1887

Abstract

A novel endophytic actinomycete, designated strain Gen 01, was isolated from the roots of and characterized by using a polyphasic approach. The predominant cellular fatty acids were iso-C, summed feature 3, iso H-C, C and iso-C. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannosides, phospholipids of unknown structure containing glucosamine inositol, phosphatidylinositol and unidentified phospholipids. The major menaquinone was MK-8 (H). The DNA G+C content of the genome sequence, consisting of 7 177 725 bp, was 74.5 mol%. Phylogenetic analysis of the full-length 16S rRNA gene sequences showed that strain Gen 01 belongs to the genus with the highest sequence similarity to CGMCC 4.1532 (98.9 %) and lower than 98.7 % similarity to other species of the genus with validly published names. The average nucleotide identity and digital DNA–DNAhybridization values between strain Gen 01 and CGMCC 4.1532 were 84.6 and 30.9 %, respectively. Furthermore, the morphological, physiological and biochemical characteristics were sufficient to categorize strain Gen 01 as being distinct from CGMCC 4.1532. Consequently, based on phenotypic and genotypic characteristics, strain Gen 01 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is Gen 01 (=CICC 24820=JCM 33840).

Funding
This study was supported by the:
  • China Postdoctoral Science Foundation (Award 2020M682602)
    • Principle Award Recipient: ZhenggangXu
  • Key Technology R&D Program of Changsha (Award kq1901145)
    • Principle Award Recipient: YunlinZhao
  • Major Science and Technology Program of Hunan Province (Award 2017NK1014)
    • Principle Award Recipient: YunlinZhao
  • Forestry Science and Technology Project of Hunan Province (Award XLK201920)
    • Principle Award Recipient: YunlinZhao
  • State Forestry and Grassland Bureau (Award 2018-01)
    • Principle Award Recipient: YunlinZhao
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004680
2021-02-02
2022-05-27
Loading full text...

Full text loading...

References

  1. Baltz RH. Marcel Faber roundtable: is our antibiotic pipeline unproductive because of starvation, constipation or lack of inspiration?. J Ind Microbiol Biotechnol 2006; 33:507–513 [View Article][PubMed]
    [Google Scholar]
  2. Henssen A. Beiträge zur Morphologie und Systematik der thermophilen Actinomyceten. Archiv Mikrobiol. 1957; 26:373–414 [View Article]
    [Google Scholar]
  3. 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 [View Article][PubMed]
    [Google Scholar]
  4. 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 Pt 2:441–449 [View Article][PubMed]
    [Google Scholar]
  5. 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 [View Article][PubMed]
    [Google Scholar]
  6. 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 [View Article][PubMed]
    [Google Scholar]
  7. Trujillo ME, Idris H, Riesco R, Nouioui I, Igual JM et al. Pseudonocardia nigra sp. nov., isolated from Atacama Desert rock. Int J Syst Evol Microbiol 2017; 67:2980–2985 [View Article][PubMed]
    [Google Scholar]
  8. Li J, Zhao GZ, Huang HY, Zhu WY, Lee JC et al. Pseudonocardia rhizophila sp. nov., a novel actinomycete isolated from a rhizosphere soil. Antonie Van Leeuwenhoek 2010; 98:77–83 [View Article][PubMed]
    [Google Scholar]
  9. Kämpfer P, Kroppenstedt RM. Pseudonocardia benzenivorans sp. nov. Int J Syst Evol Microbiol 2004; 54:749–751 [View Article][PubMed]
    [Google Scholar]
  10. 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 [View Article][PubMed]
    [Google Scholar]
  11. Qin S, Xing K, Fei SM, Lin Q, Chen XM et al. Pseudonocardia sichuanensis sp. nov., a novel endophytic actinomycete isolated from the root of Jatropha curcas L. Antonie van Leeuwenhoek 2011; 99:395–401 [View Article][PubMed]
    [Google Scholar]
  12. Zhao G-Z, Li J, Qin Y-L, Miao C-P, Wei D-Q et al. Pseudonocardia antimicrobica sp. nov., a novel endophytic actinomycete associated with Artemisia annua L. (sweet wormwood). J Antibiot 2012; 65:469–472 [View Article]
    [Google Scholar]
  13. Zhao G-Z, Zhu W-Y, Li J, Xie Q, Xu L-H et al. Pseudonocardia serianimatus sp. nov., a novel actinomycete isolated from the surface-sterilized leaves of Artemisia annua L. Antonie van Leeuwenhoek 2011; 100:521–528 [View Article][PubMed]
    [Google Scholar]
  14. Lee SD, Kim ES, Min KL, Lee WY, Kang SO et al. Pseudonocardia kongjuensis sp. nov., isolated from a gold mine cave. Int J Syst Evol Microbiol 2001; 51:1505–1510 [View Article][PubMed]
    [Google Scholar]
  15. Prabahar V, Dube S, Reddy GS, Shivaji S. Pseudonocardia antarctica sp. nov. an Actinomycetes from McMurdo Dry Valleys, Antarctica. Syst Appl Microbiol 2004; 27:66–71 [View Article][PubMed]
    [Google Scholar]
  16. Sujarit K, Sujada N, Kudo T, Ohkuma M, Pathom-Aree W et al. Pseudonocardia thailandensis sp. nov., an actinomycete isolated from a subterranean termite nest. Int J Syst Evol Microbiol 2017; 67:2773–2778 [View Article][PubMed]
    [Google Scholar]
  17. Sakiyama Y, Thao NK, Vinh HV, Giang NM, Miyadoh S et al. Pseudonocardia babensis sp. nov., isolated from plant litter. Int J Syst Evol Microbiol 2010; 60:2336–2340 [View Article][PubMed]
    [Google Scholar]
  18. Omura S, Tanaka H, Tanaka Y, Spiri-Nakagawa P, Oiwa R et al. Studies on bacterial cell wall inhibitors. VII. Azureomycins A and B, new antibiotics produced by Pseudonocardia azurea nov. sp. taxonomy of the producing organism, isolation, characterization and biological properties. J Antibiot 1979; 32:985–994 [View Article]
    [Google Scholar]
  19. Jafari N, Behroozi R, Farajzadeh D, Farsi M, Akbari-Noghabi K. Antibacterial activity of Pseudonocardia sp. JB05, a rare salty soil actinomycete against Staphylococcus aureus. Biomed Res Int 2014; 2014:1–7 [View Article][PubMed]
    [Google Scholar]
  20. Carr G, Derbyshire ER, Caldera E, Currie CR, Clardy J. Antibiotic and antimalarial quinones from fungus-growing ant-associated Pseudonocardia sp. J Nat Prod 2012; 75:1806–1809 [View Article][PubMed]
    [Google Scholar]
  21. Braña AF, Sarmiento-Vizcaíno A, Pérez-Victoria I, Otero L, Fernández J, Blanco G et al. Branimycins B and C, antibiotics produced by the abyssal actinobacterium Pseudonocardia carboxydivorans M-227. J Nat Prod 2017; 80:569–573 [View Article][PubMed]
    [Google Scholar]
  22. Malfait M, Godden B, Penninckx MJ. Growth and cellulase production of Micromonospora chalcae and Pseudonocardia thermophila . Ann Microbiol 1984; 135B:79–89 [View Article][PubMed]
    [Google Scholar]
  23. Peplowski L, Kubiak K, Nowak W. Mechanical aspects of nitrile hydratase enzymatic activity. Steered molecular dynamics simulations of Pseudonocardia thermophila JCM 3095. Chem Phys Lett 2008; 467:144–149 [View Article]
    [Google Scholar]
  24. Qin S, Li J, Chen H, Zhao Z, Zhu W et al. Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China. Appl Environ Microbiol 2009; 75:6176–6186 [View Article][PubMed]
    [Google Scholar]
  25. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7 [View Article][PubMed]
    [Google Scholar]
  26. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  27. Waksman SA. The Actinomycetes. Vol. Ii. Classification, Identification and Descriptions of Genera and Species: Vol. Ii Beijing: Science Press; 1961
    [Google Scholar]
  28. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145 [View Article][PubMed]
    [Google Scholar]
  29. Ridgway R. Color Standards and Color Nomenclature Washington, DC: 1912 pp 1–43
    [Google Scholar]
  30. LH X, WJ L, Liu ZH, Jiang CL. Actinomycete Systematic-Principle, Methods and Practice Beijing: Science press; 2007
    [Google Scholar]
  31. MIDI Sherlock Microbial Identification System Operating Manual, Version 6.0 Newark DE: MIDI Inc; 2005
    [Google Scholar]
  32. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
    [Google Scholar]
  33. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  34. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
    [Google Scholar]
  35. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, London Minnikin DE. (editors) Chemical Methods in Bacterial Systematics England: Academic Press; 1985 pp 173–199
    [Google Scholar]
  36. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  37. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article][PubMed]
    [Google Scholar]
  38. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York, USA: Wiley; 1991 pp 115–175
    [Google Scholar]
  39. Yoon SH, Ha S-M, 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 [View Article][PubMed]
    [Google Scholar]
  40. 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 [View Article][PubMed]
    [Google Scholar]
  41. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  42. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  43. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
    [Google Scholar]
  44. Xie Y, Wu G, Tang J, Luo R, Patterson J et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-seq reads. Bioinformatics 2014; 30:1660–1666 [View Article][PubMed]
    [Google Scholar]
  45. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article][PubMed]
    [Google Scholar]
  46. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60–14 [View Article]
    [Google Scholar]
  47. Grim CJ, Kotewicz ML, Power KA, Gopinath G, Franco AA et al. Pan-Genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation. BMC Genomics 2013; 14:366 [View Article][PubMed]
    [Google Scholar]
  48. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  49. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O. International committee on systematic bacteriology. Report of the AD hoc committee on the reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004680
Loading
/content/journal/ijsem/10.1099/ijsem.0.004680
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