1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 1

sp. nov., isolated from activated sludge Free

Abstract

A novel Gram-stain-negative, yellowish-pigmented bacterial strain, designated LA-38, was isolated from activated sludge of wastewater treatment plants in Hanam city, South Korea. Cell of LA-38 were rod-shaped, aerobic, motile and non-spore-forming. In phylogenetic analyses based on 16S rRNA genes, LA-38 clustered with species of the genus and appeared closely related to DSM 5680 (99.2 % similarity), DSM 63 (98.2 %), KCTC 42478 (98.1 %), DSM 15342 (98.1 %), DSM 15341 (98.0 %) and DSM 2082 (97.2 %). The average nucleotide identities between LA-38 and the closely related strains were 79.3–88.5 %, indicating that LA-38 represents a novel species of the genus . The DNA G+C content of the genomic DNA was 69.9 mol% and ubiquinone Q-8 was the predominant respiratory quinone. The major cellular fatty acids (>5 %) were C, cyclo-C, Cω7 and/or Cω6 (summed feature 3), and Cω7 and/or Cω6 (summed feature 8). The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine, the major polyamines were 2-hydroxyputrescine and putrescine. ANI calculation, physiological and biochemical characteristics indicated that LA-38 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is LA-38 (=KACC 19730=LMG 30805).

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): 16S rRNA gene sequence , genome sequence , Hydrogenophaga borbori , polyphasic taxonomy and sludge
Funding
This study was supported by the:
  • National Institute of Biological Resources
    • Principle Award Recipient: Wan-Taek Im
  • Korea Research Institute of Bioscience and Biotechnology
    • Principle Award Recipient: Wan-Taek Im
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003787
2020-02-03
2024-05-05
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/1/555.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003787&mimeType=html&fmt=ahah

References

  1. Willems A, Busse J, Goor M, Pot B, Falsen E et al. Hydrogenophaga, a new genus of hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov. (formerly Pseudomonas flava), Hydrogenophaga palleronii (formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (formerly Pseudomonas pseudoflava and "Pseudomonas carboxydoflava"), and Hydrogenophaga taeniospiralis (formerly Pseudomonas taeniospiralis). Int J Syst Bacteriol 1989; 39:319–333 [View Article]
     [Google Scholar]
  2. Contzen M, Moore ERB, Blümel S, Stolz A, Kämpfer P. Hydrogenophaga intermedia sp. nov., a 4-aminobenzene-sulfonate degrading organism. Syst Appl Microbiol 2000; 23:487–493 [View Article]
     [Google Scholar]
  3. Kämpfer P, Schulze R, Jäckel U, Malik KA, Amann R et al. Hydrogenophaga defluvii sp. nov. and Hydrogenophaga atypica sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2005; 55:341–344 [View Article]
     [Google Scholar]
  4. Lin SY, Hameed A, Wen CZ, Hsu YH, Liu YC et al. Hydrogenophaga aquatica sp. nov., isolated from a hot spring. Int J Syst Evol Microbiol 2017; 67:3716–3721 [View Article]
     [Google Scholar]
  5. Baek C, Kim E, Shin SK, Choi S, Yi H. Hydrogenophaga crassostreae sp. nov., isolated from a Pacific oyster. Int J Syst Evol Microbiol 2017; 67:4045–4049 [View Article]
     [Google Scholar]
  6. Yang D, Cha S, Choi J, Seo T. Hydrogenophaga soli sp. nov., isolated from rice field soil. Int J Syst Evol Microbiol 2017; 67:4200–4204 [View Article]
     [Google Scholar]
  7. Mantri S, Chinthalagiri MR, Gundlapally SR. Description of Hydrogenophaga laconesensis sp. nov. isolated from tube well water. Arch Microbiol 2016; 198:637–644 [View Article]
     [Google Scholar]
  8. Du J, Yang JE, Singh H, Akter S, Won K et al. Hydrogenophaga luteola sp. nov. isolated from reed pond water. Antonie van Leeuwenhoek 2015; 108:695–701 [View Article]
     [Google Scholar]
  9. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: Wiley; 1991
     [Google Scholar]
  10. 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]
  11. 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]
  12. Thompson JD, 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]
  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. 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]
  15. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  16. 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]
     [Google Scholar]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
     [Google Scholar]
  18. 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]
  19. Yoon SH, Ha SM, 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]
  20. 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; 57:725–731
     [Google Scholar]
  21. Buck JD. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993
     [Google Scholar]
  22. Weon HY, Kim BY, Joa JH, Son JA, Song MH 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]
  23. Cappuccino JG, Sherman N. Microbiology, a Laboratory Manual, 6th ed. California: Pearson Education, Inc; 2002
     [Google Scholar]
  24. Atlas RM. Handbook of Microbiological Media Boca Raton, Florida, USA: CRC Press; 1993
     [Google Scholar]
  25. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria Cambridge: Cambridge University Press; 1974
     [Google Scholar]
  26. Malik KA, Schlegel HG. Chemolithoautotrophic growth of bacteria able to grow under N2-fixing conditions. FEMS Microbiol Lett 1981; 11:63–20 [View Article]
     [Google Scholar]
  27. 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]
  28. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 1988; 11:1–8 [View Article]
     [Google Scholar]
  29. Schenkel E, Berlaimont V, Dubois J, Helson-Cambier M, Hanocq M. Improved high-performance liquid chromatographic method for the determination of polyamines as their benzoylated derivatives: application to P388 cancer cells. J Chromatogr B Biomed Appl 1995; 668:189–197 [View Article]
     [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. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI technical note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  32. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article]
     [Google Scholar]
  33. Kim M, Oh HS, Park SC, 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003787
Loading
Hydrogenophaga borbori sp. nov., isolated from activated sludge
Int J Syst Evol Microbiol 70, 555 (2020); https://doi.org/10.1099/ijsem.0.003787
/content/journal/ijsem/10.1099/ijsem.0.003787
/content/journal/ijsem/10.1099/ijsem.0.003787
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

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