1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 68, Issue 2

sp. nov., a nitrogen-fixing bacterium isolated from activated sludge Free

Abstract

A Gram-reaction-negative, catalase- and oxidase-positive, aerobic, transparent, motile and rod-shaped bacterium that was capable of fixing dinitrogen (designated strain A.slu09), isolated from activated sludge, was characterized by a polyphasic approach to clarify its taxonomic position. Strain A.slu09 was observed to grow optimally at 30 °C and at pH 7.0 on R2A agar medium. Strain A.slu09 showed -glucosidase activity, converting the major ginsenoside Rd to ginsenoside F2. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain A.slu09 belongs to the genus of the family and was most closely related to MSSRFBL1 (97.8 % similarity). The DNA G+C content was 67.2 mol%. The DNA–DNA hybridization value between strain A.slu09 and KCTC 32403 was 16.9±1.17 %. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, aminophospholipid and two glycolipids, and one unknown phospholipid as a minor lipid. The predominant quinone was ubiquinone-10 (Q-10). The major fatty acids were C cyclo 8, Cω7 and/or Cω6 (summed feature 8) and C, a profile that supported the affiliation of A.slu09 to the genus . Moreover, the physiological and biochemical characteristics and low level of DNA–DNA relatedness allowed the phenotypic and genotypic differentiation of strain A.slu09 from the recognized species of the genus . Therefore, strain A.slu09 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is A.slu09 (=KACC 19080=LMG 29962).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene sequence , bioconversion , Ciceribacter azotifigens , ginsenosides and polyphasic taxonomy
© 2018 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002438
2018-02-01
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/2/482.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002438&mimeType=html&fmt=ahah

References

  1. Kathiravan R, Jegan S, Ganga V, Prabavathy VR, Tushar L et al. Ciceribacter lividus gen. nov., sp. nov., isolated from rhizosphere soil of chick pea (Cicer arietinum L.). Int J Syst Evol Microbiol 2013; 63:4484–4488 [View Article][PubMed]
     [Google Scholar]
  2. Cavalcante VA, Dobereiner J. A new acid-tolerant nitrogen-fixing bacterium associated with sugarcane. Plant Soil 1988; 108:23–31 [View Article]
     [Google Scholar]
  3. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991 pp. 115–176
     [Google Scholar]
  4. Kim JK, Kang MS, Park SC, Kim KM, Choi K et al. Sphingosinicella ginsenosidimutans sp. nov., with ginsenoside converting activity. J Microbiol 2015; 53:435–441 [View Article][PubMed]
     [Google Scholar]
  5. 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][PubMed]
     [Google Scholar]
  6. 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]
  7. Kimura M. The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; 1983 [Crossref]
     [Google Scholar]
  8. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425[PubMed]
     [Google Scholar]
  9. 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]
  10. 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 [View Article][PubMed]
     [Google Scholar]
  11. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  12. Martens M, Delaere M, Coopman R, de Vos P, Gillis M et al. Multilocus sequence analysis of Ensifer and related taxa. Int J Syst Evol Microbiol 2007; 57:489–503 [View Article][PubMed]
     [Google Scholar]
  13. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993[PubMed]
     [Google Scholar]
  14. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria Cambridge: Cambridge University Press; 1974
     [Google Scholar]
  15. Ten LN, Im WT, Kim MK, Kang MS, Lee ST. Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 2004; 56:375–382 [View Article][PubMed]
     [Google Scholar]
  16. Siddiqi MZ, Aslam Z, Im WT. Arachidicoccus ginsenosidivorans sp. nov., with ginsenoside-converting activity isolated from ginseng cultivating soil. Int J Syst Evol Microbiol 2017; 67:1005–1010 [View Article][PubMed]
     [Google Scholar]
  17. Berge O, Guinebretière MH, Achouak W, Normand P, Heulin T. Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food. Int J Syst Evol Microbiol 2002; 52:607–616 [View Article][PubMed]
     [Google Scholar]
  18. Moore DD, Dowhan D. Preparation and analysis of DNA. In Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG et al. (editors) Current Protocols in Molecular Biology NY: Wiley; 1995 pp. 2–11
     [Google Scholar]
  19. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
     [Google Scholar]
  20. 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]
  21. 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]
  22. Sasser M. Identification of bacteria through fatty acid analysis. In Klement Z, Rudolph K, Sands DC. (editors) Methods in Phytobacteriology Budapest: Akademiai Kaido; 1990 pp. 199–204
     [Google Scholar]
  23. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989; 39:224–229 [View Article]
     [Google Scholar]
  24. Goris J, Suzuki K-Ichiro, Vos PD, Nakase T, Kersters K. Evaluation of a microplate DNA-DNA hybridization method compared with the initial renaturation method. Can J Microbiol 1998; 44:1148–1153 [View Article]
     [Google Scholar]
  25. 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.0.002438
Loading
Ciceribacter azotifigens sp. nov., a nitrogen-fixing bacterium isolated from activated sludge
Int J Syst Evol Microbiol 68, 482 (2018); https://doi.org/10.1099/ijsem.0.002438
/content/journal/ijsem/10.1099/ijsem.0.002438
/content/journal/ijsem/10.1099/ijsem.0.002438
Loading

Data & Media loading...

Supplements

Supplementary File 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