieval alum slate mine. Int J Syst Evol Microbiol 57, 1640–1646.[CrossRef]
    [Google Scholar]
  6. 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, 459–470.[CrossRef]
    [Google Scholar]
  7. Collins, M. D., Pirouz, T., Goodfellow, M. & Minnikin, D. E. ( 1977; ). Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100, 221–230.[CrossRef]
    [Google Scholar]
  8. Collins, M. D., Faulkner, M. & Keddie, R. M. ( 1984; ). Menaquinone composition of some spore forming actinomycetes. Syst Appl Microbiol 5, 20–29.[CrossRef]
    [Google Scholar]
  9. De Soete, G. ( 1983; ). A least squares algorithm for fitting additive trees to proximity data. Psychometrika 48, 621–626.[CrossRef]
    [Google Scholar]
  10. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  11. Felsenstein, J. ( 1993; ). phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  12. Garrity, G. M., Lilburn, T. G., Cole, J. R., Harrison, S. H., Euzéby, J. & Tindall, B. J. ( 2007; ). The Taxonomic Outline of Bacteria and Archaea. Part 10. The Bacteria: phylum Actinobacteria: class “Actinobacteria”. Release 7.7. http://www.taxonomicoutline.org
  13. 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, 234–239.[CrossRef]
    [Google Scholar]
  14. Groth, I., Schütze, B., Boettcher, T., Pullen, C. B., Rodriguez, C., Leistner, E. & Goodfellow, M. ( 2003; ). Kitasatospora putterlickiae sp. nov., isolated from rhizosphere soil, transfer of Streptomyces kifunensis to the genus Kitasatospora as Kitasatospora kifunensis comb. nov., and emended description of Streptomyces aureofaciens Duggar 1948. Int J Syst Evol Microbiol 53, 2033–2040.[CrossRef]
    [Google Scholar]
  15. Hahn, D., Lechevalier, M. P., Fischer, A. & Stackebrandt, E. ( 1989; ). Evidence for a close phylogenetic relationship between members of the genera Frankia, Geodermatophilus and Blastococcus and emendation of the family Frankiaceae. Syst Appl Microbiol 11, 236–242.[CrossRef]
    [Google Scholar]
  16. Hasegawa, T., Takizawa, M. & Tanida, S. ( 1983; ). A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29, 319–322.[CrossRef]
    [Google Scholar]
  17. Hayakawa, M. & Nonomura, H. ( 1987; ). Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 65, 501–509.[CrossRef]
    [Google Scholar]
  18. Itoh, T., Kudo, T., Parenti, F. & Seino, A. ( 1989; ). Amended description of the genus Kineosporia, based on chemotaxonomic and morphological studies. Int J Syst Bacteriol 39, 168–173.[CrossRef]
    [Google Scholar]
  19. Jones, K. L. ( 1949; ). Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 57, 141–145.
    [Google Scholar]
  20. Jukes, T. H. & Cantor, C. R. ( 1969; ). Evolution of protein molecules. In Mammalian Protein Metabolism, vol. 3, pp. 21–132. Edited by H. N. Munro. New York: Academic Press.
  21. Kroppenstedt, R. M. ( 1985; ). Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics, pp. 173–199. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
  22. Kudo, T., Matsushima, K., Itoh, T., Sasaki, J. & Suzuki, K. ( 1998; ). Description of four new species of the genus Kineosporia: Kineosporia succinea sp. nov., Kineosporia rhizophila sp. nov., Kineosporia mikuniensis sp. nov. and Kineosporia rhamnosa sp. nov., isolated from plant samples, and amended description of the genus Kineosporia. Int J Syst Bacteriol 48, 1245–1255.[CrossRef]
    [Google Scholar]
  23. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A. M., Alloni, G., Azevedo, V., Bertero, M. G., Bessières, P., Bolotin, A. & other authors ( 1997; ). The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390, 249–256.[CrossRef]
    [Google Scholar]
  24. Küster, E. & Williams, S. T. ( 1964; ). Selection of media for isolation of Streptomyces. Nature 202, 928–929.[CrossRef]
    [Google Scholar]
  25. Lechevalier, M. P. ( 1994; ). Taxonomy of the genus Frankia (Actinomycetales). Int J Syst Bacteriol 44, 1–8.[CrossRef]
    [Google Scholar]
  26. Lechevalier, M. P., Lechevalier, H. A. & Holbert, P. E. ( 1968; ). Sporichthya, un nouveau genre de Streptomycetaceae. Ann Inst Pasteur (Paris) 114, 277–286 (in French).
    [Google Scholar]
  27. Luedemann, G. M. ( 1968; ). Geodermatophilus, a new genus of the Dermatophilaceae (Actinomycetales). J Bacteriol 96, 1848–1858.
    [Google Scholar]
  28. Luedemann, G. M. & Fonseca, A. F. ( 1989; ). Genus Geodermatophilus Luedemann 1968, 1857AL. In Bergey's Manual of Systematic Bacteriology, vol. 4, pp. 2406–2409. Edited by S. T. Williams, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
  29. MacKenzie, S. L. ( 1987; ). Gas chromatographic analysis of amino acids as the N-heptafluorobutyryl isobutyl esters. J Assoc Off Anal Chem 70, 151–160.
    [Google Scholar]
  30. Maidak, B. L., Olsen, G. J., Larsen, N., Overbeek, R., McCaughey, M. J. & Woese, C. R. ( 1997; ). The RDP (Ribosomal Database Project). Nucleic Acids Res 25, 109–111.[CrossRef]
    [Google Scholar]
  31. Maszenan, A. M., Tay, J.-H., Schumann, P., Jiang, H.-L. & Tay, S. T.-L. ( 2005; ). Quadrisphaera granulorum gen. nov., sp. nov., a Gram-positive polyphosphate-accumulating coccus in tetrads or aggregates isolated from aerobic granules. Int J Syst Evol Microbiol 55, 1771–1777.[CrossRef]
    [Google Scholar]
  32. Mesbah, M., Premachandran, U. & Whitman, W. B. ( 1989; ). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159–167.[CrossRef]
    [Google Scholar]
  33. Mevs, U., Stackebrandt, E., Schumann, P., Gallikowski, C. A. & Hirsch, P. ( 2000; ). Modestobacter multiseptatus gen. nov., sp. nov., a budding actinomycete from soils of the Asgard Range (Transantarctic Mountains). Int J Syst Evol Microbiol 50, 337–346.[CrossRef]
    [Google Scholar]
  34. 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, 200–204.[CrossRef]
    [Google Scholar]
  35. 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, 87–95.[CrossRef]
    [Google Scholar]
  36. Mirza, M. S., Janse, J. D., Hahn, D. & Akkermans, A. D. L. ( 1991; ). Identification of atypical Frankia strains by fatty acid analysis. FEMS Microbiol Lett 83, 91–98.[CrossRef]
    [Google Scholar]
  37. Mohagheghi, A., Grohmann, K., Himmel, M., Leighton, L. & Updegraff, D. M. ( 1986; ). Isolation and characterization of Acidothermus cellulolyticus gen. nov., sp. nov., a new genus of thermophilic, acidophilic, cellulolytic bacteria. Int J Syst Bacteriol 36, 435–443.[CrossRef]
    [Google Scholar]
  38. Normand, P., Orso, S., Cournoyer, B., Jeannin, P., Chapelon, C., Dawson, J., Evtushenko, L. & Misra, K. ( 1996; ). Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae. Int J Syst Bacteriol 46, 1–9.[CrossRef]
    [Google Scholar]
  39. Pagani, H. & Parenti, F. ( 1978; ). Kineosporia, a new genus of the order Actinomycetales. Int J Syst Bacteriol 28, 401–406.[CrossRef]
    [Google Scholar]
  40. Pospiech, A. & Neumann, B. ( 1995; ). A versatile quick-prep of genomic DNA from gram-positive bacteria. Trends Genet 11, 217–218.[CrossRef]
    [Google Scholar]
  41. Prauser, H. & Falta, R. ( 1968; ). Phagensensibilität, Zellwand-Zusammensetzung und Taxonomie von Actinomyceten. Z Allg Mikrobiol 8, 39–46 (in German).[CrossRef]
    [Google Scholar]
  42. Rainey, F. A., Schumann, P., Prauser, H., Toalster, R. & Stackebrandt, E. ( 1993; ). Sporichthya polymorpha represents a novel line of descent within the order Actinomycetales. FEMS Microbiol Lett 109, 263–268.[CrossRef]
    [Google Scholar]
  43. Rhuland, L. E., Work, E., Denman, R. F. & Hoare, D. S. ( 1955; ). The behaviour of the isomers of α,ϵ-diaminopimelic acid on paper chromatograms. J Am Chem Soc 77, 4844–4846.[CrossRef]
    [Google Scholar]
  44. Schleifer, K. H. & Seidl, P. H. ( 1985; ). Chemical composition and structure of murein. In Chemical Methods in Bacterial Systematics, pp. 201–215. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
  45. Schön, R. & Groth, I. ( 2006; ). Practical thin layer chromatography techniques for diaminopimelic acid and whole cell sugar analyses in the classification of environmental actinomycetes. J Basic Microbiol 46, 243–249.[CrossRef]
    [Google Scholar]
  46. Schumann, P., Prauser, H., Rainey, F. A., Stackebrandt, E. & Hirsch, P. ( 1997; ). Friedmanniella antarctica gen. nov., sp. nov., an ll-diaminopimelic acid-containing actinomycete from Antarctic sandstone. Int J Syst Bacteriol 47, 278–283.[CrossRef]
    [Google Scholar]
  47. Shirling, E. B. & Gottlieb, D. ( 1966; ). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.[CrossRef]
    [Google Scholar]
  48. 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, 479–491.[CrossRef]
    [Google Scholar]
  49. Tamura, T., Hayakawa, M. & Hatano, K. ( 1998; ). A new genus of the order Actinomycetales, Cryptosporangium gen. nov., with descriptions of Cryptosporangium arvum sp. nov. and Cryptosporangium japonicum sp. nov. Int J Syst Bacteriol 48, 995–1005.[CrossRef]
    [Google Scholar]
  50. Tamura, T., Hayakawa, M. & Hatano, K. ( 1999; ). Sporichthya brevicatena sp. nov. Int J Syst Bacteriol 49, 1779–1784.[CrossRef]
    [Google Scholar]
  51. Tao, T.-S., Yue, Y.-Y., Chen, W.-X. & Chen, W.-F. ( 2004; ). Proposal of Nakamurella gen. nov. as a substitute for the bacterial genus Microsphaera Yoshimi et al. 1996, and Nakamurellaceae fam. nov. as a substitute for the illegitimate bacterial family Microsphaeraceae Rainey et al. 1997. Int J Syst Evol Microbiol 54, 999–1000.[CrossRef]
    [Google Scholar]
  52. Uchida, K. & Aida, K. ( 1984; ). An improved method for the glycolate test for simple identification of the acyl type of bacterial cell walls. J Gen Appl Microbiol 30, 131–134.[CrossRef]
    [Google Scholar]
  53. Urzì, C., Salamone, P., Schumann, P., Rhode, M. & Stackebrandt, E. ( 2004; ). Blastococcus saxobsidens sp. nov., and emended descriptions of the genus Blastococcus Ahrens and Moll 1970 and Blastococcus aggregatus Ahrens and Moll 1970. Int J Syst Evol Microbiol 54, 253–259.[CrossRef]
    [Google Scholar]
  54. Xu, H.-X., Kawamura, Y., Li, N., Zhao, L., Li, T.-M., Li, Z.-Y., Shu, S. & Ezaki, T. ( 2000; ). A rapid method for determining the G+C content of bacterial chromosomes by monitoring fluorescence intensity during DNA denaturation in a capillary tube. Int J Syst Evol Microbiol 50, 1463–1469.[CrossRef]
    [Google Scholar]
  55. Yokota, A., Tamura, T., Nishii, T. & Hasegawa, T. ( 1993; ). Kineococcus aurantiacus gen. nov., sp. nov., a new aerobic, gram-positive, motile coccus with meso-diaminopimelic acid and arabinogalactan in the cell wall. Int J Syst Bacteriol 43, 52–57.[CrossRef]
    [Google Scholar]
  56. Yoon, J.-H., Kang, S.-J., Jung, S.-Y. & Oh, T.-K. ( 2007; ). Humicoccus flavidus gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 57, 56–59.[CrossRef]
    [Google Scholar]
  57. Yoshimi, Y., Hiraishi, A. & Nakamura, K. ( 1996; ). Isolation and characterization of Microsphaera multipartida gen. nov., sp. nov., a polysaccharide-accumulating Gram-positive bacterium from activated sludge. Int J Syst Bacteriol 46, 519–525.[CrossRef]
    [Google Scholar]
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