1887

Abstract

A Gram-reaction-positive, motile, yellow-pigmented and rod-shaped bacterial strain, designated AR33, was isolated from the rhizosphere of L. growing in a former zinc/lead mining and processing site in Austria. A polyphasic approach was applied to determine its taxonomic position. 16S rRNA gene sequence analysis, and morphological and chemotaxonomic properties showed that strain AR33 belongs to the genus . Strain AR33 had peptidoglycan type B2 and the major menaquinones were MK-11, MK-10 and MK-12. The main branched-chain fatty acids were anteiso-C, anteiso-C and iso-C. Strain AR33 showed catalase and oxidase activity and multiple heavy metal resistances to zinc, lead and cadmium. The DNA G+C content was 70.1 mol%. Levels of 16S rRNA gene sequence similarity with closely related recognized species of the genus ranged between 98 and 99 %. However, DNA–DNA hybridization between strain AR33 and the type strains of three species showed values lower than 42 % relatedness. Therefore, differential phenotypic characteristics together with DNA–DNA relatedness suggested that strain AR33 can be recognized as representing a distinct species, for which the name sp. nov. is proposed. The type strain is AR33 (=DSM 101731=LMG 29235).

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2016-09-01
2024-03-19
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References

  1. Akimov V. N., Evtushenko L. I 2012; Genus IV. Agromyces . In Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol. 5 pp. 862–876 Edited by Goodfellow M., Kämpfer P., Busse H. J., Trujillo M. E., Suzuki K., Ludwig W., Whitman W. B. New York: Springer;
    [Google Scholar]
  2. Bankevich A., Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S., Lesin V. M., Nikolenko S. I., Pham S. et al. 2012; SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477 [View Article][PubMed]
    [Google Scholar]
  3. Bligh E. G., Dyer W. J. 1959; A rapid method of total lipid extraction and purification. Can J Biochem Physiol 37:911–917 [View Article][PubMed]
    [Google Scholar]
  4. Campisano A., Ometto L., Compant S., Pancher M., Antonielli L., Yousaf S., Varotto C., Anfora G., Pertot I. et al. 2014; Interkingdom transfer of the acne-causing agent, Propionibacterium acnes, from human to grapevine. Mol Biol Evol 31:1059–1065 [View Article][PubMed]
    [Google Scholar]
  5. Cappuccino J. G., Sherman N. 2002 Microbiology: a Laboratory Manual, 6th edn. San Francisco: Benjamin Cummings;
    [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 81:461–466 [View Article][PubMed]
    [Google Scholar]
  7. Castresana J. 2000; Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552 [View Article][PubMed]
    [Google Scholar]
  8. Cowan S. T., Steel K. J. 1965 Manual for the Identification of Medical Bacteria London: Cambridge University Press;
    [Google Scholar]
  9. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142 [View Article][PubMed]
    [Google Scholar]
  10. Dorofeeva L. V., Krausova V. I., Evtushenko L. I., Tiedje J. M. 2003; Agromyces albus sp. nov., isolated from a plant (Androsace sp.). Int J Syst Evol Microbiol 53:1435–1438 [View Article][PubMed]
    [Google Scholar]
  11. Edgar R. C. 2004; muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797 [View Article][PubMed]
    [Google Scholar]
  12. Ferooz J., Letesson J. J. 2010; Morphological analysis of the sheathed flagellum of Brucella melitensis . BMC Res Notes 3:333 [View Article][PubMed]
    [Google Scholar]
  13. García-Alcalde F., Okonechnikov K., Carbonell J., Cruz L. M., Götz S., Tarazona S., Dopazo J., Meyer T. F., Conesa A. 2012; Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics 28:2678–2679 [View Article][PubMed]
    [Google Scholar]
  14. Gledhill W. E., Casida L. E. 1969; Predominant Catalase-negative Soil Bacteria. III. Agromyces, gen. n., Microorganisms Intermediary to Actinomyces and Nocardia . Appl Microbiol 18:340–349[PubMed]
    [Google Scholar]
  15. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. H.-N. 1974; Nocardia coeliaca, Nocardia autotrophica, and the Nocardin Strain. Int J Syst Evol Microbiol 24:54–63
    [Google Scholar]
  16. Hamada M., Shibata C., Tamura T., Suzuki K. 2014; Agromyces marinus sp. nov., a novel actinobacterium isolated from sea sediment. J Antibiot 67:703–706 [View Article][PubMed]
    [Google Scholar]
  17. Huss V. A., Festl H., Schleifer K. H. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192 [View Article][PubMed]
    [Google Scholar]
  18. Jung S. Y., Lee S. Y., Oh T. K., Yoon J. H. 2007; Agromyces allii sp. nov., isolated from the rhizosphere of Allium victorialis var. platyphyllum . Int J Syst Evol Microbiol 57:588–593 [View Article][PubMed]
    [Google Scholar]
  19. Jurado V., Groth I., Gonzalez J. M., Laiz L., Saiz-Jimenez C. 2005a; Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov. Int J Syst Evol Microbiol 55:153–157 [View Article][PubMed]
    [Google Scholar]
  20. Jurado V., Groth I., Gonzalez J. M., Laiz L., Saiz-Jimenez C. 2005b; Agromyces subbeticus sp. nov., isolated from a cave in southern Spain. Int J Syst Evol Microbiol 55:1897–1901 [View Article][PubMed]
    [Google Scholar]
  21. Jurado V., Groth I., Gonzalez J. M., Laiz L., Schuetze B., Saiz-Jimenez C. 2005c; Agromyces italicus sp. nov., Agromyces humatus sp. nov. and Agromyces lapidis sp. nov., isolated from Roman catacombs. Int J Syst Evol Microbiol 55:871–875 [View Article][PubMed]
    [Google Scholar]
  22. Kim M., Park S. C., Baek I., Chun J. 2015; Large-scale evaluation of experimentally determined DNA G+C contents with whole genome sequences of prokaryotes. Syst Appl Microbiol 38:79–83 [View Article][PubMed]
    [Google Scholar]
  23. Kuffner M., Puschenreiter M., Wieshammer G., Gorfer M., Sessitsch A. 2008; Rhizosphere bacteria affect growth and metal uptake of heavy metal accumulating willows. Plant and Soil 304:35–44 [View Article]
    [Google Scholar]
  24. Kuykendall L. D., Roy M. A., O'Neill J. J., Devine T. E. 1988; Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum . Int J Syst Bacteriol 38:358–361 [View Article]
    [Google Scholar]
  25. Lagesen K., Hallin P., Rødland E. A., Staerfeldt H. H., Rognes T., Ussery D. W. 2007; RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108 [View Article][PubMed]
    [Google Scholar]
  26. Lanyi B. 1987; Classical and rapid identification methods for medically important bacteria. Methods Microbiol 19:1–67 [CrossRef]
    [Google Scholar]
  27. Lee M., Ten L. N., Woo S. G., Park J. 2011; Agromyces soli sp. nov., isolated from farm soil. Int J Syst Evol Microbiol 61:1286–1292 [View Article][PubMed]
    [Google Scholar]
  28. Miller L. T. 1982; A single derivatization method for bacterial fatty acid methyl esters including hydroxy acids. J Clin Microbiol 16:584–586
    [Google Scholar]
  29. Rivas R., Trujillo M. E., Mateos P. F., Martínez-Molina E., Velázquez E. 2004; Agromyces ulmi sp. nov., a xylanolytic bacterium isolated from Ulmus nigra in Spain. Int J Syst Evol Microbiol 54:1987–1990 [View Article][PubMed]
    [Google Scholar]
  30. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  31. Schleifer K. H. 1985; Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156 [CrossRef]
    [Google Scholar]
  32. Schleifer K. H., Kandler O. 1972; Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477[PubMed]
    [Google Scholar]
  33. Schneider C. A., Rasband W. S., Eliceiri K. W. 2012; NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9:671–675 [View Article][PubMed]
    [Google Scholar]
  34. Staneck J. L., Roberts G. D. 1974; Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231[PubMed]
    [Google Scholar]
  35. Takeuchi M., Hatano K. 2001; Agromyces luteolus sp. nov., Agromyces rhizospherae sp. nov. and Agromyces bracchium sp. nov., from the mangrove rhizosphere. Int J of Evol Microbiol 51:1529–1537 [View Article]
    [Google Scholar]
  36. Tamura K., Nei M., Kumar S. 2004; Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A 101:11030–11035 [View Article][PubMed]
    [Google Scholar]
  37. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  38. Tindall B. J. 1990a; A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130 [View Article]
    [Google Scholar]
  39. Tindall B. J. 1990b; Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 66:199–202 [View Article]
    [Google Scholar]
  40. Tindall B. J., Rosselló-Móra R., Busse H. J., Ludwig W., Kämpfer P. 2010; Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266 [View Article][PubMed]
    [Google Scholar]
  41. Tindall B. J., Sikorski J., Smibert R. M., Kreig N. R. 2007; Phenotypic characterization and the principles of comparative systematics. In Methods for General and Molecular Microbiology, 3rd edn. pp. 330–393 . Edited by Reddy C. A., Beveridge T. J., Breznak J. A., Marzluf G., Schmidt T. M. Washington DC: L. R. Snyder ASM Press;
    [Google Scholar]
  42. Wenzel W. W., Jockwer F. 1999; Accumulation of heavy metals in plants grown on mineralised soils of the Austrian Alps. Environmental Pollution 104:145–155 [View Article]
    [Google Scholar]
  43. Yoon J. H., Schumann P., Kang S. J., Park S., Oh T. K. 2008; Agromyces terreus sp. nov., isolated from soil. Int J Syst Evol Microbiol 58:1308–1312 [View Article][PubMed]
    [Google Scholar]
  44. Zgurskaya H. I., Evtushenko L. I., Akimov V. N., Voyevoda H. V., Dobrovolskaya T. G., Lysak L. V., Kalakoutskii L. V. 1992; Emended description of the genus Agromyces and description of Agromyces cerinus subsp. cerinus sp. nov., subsp. nov., Agromyces cerinus subsp. nitratus sp. nov., subsp. nov., Agromyces fucosus subsp. fucosus sp. nov., subsp. nov., and Agromyces fucosus subsp. hippuratus sp. nov., subsp. nov. IntJ Syst Bacteriol 42:635–641 [View Article]
    [Google Scholar]
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