1887

Abstract

A Gram-stain-negative, rod-shaped bacterium, strain 4-12, was isolated from the rhizosphere of Triticum aestivum L. from the Xiaokai River irrigation area, China. The isolate grew optimally at 30 °C, pH 7.5–8.0 and with 1.0 % (w/v) NaCl. Based on the 16S rRNA gene sequence and phylogenetic analysis, strain 4-12 belonged to the genus Luteimonas with the highest degree of 16S rRNA gene sequence similarity to Luteimonas tolerans UM1 (97.68 %), followed by Luteimonas terrae THG-MD21 (97.67 %), Lysobacter panaciterrae Gsoil 068 (97.21 %) and Luteimonas aestuarii B9 (97.16 %). However, the DNA–DNA relatedness values between strain 4-12 and closely related Luteimonas strains were well below 40 %. The average nucleotide identity and the Genome-to-Genome Distance Calculator also showed low relatedness (below 95 and 70 %, respectively) between strain 4-12 and the type strains in genus Luteimonas . Ubiquinone-8 was the predominant quinone. The major fatty acids were iso-C15 : 0, iso-C11 : 0, iso-C17 : 0 and iso-C17 : 1ω9c. Polar lipids were dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unidentified phospholipids. The DNA G+C content was 69.5 %. According to the phenotypic, genetic and chemotaxonomic data, strain 4-12 is considered to represent a novel species in the genus Luteimonas , for which the name >Luteimonas rhizosphaerae sp. nov. is proposed, with strain 4-12 (=CCTCC AB 2016261=KCTC 52585) as the type strain.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002649
2018-02-23
2019-09-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/4/1197.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002649&mimeType=html&fmt=ahah

References

  1. Finkmann W, Altendorf K, Stackebrandt E, Lipski A. Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov. Int J Syst Evol Microbiol 2000; 50: 273– 282 [CrossRef] [PubMed]
    [Google Scholar]
  2. Baik KS, Park SC, Kim MS, Kim EM, Park C et al. Luteimonas marina sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2008; 58: 2904– 2908 [CrossRef] [PubMed]
    [Google Scholar]
  3. Chou JH, Cho NT, Arun AB, Young CC, Chen WM. Luteimonas aquatica sp. nov., isolated from fresh water from Southern Taiwan. Int J Syst Evol Microbiol 2008; 58: 2051– 2055 [CrossRef] [PubMed]
    [Google Scholar]
  4. Wu G, Liu Y, Li Q, du H, You J et al. Luteimonas huabeiensis sp. nov., isolated from stratum water. Int J Syst Evol Microbiol 2013; 63: 3352– 3357 [CrossRef] [PubMed]
    [Google Scholar]
  5. Ten LN, Jung HM, Im WT, Yoo SA, Oh HM et al. Lysobacter panaciterrae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2009; 59: 958– 963 [CrossRef] [PubMed]
    [Google Scholar]
  6. Zhang DC, Liu HC, Xin YH, Zhou YG, Schinner F et al. Luteimonas terricola sp. nov., a psychrophilic bacterium isolated from soil. Int J Syst Evol Microbiol 2010; 60: 1581– 1584 [CrossRef] [PubMed]
    [Google Scholar]
  7. Ngo HT, Yin CS. Luteimonas terrae sp. nov., isolated from rhizosphere soil of Radix ophiopogonis. Int J Syst Evol Microbiol 2016; 66: 1920– 1925 [CrossRef] [PubMed]
    [Google Scholar]
  8. Cheng J, Zhang MY, Wang WX, Manikprabhu D, Salam N et al. Luteimonas notoginsengisoli sp. nov., isolated from rhizosphere. Int J Syst Evol Microbiol 2016; 66: 946– 950 [CrossRef] [PubMed]
    [Google Scholar]
  9. Rani P, Mukherjee U, Verma H, Kamra K, Lal R. Luteimonas tolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 2016; 66: 1851– 1856 [CrossRef] [PubMed]
    [Google Scholar]
  10. Romanenko LA, Tanaka N, Svetashev VI, Kurilenko VV, Mikhailov VV. Luteimonas vadosa sp. nov., isolated from seashore sediment. Int J Syst Evol Microbiol 2013; 63: 1261– 1266 [CrossRef] [PubMed]
    [Google Scholar]
  11. Roh SW, Kim KH, Nam YD, Chang HW, Kim MS et al. Luteimonas aestuarii sp. nov., isolated from tidal flat sediment. J Microbiol 2008; 46: 525– 529 [CrossRef] [PubMed]
    [Google Scholar]
  12. Fan X, Yu T, Li Z, Zhang XH. Luteimonas abyssi sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2014; 64: 668– 674 [CrossRef] [PubMed]
    [Google Scholar]
  13. Young CC, Kämpfer P, Chen WM, Yen WS, Arun AB et al. Luteimonas composti sp. nov., a moderately thermophilic bacterium isolated from food waste. Int J Syst Evol Microbiol 2007; 57: 741– 744 [CrossRef] [PubMed]
    [Google Scholar]
  14. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74: 2461– 2470 [CrossRef] [PubMed]
    [Google Scholar]
  15. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62: 716– 721 [CrossRef] [PubMed]
    [Google Scholar]
  16. Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23: 2947– 2948 [CrossRef] [PubMed]
    [Google Scholar]
  17. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406– 425 [CrossRef] [PubMed]
    [Google Scholar]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368– 376 [CrossRef] [PubMed]
    [Google Scholar]
  19. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20: 406– 416 [CrossRef]
    [Google Scholar]
  20. 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 [CrossRef] [PubMed]
    [Google Scholar]
  21. 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 [CrossRef] [PubMed]
    [Google Scholar]
  22. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983; 4: 184– 192 [CrossRef] [PubMed]
    [Google Scholar]
  23. Stackebrandt E, Goebel BM. Taxonomic Note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44: 846– 849 [CrossRef]
    [Google Scholar]
  24. 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 [CrossRef] [PubMed]
    [Google Scholar]
  25. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14: 60 [CrossRef] [PubMed]
    [Google Scholar]
  26. Claus D. A standardized Gram staining procedure. World J Microbiol Biotechnol 1992; 8: 451– 452 [CrossRef] [PubMed]
    [Google Scholar]
  27. Tarrand JJ, Gröschel DH. Rapid, modified oxidase test for oxidase-variable bacterial isolates. J Clin Microbiol 1982; 16: 772– 774 [PubMed]
    [Google Scholar]
  28. Mata JA, Martínez-Cánovas J, Quesada E, Béjar V. A detailed phenotypic characterisation of the type strains of Halomonas species. Syst Appl Microbiol 2002; 25: 360– 375 [CrossRef] [PubMed]
    [Google Scholar]
  29. Bauer AW, Kirby WM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45: 493– 496 [PubMed] [Crossref]
    [Google Scholar]
  30. Stead DE, Sellwood JE, Wilson J, Viney I. Evaluation of a commercial microbial identification system based on fatty acid profiles for rapid, accurate identification of plant pathogenic bacteria. J Appl Bacteriol 1992; 72: 315– 321 [CrossRef]
    [Google Scholar]
  31. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42: 989– 1005 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002649
Loading
/content/journal/ijsem/10.1099/ijsem.0.002649
Loading

Data & Media loading...

Supplementary File 1

PDF

Most Cited This Month

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