sp. nov., a novel denitrifying bacterium isolated from sludge Free

Abstract

A novel Gram-reaction-negative, facultative-aerobic, motile, non-spore-forming, oval-shaped and denitrifying bacterium, designated BO-81, was isolated from sludge sampled in the Republic of Korea. This bacterium was investigated via a polyphasic approach to reveal its taxonomic position. The results of phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain BO-81 belonged to the family and was related to the closest species (98.8 % sequence similarity), ‘’ (98.4 %), (97.8 %), (96.8 %) and (96.2 %). The average nucleotide identity and DNA–DNA hybridization values between strain BO-81 and its closely related strains were 77.7–94.2 % and 20.1–55.9 %, respectively, indicating that BO-81 represents a novel species of the genus . Growth occurred at 18–40 °C on Reasoner's 2A medium in the presence of 0–7 % NaCl (w/v) and at pH 6.0–9.0. Strain BO-81 was characterized chemotaxonomically as having ubiquinone 10 as its predominant respiratory quinone, summed feature 8 (C 6 and/or C 7) as its major fatty acid and phosphatidylglycerol and phosphatidylethanolamine as its predominant polar lipids. The G+C content of the genomic DNA was 68.3 mol%. The results of physiological and biochemical tests allowed phenotypic differentiation of strain BO-81 from other species with validly published names. Therefore, the isolate represented a novel species, for which the name sp. nov. (type strain BO-81=KACC 19677=LMG 30808) is proposed.

Funding
This study was supported by the:
  • Korea Research Institute of Bioscience and Biotechnology
    • Principle Award Recipient: Wan-Taek Im
  • National Institute of Biological Resources
    • Principle Award Recipient: Wan-Taek Im
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2020-02-03
2024-03-28
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References

  1. Yang G, Chen M, Zhou S, Liu Z, Yuan Y. Sinorhodobacter ferrireducens gen. nov., sp. nov., a non-phototrophic iron-reducing bacterium closely related to phototrophic Rhodobacter species. Antonie van Leeuwenhoek 2013; 104:715–724 [View Article]
    [Google Scholar]
  2. Imhoff JF, Trüper HG, Pfennig N. Rearrangement of the species and genera of the phototrophic "Purple Nonsulfur Bacteria". Int J Syst Bacteriol 1984; 34:340–343 [View Article]
    [Google Scholar]
  3. Xu G-T, Piao C, Chang J-P, Guo L-M, Yang X-Q et al. Sinorhodobacter populi sp. nov., isolated from the symptomatic bark tissue of Populus × euramericana canker. Int J Syst Evol Microbiol 2019; 69:1220–1224 [View Article]
    [Google Scholar]
  4. Xi L, Qiao N, Zhang Z, Yan L, Li F et al. Sinorhodobacter hungdaonensis sp. nov. isolated from activated sludge collected from a municipal wastewater treatment plant. Antonie van Leeuwenhoek 2017; 110:27–32 [View Article]
    [Google Scholar]
  5. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: Wiley; 1991 pp 115–175
    [Google Scholar]
  6. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article]
    [Google Scholar]
  7. Yoon SH, SM H, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically United database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617
    [Google Scholar]
  8. Thompson J, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article]
    [Google Scholar]
  9. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  10. Kimura M. The Neutral Theory of Molecular Evolution Cambridge University Press;
    [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425
    [Google Scholar]
  12. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  13. 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]
    [Google Scholar]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  15. Suresh G, Sailaja B, Ashif A, Dave BP, Sasikala C et al. Description of Rhodobacter azollae sp. nov. and Rhodobacter lacus sp. nov. Int J Syst Evol Microbiol 2017; 67:3289–3295 [View Article]
    [Google Scholar]
  16. Venkata Ramana V, Sasikala C, Ramana CV. Rhodobacter maris sp. nov., a phototrophic alphaproteobacterium isolated from a marine habitat of India. Int J Syst Evol Microbiol 2008; 58:1719–1722 [View Article]
    [Google Scholar]
  17. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article]
    [Google Scholar]
  18. Yoon S-H, Ha S-min, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
    [Google Scholar]
  19. FN L, Liao SL, Liu SW, Jin T, Sun CH. Aeromicrobium endophyticum sp. nov., an endophytic actinobacterium isolated from reed (Phragmites australis). J Microbiol 2019; 57:
    [Google Scholar]
  20. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article]
    [Google Scholar]
  21. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc Committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
    [Google Scholar]
  22. Buck JD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993
    [Google Scholar]
  23. Weon H-Y, Kim B-Y, Joa J-H, Son J-A, Song M-H et al. Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea. Int J Syst Evol Microbiol 2008; 58:93–96 [View Article]
    [Google Scholar]
  24. Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA et al. Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature 2016; 533:543–546 [View Article]
    [Google Scholar]
  25. Cappuccino JG, Sherman N. A Laboratory Manual, 6th ed. Benjamin Cummings, CA. Microbiology: Pearson Education, Inc; 2002
    [Google Scholar]
  26. Atlas RM. Handbook of Microbiological Media Boca Raton, Florida, USA: CRC Press; 1993
    [Google Scholar]
  27. Dong X-zhu, Cai M-ying. Manual of Systematic and Determinative Bacteriology Science Press; 2001
    [Google Scholar]
  28. Breznak JA, Costilow RN. Physicochemical factors in growth. in methods for general and molecular microbiology. American Society of Microbiology 2007; 3:309–329
    [Google Scholar]
  29. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI technical note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  30. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
    [Google Scholar]
  31. 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]
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