1887

Abstract

A novel actinomycete, designated strain NEAU-G57 was isolated from a soil sample collected from the bottom of a river in Chad. A polyphasic approach was employed to determine the status of strain NEAU-G57. Phylogenetic analysis based on its 16S rRNA gene sequence indicated that the organism should be assigned to the genus Pseudonocardia and formed a monophyletic clade with its closest relatives Pseudonocardia yuanmoensis YIM 75926 (98.8 %), Pseudonocardia halophobica DSM 43089 (98.2 %) and Pseudonocardia kujensis A 4038 (97.6 %). Moreover, morphological and chemotaxonomic properties of strain NEAU-G57 also confirmed the affiliation of the isolate to the genus Pseudonocardia . The cell wall contained meso-diaminopimelic acid and whole-cell sugars were glucose, xylose, arabinose and galactose. The predominant menaquinone was MK-8(H4). The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxyphosphatidylmethylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol mannosides, one unidentified glycolipid and one unidentified lipid. The major fatty acids were C16 : 0 and C16 : 1ω7c. The DNA G+C content was 73.3 mol%. However, the low level of DNA–DNA relatedness and some phenotypic characteristics allowed the isolate to be differentiated from its closely related species. Therefore, it is concluded that strain NEAU-G57 can be classified as representing a novel species of the genus Pseudonocardia , for which the name Pseudonocardia lutea sp. nov. is proposed. The type strain is NEAU-G57 (=JCM 32387=CGMCC 4.7397).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002780
2018-04-23
2019-10-15
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/6/1992.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002780&mimeType=html&fmt=ahah

References

  1. Henssen A. Beiträge zur Morphologie und Systematik der thermophilen Actinomyceten. Archiv für Mikrobiologie 1957; 26: 373– 414 [CrossRef]
    [Google Scholar]
  2. Warwick S, Bowen T, McVeigh H, Embley TM. A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and a proposal to combine the genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia. Int J Syst Bacteriol 1994; 44: 293– 299 [CrossRef] [PubMed]
    [Google Scholar]
  3. Reichert K, Lipski A, Pradella S, Stackebrandt E, Altendorf K. Pseudonocardia asaccharolytica sp. nov. and Pseudonocardia sulfidoxydans sp. nov., two new dimethyl disulfide-degrading actinomycetes and emended description of the genus Pseudonocardia. Int J Syst Bacteriol 1998; 48: 441– 449 [CrossRef] [PubMed]
    [Google Scholar]
  4. Huang Y, Wang L, Lu Z, Hong L, Liu Z et al. Proposal to combine the genera Actinobispora and Pseudonocardia in an emended genus Pseudonocardia, and description of Pseudonocardia zijingensis sp. nov. Int J Syst Evol Microbiol 2002; 52: 977– 982 [CrossRef] [PubMed]
    [Google Scholar]
  5. Park SW, Park ST, Lee JE, Kim YM. Pseudonocardia carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete, and an emended description of the genus Pseudonocardia. Int J Syst Evol Microbiol 2008; 58: 2475– 2478 [CrossRef] [PubMed]
    [Google Scholar]
  6. Kämpfer P, Kohlweyer U, Thiemer B, Andreesen JR. Pseudonocardia tetrahydrofuranoxydans sp. nov. Int J Syst Evol Microbiol 2006; 56: 1535– 1538 [CrossRef] [PubMed]
    [Google Scholar]
  7. Cuesta G, Soler A, Alonso JL, Ruvira MA, Lucena T et al. Pseudonocardia hispaniensis sp. nov., a novel actinomycete isolated from industrial wastewater activated sludge. Antonie van Leeuwenhoek 2013; 103: 135– 142 [CrossRef] [PubMed]
    [Google Scholar]
  8. Zhao GZ, Li J, Zhu WY, Li XP, Tian SZ et al. Pseudonocardia bannaensis sp. nov., a novel actinomycete isolated from the surface-sterilized roots of Artemisia annua L. Antonie van Leeuwenhoek 2011; 100: 35– 42 [CrossRef] [PubMed]
    [Google Scholar]
  9. Xing K, Qin S, Bian GK, Zhang YJ, Zhang WD et al. Pseudonocardia nantongensis sp. nov., a novel endophytic actinomycete isolated from the coastal halophyte Tamarix chinensis Lour. Antonie van Leeuwenhoek 2012; 102: 659– 667 [CrossRef] [PubMed]
    [Google Scholar]
  10. Ara I, Tsetseg B, Daram D, Suto M, Ando K. Pseudonocardia mongoliensis sp. nov. and Pseudonocardia khuvsgulensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011; 61: 747– 756 [CrossRef] [PubMed]
    [Google Scholar]
  11. Sahin N, Veyisoglu A, Tatar D, Spröer C, Cetin D et al. Pseudonocardia cypriaca sp. nov., Pseudonocardia salamisensis sp. nov., Pseudonocardia hierapolitana sp. nov. and Pseudonocardia kujensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64: 1703– 1711 [CrossRef] [PubMed]
    [Google Scholar]
  12. Zhang DF, Jiang Z, Li L, Liu BB, Zhang XM et al. Pseudonocardia sediminis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2014; 64: 745– 750 [CrossRef] [PubMed]
    [Google Scholar]
  13. Zhang G, Wang L, Li J, Zhou Y. Pseudonocardia profundimaris sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2017; 67: 1693– 1697 [CrossRef] [PubMed]
    [Google Scholar]
  14. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16: 313– 340 [CrossRef]
    [Google Scholar]
  15. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57: 141– 145 [PubMed]
    [Google Scholar]
  16. Waksman SA. The Actinobacteria, Classification, Identification and Descriptions of Genera and Speciesvol. 2 Baltimore: Williams and Wilkins; 1961
    [Google Scholar]
  17. Kelly KL. Inter-Society Color Council-National Bureau of Standards Color-Name Charts Illustrated with Centroid Colors Published in US 1964
    [Google Scholar]
  18. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp. 607– 654
    [Google Scholar]
  19. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 1974; 24: 54– 63 [CrossRef]
    [Google Scholar]
  20. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicus gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 1993; 43: 805– 812 [CrossRef]
    [Google Scholar]
  21. Jia F, Liu C, Wang X, Zhao J, Liu Q et al. Wangella harbinensis gen. nov., sp. nov., a new member of the family Micromonosporaceae. Antonie van Leeuwenhoek 2013; 103: 399– 408 [CrossRef] [PubMed]
    [Google Scholar]
  22. Xie QY, Lin HP, Li L, Brown R, Goodfellow M et al. Verrucosispora wenchangensis sp. nov., isolated from mangrove soil. Antonie van Leeuwenhoek 2012; 102: 1– 7 [CrossRef] [PubMed]
    [Google Scholar]
  23. McKerrow J, Vagg S, McKinney T, Seviour EM, Maszenan AM et al. A simple HPLC method for analysing diaminopimelic acid diastereomers in cell walls of Gram-positive bacteria. Lett Appl Microbiol 2000; 30: 178– 182 [CrossRef] [PubMed]
    [Google Scholar]
  24. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. (editors) Actinomycete Taxonomy (Special Publication No. 6) Arlington: Society for Industrial Microbiology; 1980; pp. 227– 291
    [Google Scholar]
  25. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2: 233– 241 [CrossRef]
    [Google Scholar]
  26. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985; pp. 267– 284
    [Google Scholar]
  27. Wu C, Lu X, Qin M, Wang Y, Ruan J. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology [English translation of Microbiology (Beijing)] 1989; 16: 176– 178
    [Google Scholar]
  28. Gao R, Liu C, Zhao J, Jia F, Yu C et al. Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora. Antonie van Leeuwenhoek 2014; 105: 307– 315 [CrossRef] [PubMed]
    [Google Scholar]
  29. Xiang W, Liu C, Wang X, Du J, Xi L et al. Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa). Int J Syst Evol Microbiol 2011; 61: 1165– 1169 [CrossRef] [PubMed]
    [Google Scholar]
  30. Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S et al. Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 2000; 50: 2031– 2036 [CrossRef] [PubMed]
    [Google Scholar]
  31. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 06– 425 [CrossRef] [PubMed]
    [Google Scholar]
  32. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368– 376 [CrossRef] [PubMed]
    [Google Scholar]
  33. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30: 2725– 2729 [CrossRef] [PubMed]
    [Google Scholar]
  34. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  35. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16: 111– 120 [CrossRef] [PubMed]
    [Google Scholar]
  36. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67: 1613– 1617 [CrossRef] [PubMed]
    [Google Scholar]
  37. Mandel M, Marmur J. Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 1968; 12B: 195– 206 [Crossref]
    [Google Scholar]
  38. De Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12: 133– 142 [CrossRef] [PubMed]
    [Google Scholar]
  39. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983; 4: 184– 192 [CrossRef] [PubMed]
    [Google Scholar]
  40. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37: 463– 464 [Crossref]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002780
Loading
/content/journal/ijsem/10.1099/ijsem.0.002780
Loading

Data & Media loading...

Supplementary File 1

PDF

Most Cited This Month

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