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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 8

sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan Free

Abstract

A novel actinobacterium, designated strain HNM0687, was isolated from mangrove soil samples collected from Hainan Province, PR China and its polyphasic taxonomy was studied. Based on the results of 16S rRNA gene sequence analysis, strain HNM0687 was closely related to NBRC 16047 (98.7 %), NBRC 16068 (98.2 %), RS15-1S (97.9 %), NBRC 16320 (97.7 %) and AMA 120 (97.7 %). Genome-based comparisons revealed a clear distinction in average nucleotide identity values between strain HNM0687 and its closely related strains (74.4–78.3 %). Strain HNM0687 contained -diaminopimelic acid, arabinose and galactose in whole-cell hydrolysates. Mycolic acid was present. The menaquinones of strain HNM0687 were MK-9(H) and MK-7(H). The phospholipids of the isolate were composed of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major fatty acids were C, C 7/C 6, C10-methyl (TBSA), C and C 9. Based on its genotypic, chemotaxonomic and phenotypic characteristics, it is concluded that strain HNM0687 represents a novel species of the genus for which the name sp. nov. is proposed. The type strain is HNM0687 (=CCTCC AA 2019074 =KCTC 49383 ).

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Keyword(s): Gordonia mangrovi sp. nov. and mangrove soil
Funding
This study was supported by the:
  • High education teaching and reform research fund program of Hainan province (Award Hnjg2017ZD-3)
    • Principle Award Recipient: Xiaolong Huang
  • High-level talent grant of basic and applied basic research project (natural science) of Hainan province in 2019 (Award 2019RC069)
    • Principle Award Recipient: Xiaolong Huang
  • High-level talent grant of basic and applied basic research project (natural science) of Hainan province in 2019 (Award 2019RC133)
    • Principle Award Recipient: Shuangqing Zhou
© 2020 The Authors
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2020-07-15
2024-09-14
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References

  1. Tsukamura M. Proposal of a new genus, Gordona, for slightly acid-fast organisms occurring in sputa of patients with pulmonary disease and in soil. J Gen Microbiol 1971; 68:15–26 [View Article][PubMed]
     [Google Scholar]
  2. Lin Z, Marett L, Hughen RW, Flores M, Forteza I et al. Neuroactive diol and acyloin metabolites from cone snail-associated bacteria. Bioorg Med Chem Lett 2013; 23:4867–4869 [View Article][PubMed]
     [Google Scholar]
  3. Elfalah HWA, Ahmad A, Usup G. Anti-microbial properties of secondary metabolites of marine Gordonia tearrae extract. J Agric Sci 2013; 5:94–101 [View Article]
     [Google Scholar]
  4. Romanowska I, Kwapisz E, Mitka M, Bielecki S. Isolation and preliminary characterization of a respiratory nitrate reductase from hydrocarbon-degrading bacterium Gordonia alkanivorans S7. J Ind Microbiol Biotechnol 2010; 37:625–629 [View Article][PubMed]
     [Google Scholar]
  5. Arenskötter M, Baumeister D, Berekaa MM, Pötter G, Kroppenstedt RM et al. Taxonomic characterization of two rubber degrading bacteria belonging to the species Gordonia polyisoprenivorans and analysis of hyper variable regions of 16S rDNA sequences. FEMS Microbiol Lett 2001; 205:277–282 [View Article][PubMed]
     [Google Scholar]
  6. Stobdan T, Sinha A, Singh RP, Adhikari DK. Degradation of pyridine and 4-methylpyridine by Gordonia terrea IIPN1. Biodegradation 2008; 19:481–487 [View Article][PubMed]
     [Google Scholar]
  7. Sowani H, Kulkarni M, Zinjarde S. An insight into the ecology, diversity and adaptations of Gordonia species. Crit Rev Microbiol 2018; 44:1–21 [View Article][PubMed]
     [Google Scholar]
  8. Drzyzga O. The strengths and weaknesses of Gordonia: a review of an emerging genus with increasing biotechnological potential. Crit Rev Microbiol 2012; 38:300–316 [View Article][PubMed]
     [Google Scholar]
  9. Sangkanu S, Suriyachadkun C, Phongpaichit S. Gordonia sediminis sp. nov., an actinomycete isolated from mangrove sediment. Int J Syst Evol Microbiol 2019; 69:1814–1820 [View Article][PubMed]
     [Google Scholar]
  10. Takeuchi M, Hatano K. Gordonia rhizosphera sp. nov. isolated from the mangrove rhizosphere. Int J Syst Bacteriol 1998; 48 Pt 3:907–912 [View Article][PubMed]
     [Google Scholar]
  11. Cha JH, Cha CJ. Gordonia alkaliphila sp. nov., an actinomycete isolated from tidal flat sediment. Int J Syst Evol Microbiol 2013; 63:327–331 [View Article][PubMed]
     [Google Scholar]
  12. de Menezes CBA, Afonso RS, de Souza WR, Parma M, de Melo IS et al. Gordonia didemni sp. nov. an actinomycete isolated from the marine ascidium Didemnum sp . Antonie van Leeuwenhoek 2016; 109:297–303 [View Article][PubMed]
     [Google Scholar]
  13. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
     [Google Scholar]
  14. Huang XL, Zhuang L, Lin HP, Li J, Goodfellow M et al. Isolation and bioactivity of endophytic filamentous actinobacteria from tropical medicinal plants. Afr. J. Biotechnol. 2012; 11:9855–9864 [View Article]
     [Google Scholar]
  15. 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 [View Article][PubMed]
     [Google Scholar]
  16. 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]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  18. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  19. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  20. 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]
  21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  22. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:1–10 [View Article]
     [Google Scholar]
  23. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
     [Google Scholar]
  24. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  25. Kelly KL. Inter-Society Color Council-National Bureau of Standards Color-Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
     [Google Scholar]
  26. Williams ST, Goodfellow M, Alderson G, Wellington EM, Sneath PH, Sackin MJ et al. Numerical classification of Streptomyces and related genera. J Gen Microbiol 1983; 129:1743–1813 [View Article][PubMed]
     [Google Scholar]
  27. Huang X, Zhou S, Huang D, Chen J, Zhu W et al. Streptomyces spongiicola sp. nov., an actinomycete derived from marine sponge. Int J Syst Evol Microbiol 2016; 66:738–743 [View Article][PubMed]
     [Google Scholar]
  28. 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]
  29. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 1990
     [Google Scholar]
  30. 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 [View Article]
     [Google Scholar]
  31. Tomiyasu I. Mycolic acid composition and thermally adaptative changes in Nocardia asteroides . J Bacteriol 1982; 151:828–837 [View Article][PubMed]
     [Google Scholar]
  32. 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]
  33. Collins MD, Goodfellow M, Minnikin DE, Alderson G. Menaquinone composition of mycolic acid-containing actinomycetes and some sporoactinomycetes. J Appl Bacteriol 1985; 58:77–86 [View Article][PubMed]
     [Google Scholar]
  34. Kämpfer P, Young CC, Chu JN, Frischmann A, Busse HJ et al. Gordonia humi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2011; 61:65–70 [View Article][PubMed]
     [Google Scholar]
  35. Kämpfer P, Martin K, Dott W. Gordonia phosphorivorans sp. nov., isolated from a wastewater bioreactor with phosphorus removal. Int J Syst Evol Microbiol 2013; 63:230–235 [View Article][PubMed]
     [Google Scholar]
  36. Lefort V, Desper R, Gascuel O. FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article][PubMed]
     [Google Scholar]
  37. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
     [Google Scholar]
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Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan
Int J Syst Evol Microbiol 70, 4537 (2020); https://doi.org/10.1099/ijsem.0.004310
/content/journal/ijsem/10.1099/ijsem.0.004310
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