1887

Abstract

A novel filamentous bacterium, designated strain JIR-001, was isolated from hemipelagic sediment in deep seawater. This strain was non-motile, Gram-positive, aerobic, heterotrophic and thermophilic; colonies were of infinite form and ivory coloured with wrinkles between the centre and the edge of the colony on ISP2 medium. The isolate grew aerobically at 55–73 °C with the formation of aerial mycelia; spores were produced singly along the aerial mycelium. These morphological features show some similarities to those of the type strains of some species belonging to the family . Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain JIR-001 belongs to the family within the class . Similarity levels between the 16S rRNA gene sequence of strain JIR-001 and those of the type strains of species were 85.5–93.5 %; highest sequence similarity was with NariEX. In the DNA–DNA hybridization assays between strain JIR-001 and its phylogenetic neighbours the mean hybridization levels with NariEX, H0165, 500275 and LA5 were 5.3–7.5, 2.3–4.7, 2.1–4.8 and 2.5–4.9 %, respectively. The DNA G+C content of strain JIR-001 was 55.1 mol%. The major fatty acids were iso-C, iso-C, iso-C and C. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, glucolipid, phosphatidylserine, an amino-group containing phospholipid, an unknown phospholipid and two unknown lipids. The predominant menaquinone was MK-7 and the cell-wall peptidoglycan contained -diaminopimelic acid, glutamic acid and alanine. On the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons, strain JIR-001 is considered to represent a novel species in a new genus of the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is JIR-001 ( = JCM 18147 = CECT 8074).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.043596-0
2013-06-01
2020-10-31
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/6/1972.html?itemId=/content/journal/ijsem/10.1099/ijs.0.043596-0&mimeType=html&fmt=ahah

References

  1. Addou A. N., Schumann P., Spröer C., Hacene H., Cayol J. L., Fardeau M. L. ( 2012 ). Melghirimyces algeriensis gen. nov., sp. nov., a member of the family Thermoactinomycetaceae, isolated from a salt lake. . Int J Syst Evol Microbiol 62, 14911498. [CrossRef] [PubMed]
    [Google Scholar]
  2. Barrow G. I., Feltham R. K. A. (editors) ( 1993 ). Cowan and Steel’s Manual for the Identification of Medical Bacteria, , 3rd edn.. Cambridge:: Cambridge University Press;. [CrossRef]
    [Google Scholar]
  3. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. ( 1977 ). Distribution of menaquinones in actinomycetes and corynebacteria. . J Gen Microbiol 100, 221230.[PubMed] [CrossRef]
    [Google Scholar]
  4. Cross T., Walker P. D., Gould G. W. ( 1968 ). Thermophilic actinomycetes producing resistant endospores. . Nature 220, 352354. [CrossRef] [PubMed]
    [Google Scholar]
  5. Cross T., Davies F. L., Walker P. D. ( 1971 ). Thermoactinomyces vulgaris. I. Fine structure of the developing endospores. . In Spore Research, pp. 175187. Edited by Barker A. N., Gould G. W., Wolf J. A. . London:: Academic Press;.
    [Google Scholar]
  6. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989 ). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. . Int J Syst Bacteriol 39, 224229. [CrossRef]
    [Google Scholar]
  7. Fardeau M.-L., Ollivier B., Patel B. K. C., Magot M., Thomas P., Rimbault A., Rocchiccioli F., Garcia J.-L. ( 1997 ). Thermotoga hypogea sp. nov., a xylanolytic, thermophilic bacterium from an oil-producing well. . Int J Syst Bacteriol 47, 10131019. [CrossRef] [PubMed]
    [Google Scholar]
  8. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [CrossRef] [PubMed]
    [Google Scholar]
  9. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [CrossRef]
    [Google Scholar]
  10. Fitch W. M. ( 1971 ). Towards defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20, 406416. [CrossRef]
    [Google Scholar]
  11. Gordon R. E. ( 1966 ). Some criteria for the recognition of Nocardia madurae (Vincent) Blanchard. . J Gen Microbiol 45, 355364.[PubMed] [CrossRef]
    [Google Scholar]
  12. Gordon R. E., Mihm J. M. ( 1957 ). A comparative study of some strains received as nocardiae. . J Bacteriol 73, 1527.[PubMed]
    [Google Scholar]
  13. Gottlieb D. ( 1974 ). Actinomycetales . . In Bergey’s Manual of Determinative Bacteriology, , 8th edn., pp. 657688. Edited by Buchanan R. E., Gibbons N. E. . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  14. 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. [CrossRef] [PubMed]
    [Google Scholar]
  15. Hatayama K., Shoun H., Ueda Y., Nakamura A. ( 2005 ). Planifilum fimeticola gen. nov., sp. nov. and Planifilum fulgidum sp. nov., novel members of the family ‘Thermoactinomycetaceae’ isolated from compost. . Int J Syst Evol Microbiol 55, 21012104. [CrossRef] [PubMed]
    [Google Scholar]
  16. Ivanova E. P., Zhukova N. V., Lysenko A. M., Gorshkova N. M., Sergeev A. F., Mikhailov V. V., Bowman J. P. ( 2005 ). Loktanella agnita sp. nov. and Loktanella rosea sp. nov., from the north-west Pacific Ocean. . Int J Syst Evol Microbiol 55, 22032207. [CrossRef] [PubMed]
    [Google Scholar]
  17. Joffin J.-N., Leyral G. ( 2006 ). Dictionnaire des Techniques, , 4th edn. , vol. 1. Microbiologie Technique. Bordeaux:: CRDP d’Aquitaine;.
    [Google Scholar]
  18. Jukes T. H., Cantor C. R. ( 1969 ). Evolution of protein molecules. . In Mammalian Protein Metabolism, pp. 21132. Edited by Munro H. N. . New York:: Academic Press;.
    [Google Scholar]
  19. Kroppenstedt R. M., Goodfellow M. ( 2006 ). The family Thermomonosporaceae . . In The Prokaryotes, , 3rd edn., vol. 3, pp. 682724. Edited by Dworkin M., Falkow N., Rosenberg E., Schleifer K. H., Stackebrandt E. . New York:: Springer;. [CrossRef]
    [Google Scholar]
  20. Kumar Y., Westram R., Behrens S., Fuchs B., Glöckner F. O., Amann R., Meier H., Ludwig W. ( 2005 ). Graphical representation of ribosomal RNA probe accessibility data using ARB software package. . BMC Bioinformatics 6, 61. [CrossRef] [PubMed]
    [Google Scholar]
  21. Kumar Y., Westram R., Kipfer P., Meier H., Ludwig W. ( 2006 ). Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package. . BMC Bioinformatics 7, 240. [CrossRef] [PubMed]
    [Google Scholar]
  22. Lacey J., Cross T. ( 1989 ). Genus Thermoactinomyce Tsiklinsky 1899, 501AL . . In Bergey’s Manual of Systematic Bacteriology, vol. 4, pp. 25742585. Edited by Williams S. T., Sharpe M. E., Holt J. G. . Baltimore:: Williams & Wilkins;.
    [Google Scholar]
  23. Lacey J., Vince D. A. ( 1971 ). Endospore formation and germination in a new Thermoactinomyces species. . In Spore Research, pp. 181187. Edited by Barker A. N., Gould G. W., Wolf J. A. . London:: Academic Press;.
    [Google Scholar]
  24. Lane D. J. ( 1991 ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E., Goodfellow M. . Chichester:: Wiley;.
    [Google Scholar]
  25. Lányí B. ( 1987 ). Classical and rapid identification methods for medically important bacteria. . Methods Microbiol 19, 167. [CrossRef]
    [Google Scholar]
  26. Lechevalier M. P., Lechevalier H. A. ( 1970 ). A critical evaluation of the genera of aerobic actinomycetes. . In The Actinomycetales, pp. 393405. Edited by Prauser H. . Jena:: Gustav Fischer;.
    [Google Scholar]
  27. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S. et al. ( 2004 ). ARB: a software environment for sequence data. . Nucleic Acids Res 32, 13631371. [CrossRef] [PubMed]
    [Google Scholar]
  28. MacKenzie S. L. ( 1987 ). Gas chromatographic analysis of amino acids as the N-heptafluorobutyryl isobutyl esters. . J Assoc Off Anal Chem 70, 151160.[PubMed]
    [Google Scholar]
  29. Matsuo Y., Katsuta A., Matsuda S., Shizuri Y., Yokota A., Kasai H. ( 2006 ). Mechercharimyces mesophilus gen. nov., sp. nov. and Mechercharimyces asporophorigenens sp. nov., antitumour substance-producing marine bacteria, and description of Thermoactinomycetaceae fam. nov.. Int J Syst Evol Microbiol 56, 28372842. [CrossRef] [PubMed]
    [Google Scholar]
  30. 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, 159167. [CrossRef]
    [Google Scholar]
  31. Minnikin D. E., O’Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. ( 1984 ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2, 233241. [CrossRef]
    [Google Scholar]
  32. Nonomura H., Ohara Y. ( 1971 ). Distribution of actinomycetes in soil. X. New genus and species of monosporic actinomycetes in soil. . J Ferment Technol 49, 895903.
    [Google Scholar]
  33. Park Y.-H., Kim E., Yim D.-G., Kho Y.-H., Mheen T.-I., Goodfellow M. ( 1993 ). Suprageneric classification of Thermoactinomyces vulgaris by nucleotide sequencing of 5S ribosomal RNA. . Zentralbl Bakteriol 278, 469478. [CrossRef] [PubMed]
    [Google Scholar]
  34. Park D. J., Dastager S. G., Lee J. C., Yeo S. H., Yoon J. H., Kim C. J. ( 2007 ). Shimazuella kribbensis gen. nov., sp. nov., a mesophilic representative of the family Thermoactinomycetaceae . . Int J Syst Evol Microbiol 57, 26602664. [CrossRef] [PubMed]
    [Google Scholar]
  35. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  36. Schleifer K. H. ( 1985 ). Analysis of the chemical composition and primary structure of murein. . Methods Microbiol 18, 123156. [CrossRef]
    [Google Scholar]
  37. Schleifer K. H., Kandler O. ( 1972 ). Peptidoglycan types of bacterial cell walls and their taxonomic implications. . Bacteriol Rev 36, 407477.[PubMed]
    [Google Scholar]
  38. Shirling E. B., Gottlieb D. ( 1966 ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16, 313340. [CrossRef]
    [Google Scholar]
  39. Stackebrandt E., Woese C. R. ( 1981 ). Towards a phylogeny of the actinomycetes and related organisms. . Curr Microbiol 5, 197202. [CrossRef]
    [Google Scholar]
  40. Staneck J. L., Roberts G. D. ( 1974 ). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. . Appl Microbiol 28, 226231.[PubMed]
    [Google Scholar]
  41. Tsilinsky P. ( 1899 ). Sur les mucedinéés thermophiles. . Ann Inst Pasteur (Paris) 13, 500505. (in French).
    [Google Scholar]
  42. Tsukamura M. ( 1966 ). Adansonian classification of mycobacteria. . J Gen Microbiol 45, 253273.[PubMed] [CrossRef]
    [Google Scholar]
  43. von Jan M., Riegger N., Pötter G., Schumann P., Verbarg S., Spröer C., Rohde M., Lauer B., Labeda D. P., Klenk H. P. ( 2011 ). Kroppenstedtia eburnea gen. nov., sp. nov., a thermoactinomycete isolated by environmental screening, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006 emend. Yassin et al. 2009. . Int J Syst Evol Microbiol 61, 23042310. [CrossRef] [PubMed]
    [Google Scholar]
  44. Wilson K. ( 2001 ). Preparation of genomic DNA from bacteria. . In Current Protocols in Molecular Biology, pp. 2.4.12.4.5. Edited by Ausubel F. M., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. . New York:: Green Publishing & Wiley-Interscience;. [CrossRef]
    [Google Scholar]
  45. Yassin A. F., Hupfer H., Klenk H. P., Siering C. ( 2009 ). Desmospora activa gen. nov., sp. nov., a thermoactinomycete isolated from sputum of a patient with suspected pulmonary tuberculosis, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006. . Int J Syst Evol Microbiol 59, 454459. [CrossRef] [PubMed]
    [Google Scholar]
  46. Yoon J.-H., Park Y.-H. ( 2000 ). Phylogenetic analysis if the genus Thermoactinomyces based on 16S rDNA sequences. . Int J Syst Evol Microbiol 50, 10811086. [CrossRef] [PubMed]
    [Google Scholar]
  47. Yoon J.-H., Shin Y. K., Park Y.-H. ( 2000 ). DNA–DNA relatedness among Thermoactinomyces species: Thermoactinomyces candidus as a synonym of Thermoactinomyces vulgaris and Thermoactinomyces thalpophilus as a synonym of Thermoactinomyces sacchari . . Int J Syst Evol Microbiol 50, 19051908.[PubMed]
    [Google Scholar]
  48. Yoon J. H., Kim I. G., Shin Y. K., Park Y.-H. ( 2005 ). Proposal of the genus Thermoactinomyces sensu stricto and three new genera, Laceyella, Thermoflavimicrobium and Seinonella, on the basis of phenotypic, phylogenetic and chemotaxonomic analysis. . Int J Syst Evol Microbiol 55, 395400. [CrossRef] [PubMed]
    [Google Scholar]
  49. Zhang Y. X., Dong C., Biao S. ( 2007 ). Planifilum yunnanense sp. nov., a thermophilic thermoactinomycete isolated from a hot spring. . Int J Syst Evol Microbiol 57, 18511854. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.043596-0
Loading
/content/journal/ijsem/10.1099/ijs.0.043596-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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