1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 61, Issue 3

gen. nov., sp. nov., a new member of the suborder Free

Abstract

A thermotolerant, Gram-stain-positive, aerobic, sporangium-forming actinomycete, strain RA45, was isolated from a desert region in Xinjiang Uigur Autonomous Region, north-western China. Comparative analysis of the 16S rRNA gene sequence and phenotypic characterization revealed that strain RA45 belonged phylogenetically to the family of the suborder . Strain RA45 showed more than 5 % 16S rRNA gene sequence divergence from recognized species of genera in the family , forming a distinct lineage within the evolutionary radiation occupied by the genera , , , , and , but distinct from each of them. The affiliation to the family was supported by the presence of suborder- and family-specific 16S rRNA signature nucleotides, a DNA G+C content of 69.9 mol%, the presence of -diaminopimelic acid, ribose, arabinose, glucose and galactose, which are characteristic components of cell-wall chemotype IV of actinomycetes, the presence of menaquinone MK-9(H) as the major respiratory lipoquinone, a lack of mycolic acids and the presence of an -acetylated type of muramic acid. However, strain RA45 differed from known genera of the family in its polar lipid composition: the major phospholipids were phosphatidylethanolamine, phosphatidylinositol mannosides, phosphatidylmethylethanolamine, diphosphatidylglycerol, phospholipids of unknown structure and phospholipids of unknown structure containing glucosamine (phospholipid type IV). Based on its morphological, chemotaxonomic and phylogenetic characteristics, strain RA45 is considered to represent a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain of is RA45 (=CGMCC 4.5579 =JCM 16584).

  • Published Online:
Keyword(s): ML, maximum-likelihood , MP, maximum-parsimony and NJ, neighbour-joining
SGM
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.019588-0
2011-03-01
2024-04-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/61/3/621.html?itemId=/content/journal/ijsem/10.1099/ijs.0.019588-0&mimeType=html&fmt=ahah

References

  1. Al-Zarban S. S., Al-Musallam A. A., Abbas I., Stackebrandt E., Kroppenstedt R. M. 2002; Saccharomonospora halophila sp. nov., a novel halophilic actinomycete isolated from marsh soil in Kuwait. Int J Syst Evol Microbiol 52:555–558
     [Google Scholar]
  2. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [CrossRef]
     [Google Scholar]
  3. Bian J., Li Y., Wang J., Song F. H., Liu M., Dai H. Q., Ren B., Gao H., Hu X. other authors 2009; Amycolatopsis marina sp. nov., an actinomycete isolated from an ocean sediment. Int J Syst Evol Microbiol 59:477–481 [CrossRef]
     [Google Scholar]
  4. Chun J., Kim S. B., Oh Y. K., Seong C. N., Lee D. H., Bae K. S., Lee K. J., Kang S. O., Hah Y. C., Goodfellow M. 1999 Amycolatopsis thermoflava sp. nov., a novel soil actinomycete from Hainan Island, China. Int J Syst Bacteriol 49, 1369–1373 [CrossRef]
  5. Dolashka P., Georgieva D. N., Stoeva S., Genov N., Rachev R., Gusterova A., Voelter W. 1998; A novel thermostable neutral proteinase from Saccharomonospora canescens . Biochim Biophys Acta 1382:207–216 [CrossRef]
     [Google Scholar]
  6. Embley T. M., Smida J., Stackebrandt E. 1988; Reverse transcriptase sequencing of 16S ribosomal RNA from Faenia rectivirgula , Pseudonocardia thermophila and Saccharopolyspora hirsuta , three wall type IV actinomycetes which lack mycolic acids. J Gen Microbiol 134:961–966
     [Google Scholar]
  7. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376 [CrossRef]
     [Google Scholar]
  8. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [CrossRef]
     [Google Scholar]
  9. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [CrossRef]
     [Google Scholar]
  10. Gause G. F., Preobrazhenskaya T. P., Sveshnikova G. V., Terekhova L. P., Maksimova T. S. 1983; A Guide for Determination of Actinomycetes. Moscow: : Nauka (in Russian)
  11. Goodfellow M., Kim S. B., Minnikin D. E., Whitehead D., Zhou Z. H., Mattinson-Rose A. D. 2001; Amycolatopsis sacchari sp. nov., a moderately thermophilic actinomycete isolated from vegetable matter. Int J Syst Evol Microbiol 51:187–193
     [Google Scholar]
  12. Gordon R. E. 1967; The taxonomy of soil bacteria. In The Ecology of Soil Bacteria pp 293–321 Edited by Gray T. R. G., Parkinson D. Liverpool: Liverpool University Press;
     [Google Scholar]
  13. Guindon S., Lethiec F., Duroux P., Gascuel O. 2005; phyml Online – a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33:W557–W559 [CrossRef]
     [Google Scholar]
  14. Hamid M. E., Minnikin D. E., Goodfellow M., Ridell M. 1993; Thin-layer chromatographic analysis of glycolipids and mycolic acids from Mycobacterium farcinogenes , Mycobacterium senegalense and related taxa. Zentralbl Bakteriol 279:354–367 [CrossRef]
     [Google Scholar]
  15. Henssen A. 1957; Beiträge zur Morphologie und Systematik der thermophilen Actinomyceten. Arch Mikrobiol 26:373–414 (in German) [CrossRef]
     [Google Scholar]
  16. Huang Y., Paściak M., Liu Z., Xie Q., Gamian A. 2004; Amycolatopsis palatopharyngis sp. nov., a potentially pathogenic actinomycete isolated from a human clinical source. Int J Syst Evol Microbiol 54:359–363 [CrossRef]
     [Google Scholar]
  17. Hucker G. J. 1921; A new modification and application of the Gram stain. J Bacteriol 6:395–397
     [Google Scholar]
  18. Jiang Y., Wiese J., Tang S. K., Xu L. H., Imhoff J. F., Jiang C. L. 2008; Actinomycetospora chiangmaiensis gen. nov., sp. nov., a new member of the family Pseudonocardiaceae . Int J Syst Evol Microbiol 58:408–413 [CrossRef]
     [Google Scholar]
  19. Jin X., Xu L. H., Mao P. H., Hseu T. H., Jiang C. L. 1998; Description of Saccharomonospora xinjiangensis sp. nov. based on chemical and molecular classification. Int J Syst Bacteriol 48:1095–1099 [CrossRef]
     [Google Scholar]
  20. 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]
  21. Kelly K. L. 1964 Inter-Society Color Council-National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office;
     [Google Scholar]
  22. Kim S. B., Goodfellow M. 1999; Reclassification of Amycolatopsis rugosa Lechevalier et al. 1986 as Prauserella rugosa gen. nov., comb. nov. Int J Syst Bacteriol 49:507–512 [CrossRef]
     [Google Scholar]
  23. Kim B., Sahin N., Tan G. Y. A., Zakrzewska-Czerwinska J., Goodfellow M. 2002; Amycolatopsis eurytherma sp. nov., a thermophilic actinomycete isolated from soil. Int J Syst Evol Microbiol 52:889–894 [CrossRef]
     [Google Scholar]
  24. Kimura M. 1980; A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120 [CrossRef]
     [Google Scholar]
  25. Kimura M. 1983 The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press;
     [Google Scholar]
  26. Korn-Wendisch F., Kempf A., Grund E., Kroppenstedt R. M., Kutzner H. J. 1989; Transfer of Faenia rectivirgula Kurup and Agre 1983 to the genus Saccharopolyspora Lacey and Goodfellow 1975, elevation of Saccharopolyspora hirsuta subsp. taberi Labeda 1987 to species level, and emended description of the genus Saccharopolyspora . Int J Syst Bacteriol 39:430–441 [CrossRef]
     [Google Scholar]
  27. Korn-Wendisch F., Rainey F., Kroppenstedt R. M., Kempf A., Majazza A., Kutzner H. J., Stackebrandt E. 1995; Thermocrispum gen. nov., a new genus of the order Actinomycetales , and description of Thermocrispum municipale sp.nov. and Thermocrispum agreste sp. nov. Int J Syst Bacteriol 45:67–77 [CrossRef]
     [Google Scholar]
  28. Kroppenstedt R. M. 1982; Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367 [CrossRef]
     [Google Scholar]
  29. Kumar Y., Goodfellow M. 2008; Five new members of the Streptomyces violaceusniger 16S rRNA gene clade: Streptomyces castelarensis sp.nov., comb. nov., Streptomyces himastatinicus sp. nov.,Streptomyces mordarskii sp. nov., Streptomyces rapamycinicus sp.nov. and Streptomyces ruanii sp. nov. Int J Syst Evol Microbiol 58:1369–1378 [CrossRef]
     [Google Scholar]
  30. Labeda D. P. 1998; Phylogenetic analysis of the genus Saccharothrix and related taxa. In Abstracts of the 98th General Meeting of the American Society for Microbiology Atlanta, GA:p–485 Washington, DC: American Society for Microbiology;
     [Google Scholar]
  31. Labeda D. P. 2001; Crossiella gen. nov., a new genus related to Streptoalloteichus . Int J Syst Evol Microbiol 51:1575–1579
     [Google Scholar]
  32. Labeda D. P., Kroppenstedt R. M. 2000; Phylogenetic analysis of Saccharothrix and related taxa: proposal for Actinosynnemataceae fam. nov. Int J Syst Evol Microbiol 50:331–336 [CrossRef]
     [Google Scholar]
  33. Labeda D. P., Kroppenstedt R. M. 2006; Goodfellowia gen. nov., a new genus of the Pseudonocardineae related to Actinoalloteichus , containing Goodfellowia coeruleoviolacea gen. nov., comb. nov. Int J Syst Evol Microbiol 56:1203–1207 [CrossRef]
     [Google Scholar]
  34. Labeda D. P., Kroppenstedt R. M. 2008; Proposal for the new genus Allokutzneria gen. nov. within the suborder Pseudonocardineae and transfer of Kibdelosporangium albatum Tomita et al. 1993 as Allokutzneria albata comb. nov. Int J Syst Evol Microbiol 58:1472–1475 [CrossRef]
     [Google Scholar]
  35. Labeda D. P., Kroppenstedt R. M., Euzéby J. P., Tindall B. J. 2008; Proposal of Goodfellowiella gen. nov. to replace the illegitimate genus name Goodfellowia Labeda and Kroppenstedt 2006. Int J Syst Evol Microbiol 58:1047–1048 [CrossRef]
     [Google Scholar]
  36. Lacey J., Goodfellow M. 1975; A novel actinomycete from sugar-cane bagasse: Saccharopolyspora hirsuta gen. et sp. nov. J Gen Microbiol 88:75–85 [CrossRef]
     [Google Scholar]
  37. Lechevalier M. P., Lechevalier H. A. 1970; Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443 [CrossRef]
     [Google Scholar]
  38. Lechevalier M. P., De Bièvre C., Lechevalier H. A. 1977; Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5:249–260 [CrossRef]
     [Google Scholar]
  39. Lechevalier M. P., Prauser H., Labeda D. P., Ruan J. S. 1986; Two new genera of nocardioform actinomycetes: Amycolata gen.nov. and Amycolatopsis gen. nov. Int J Syst Bacteriol 36:29–37 [CrossRef]
     [Google Scholar]
  40. Li W. J., Tang S. K., Stackebrandt E., Kroppenstedt R. M., Schumann P., Xu L. H., Jiang C. L. 2003a; Saccharomonospora paurometabolica sp. nov., a moderately halophilic actinomycete isolated from soil in China. Int J Syst Evol Microbiol 53:1591–1594 [CrossRef]
     [Google Scholar]
  41. Li W. J., Xu P., Tang S. K., Xu L. H., Kroppenstedt R. M., Stackebrandt E., Jiang C. L. 2003b; Prauserella halophila sp. nov. and Prauserella alba sp. nov., moderately halophilic actinomycetes from saline soil. Int J Syst Evol Microbiol 53:1545–1549 [CrossRef]
     [Google Scholar]
  42. Lu Z., Liu Z., Wang L., Zhang Y., Qi W., Goodfellow M. 2001; Saccharopolyspora flava sp. nov. and Saccharopolyspora thermophila sp. nov., novel actinomycetes from soil. Int J Syst Evol Microbiol 51:319–325
     [Google Scholar]
  43. Mandel M., Marmur J. 1968; Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 12B:195–206
     [Google Scholar]
  44. Marmur J. 1961; A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218 [CrossRef]
     [Google Scholar]
  45. McVeigh H. P., Divers M., Warwick S., Munro J., Embley T. M. 1994; Exploration of actinomycete diversity using ribosomal RNA sequences. Biotechnologia 7:8253–260
     [Google Scholar]
  46. 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 2:233–241 [CrossRef]
     [Google Scholar]
  47. Morón R., González I., Genilloud O. 1999; New genus-specific primers for the PCR identification of members of the genera Pseudonocardia and Saccharopolyspora . Int J Syst Bacteriol 49:149–162 [CrossRef]
     [Google Scholar]
  48. Nonomura H., Ohara Y. 1971; Distribution of actinomycetes in soil. X. New genus and species of monosporic actinomycetes. J Ferment Technol 49:895–903
     [Google Scholar]
  49. Pimentel-Elardo S. M., Tiro L. P., Grozdanov L., Hentschel U. 2008; Saccharopolyspora cebuensis sp. nov., a novel actinomycete isolated from a Philippine sponge (Porifera). Int J Syst Evol Microbiol 58:628–632 [CrossRef]
     [Google Scholar]
  50. Qin S., Li J., Zhao G. Z., Chen H. H., Xu L. H., Li W. J. 2008; Saccharopolyspora endophytica sp. nov., an endophytic actinomycete isolated from the root of Maytenus austroyunnanensis . Syst Appl Microbiol 31:352–357 [CrossRef]
     [Google Scholar]
  51. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
     [Google Scholar]
  52. Salazar O., Morón R., Genilloud O. 2000; New genus-specific primers for the PCR identification of members of the genus Saccharomonospora and evaluation of the microbial diversity of wild-type isolates of Saccharomonospora detected from soil DNAs. Int J Syst Evol Microbiol 50:2043–2055 [CrossRef]
     [Google Scholar]
  53. Sambrook J., Russell D. W. 2001 Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  54. Sasser M. 1990; Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20: 16
    [Google Scholar]
  55. Shearer M. C., Colman P. M., Ferrin R. M., Nisbet L. J., Nash C. H. III 1986; New genus of the Actinomycetales : Kibdelosporangium aridum gen. nov., sp. nov.. Int J Syst Bacteriol 36:47–54 [CrossRef]
     [Google Scholar]
  56. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340 [CrossRef]
     [Google Scholar]
  57. Stach J. E., Maldonado L. A., Ward A. C., Goodfellow M., Bull A. T. 2003; New primers for the class Actinobacteria : application to marine and terrestrial environments. Environ Microbiol 5:828–841 [CrossRef]
     [Google Scholar]
  58. Stackebrandt E., Kroppenstedt R. M., Jahnke K.-D., Kemmerling C., Gürtler H. 1994; Transfer of Streptosporangium viridogriseum (Okuda et al. 1966), Streptosporangium viridogriseum subsp. kofuense (Nonomura and Ohara 1969), and Streptosporangium albidum (Furumai et al. 1968) to Kutzneria gen.nov. as Kutzneria viridogrisea comb. nov., Kutzneria kofuensis comb. nov., and Kutzneria albida comb. nov., respectively, and emendation of the genus Streptosporangium . Int J Syst Bacteriol 44:265–269 [CrossRef]
     [Google Scholar]
  59. 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]
  60. Staneck J. L., Roberts G. D. 1974; Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231
     [Google Scholar]
  61. Syed D. G., Tang S. K., Cai M., Zhi X. Y., Agasar D., Lee J. C., Kim C. J., Jiang C. L., Xu L. H., Li W. J. 2008; Saccharomonospora saliphila sp. nov., a halophilic actinomycete from an Indian soil. Int J Syst Evol Microbiol 58:570–573 [CrossRef]
     [Google Scholar]
  62. Tamura T., Liu Z., Zhang Y., Hatano K. 2000; Actinoalloteichus cyanogriseus gen. nov., sp. nov. Int J Syst Evol Microbiol 50:1435–1440 [CrossRef]
     [Google Scholar]
  63. Tamura K., Dudley J., Nei M., Kumar S. 2007; mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599 [CrossRef]
     [Google Scholar]
  64. Tan G. Y., Ward A. C., Goodfellow M. 2006; Exploration of Amycolatopsis diversity in soil using genus-specific primers and novel selective media. Syst Appl Microbiol 29:557–569 [CrossRef]
     [Google Scholar]
  65. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [CrossRef]
     [Google Scholar]
  66. Tian X. P., Zhi X. Y., Qiu Y. Q., Zhang Y. Q., Tang S. K., Xu L. H., Zhang S., Li W. J. 2009; Sciscionella marina gen. nov., sp. nov., a marine actinomycete isolated from a sediment in the northern South China Sea. Int J Syst Evol Microbiol 59:222–228 [CrossRef]
     [Google Scholar]
  67. Tomita K., Uenoyama Y., Numata E. I., Sasahira T., Hoshino Y., Fujisawa K. I., Tsukiura H., Kawaguchi H. 1978; Streptoalloteichus , a new genus of the family Actinoplanaceae . J Antibiot (Tokyo 31:497–510 [CrossRef]
     [Google Scholar]
  68. Tseng M., Yang S. F., Li W. J., Jiang C. L. 2006; Amycolatopsis taiwanensis sp. nov., from soil. Int J Syst Evol Microbiol 56:1811–1815 [CrossRef]
     [Google Scholar]
  69. Uchida K., Kudo T., Suzuki K. I., Nakase T. 1999; A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 45:49–56 [CrossRef]
     [Google Scholar]
  70. Van de Peer Y., De Wachter R. 1994; treecon for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10:569–570
     [Google Scholar]
  71. Van de Peer Y., De Wachter R. 1997; Construction of evolutionary distance trees with treecon for Windows: accounting for variation in nucleotide substitution rate among sites. Comput Appl Biosci 13:227–230
     [Google Scholar]
  72. Xu P., Li W. J., Xu L. H., Jiang C. L. 2003 A microwave-based method for genomic DNA extraction from actinomycetes. Microbiology [English translation of Microbiology (Beijing) ] 3082–84
  73. Yoon J. H., Lee K. C., Shin Y. K., Park Y. H. 2000; Transfer of ‘ Thermoactinomyces glaucus ’ IFO 12530 and ‘ Thermoactinomyces monosporus ’ IFO 14050 to the genus Saccharomonospora as members of Saccharomonospora glauca . J Gen Appl Microbiol 46:251–256 [CrossRef]
     [Google Scholar]
  74. Zhang J., Wu D., Zhang J., Liu Z., Song F. 2008; Saccharopolyspora shandongensis sp. nov., isolated from wheat-field soil. Int J Syst Evol Microbiol 58:1094–1099 [CrossRef]
     [Google Scholar]
  75. 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 59:589–608 [CrossRef]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.019588-0
Loading
Yuhushiella deserti gen. nov., sp. nov., a new member of the suborder Pseudonocardineae
Int J Syst Evol Microbiol 61, 621 (2011); https://doi.org/10.1099/ijs.0.019588-0
/content/journal/ijsem/10.1099/ijs.0.019588-0
/content/journal/ijsem/10.1099/ijs.0.019588-0
Loading

Data & Media loading...

Most cited 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