1887

Abstract

An aerobic, Gram-stain-negative, rod-shaped bacterium, designated strain CC-LY845, was isolated from the surface of rice straw in Taiwan. Cells were non-motile, and no flagellum was detected. Comparison of 16S rRNA gene sequences indicated that the strain was phylogenetically related to species of the genus , with closest similarity to KCTC 23294 (97.6 %), KCTC 23652 (97.0 %) and LMG 24253 (96.7 %); other species showed lower levels of similarity (<96.6 %). The DNA–DNA relatedness of strain CC-LY845 and KCTC 23294 was 34.8±3.1 % (reciprocal value 39.2±2.2 %). Phylogenetic analysis based on the housekeeping and genes showed that the novel strain could be distinguished from KCTC 23294 (92.7 and 91.5 %, respectively) and other species of the genus . The temperature range for growth was 25–42 °C, the pH range was 5.0–9.0 and NaCl concentrations up to 4.0 % (w/v) were tolerated. Strain CC-LY845 did not form nodules on four different legumes, and the and genes were not detected by PCR. The major fatty acids were C and summed feature 8 (Cω7/Cω6). The polyamine pattern of strain CC-LY845 showed spermidine and putrescine as major polyamines. The predominant quinone system was ubiquinone 10 (Q-10). The DNA G+C content was 68.3±2.4 mol%. Base on its phylogenetic, phenotypic and chemotaxonomic features, strain CC-LY845 is proposed to represent a novel species within the genus , for which the name sp. nov. is proposed. The type strain is strain CC-LY845 ( = BCRC 80698 = JCM 19536).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.062117-0
2014-09-01
2019-11-22
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/9/2962.html?itemId=/content/journal/ijsem/10.1099/ijs.0.062117-0&mimeType=html&fmt=ahah

References

  1. Berge O. , Lodhi A. , Brandelet G. , Santaella C. , Roncato M. A. , Christen R. , Heulin T. , Achouak W. . ( 2009; ). Rhizobium alamii sp. nov., an exopolysaccharide-producing species isolated from legume and non-legume rhizospheres. . Int J Syst Evol Microbiol 59:, 367–372. [CrossRef] [PubMed]
    [Google Scholar]
  2. Collins M. D. . ( 1985; ). Isoprenoid quinone analysis in classification and identification. . In Chemical Methods in Bacterial Systematics, pp. 267–287. Edited by Goodfellow M. , Minnikin D. E. . . London:: Academic Press;.
    [Google Scholar]
  3. Conn H. J. . ( 1942; ). Validity of the genus Alcaligenes . . J Bacteriol 44:, 353–360.[PubMed]
    [Google Scholar]
  4. de Bruijn F. J. . ( 1992; ). Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. . Appl Environ Microbiol 58:, 2180–2187.[PubMed]
    [Google Scholar]
  5. de Lajudie P. , Laurent-Fulele E. , Willems A. , Torek U. , Coopman R. , Collins M. D. , Kersters K. , Dreyfus B. , Gillis M. . ( 1998; ). Allorhizobium undicola gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate Neptunia natans in Senegal. . Int J Syst Bacteriol 48:, 1277–1290. [CrossRef] [PubMed]
    [Google Scholar]
  6. Edwards U. , Rogall T. , Blöcker H. , Emde M. , Böttger E. C. . ( 1989; ). Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. . Nucleic Acids Res 17:, 7843–7853. [CrossRef] [PubMed]
    [Google Scholar]
  7. Farrand S. K. , Van Berkum P. B. , Oger P. . ( 2003; ). Agrobacterium is a definable genus of the family Rhizobiaceae . . Int J Syst Evol Microbiol 53:, 1681–1687. [CrossRef] [PubMed]
    [Google Scholar]
  8. Felsenstein J. . ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368–376. [CrossRef] [PubMed]
    [Google Scholar]
  9. Felsenstein J. . ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  10. Fitch W. M. . ( 1971; ). Toward defining the course of evolution: minimum change for a specific tree topology. . Syst Zool 20:, 406–416. [CrossRef]
    [Google Scholar]
  11. Frank B. . ( 1889; ). Über die Pilzsymbiose der Leguminosen. . Ber Dtsch Bot Ges 7:, 332–346 (in German).
    [Google Scholar]
  12. García-Fraile P. , Rivas R. , Willems A. , Peix A. , Martens M. , Martínez-Molina E. , Mateos P. F. , Velázquez E. . ( 2007; ). Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba . . Int J Syst Evol Microbiol 57:, 844–848. [CrossRef] [PubMed]
    [Google Scholar]
  13. Gaunt M. W. , Turner S. L. , Rigottier-Gois L. , Lloyd-Macgilp S. A. , Young J. P. W. . ( 2001; ). Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. . Int J Syst Evol Microbiol 51:, 2037–2048. [CrossRef] [PubMed]
    [Google Scholar]
  14. Graham P. H. , Sadowsky M. J. , Keyser H. H. , Barnet Y. M. , Bradley R. S. , Cooper J. E. , De Ley D. J. , Jarvis B. D. W. , Roslycky E. B. . & other authors ( 1991; ). Proposed minimal standards for the description of new genera and species of root-and stem-nodulating bacteria. . Int J Syst Bacteriol 41:, 582–587. [CrossRef]
    [Google Scholar]
  15. Heiner C. R. , Hunkapiller K. L. , Chen S. M. , Glass J. I. , Chen E. Y. . ( 1998; ). Sequencing multimegabase-template DNA with BigDye terminator chemistry. . Genome Res 8:, 557–561.[PubMed]
    [Google Scholar]
  16. Huber I. , Selenska-Pobell S. . ( 1994; ). Characterization of Rhizobium galegae by REP-PCR, PFGE and 16S rRNA sequencing. . In Symbiotic Nitrogen Fixation, pp. 153–158. Edited by Graham P. H. , Sadowsky M. J. , Vance C. P. . . Dordrecht:: Kluwer;. [CrossRef]
    [Google Scholar]
  17. Hunter W. J. , Kuykendall L. D. , Manter D. K. . ( 2007; ). Rhizobium selenireducens sp. nov.: a selenite-reducing α-Proteobacteria isolated from a bioreactor. . Curr Microbiol 55:, 455–460. [CrossRef] [PubMed]
    [Google Scholar]
  18. Judd A. K. , Schneider M. , Sadowsky M. J. , de Bruijn F. J. . ( 1993; ). Use of repetitive sequences and the polymerase chain reaction technique to classify genetically related Bradyrhizobium japonicum serocluster 123 strains. . Appl Environ Microbiol 59:, 1702–1708.[PubMed]
    [Google Scholar]
  19. Kim O. S. , Cho Y. J. , Lee K. , Yoon S. H. , Kim M. , Na H. , Park S. C. , Jeon Y. S. , Lee J. H. . & other authors ( 2012; ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62:, 716–721. [CrossRef] [PubMed]
    [Google Scholar]
  20. Kittiwongwattana C. , Thawai C. . ( 2013; ). Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis). . Int J Syst Evol Microbiol 63:, 3823–3828. [CrossRef] [PubMed]
    [Google Scholar]
  21. Koeuth T. , Versalovic J. , Lupski J. R. . ( 1995; ). Differential subsequence conservation of interspersed repetitive Streptococcus pneumoniae BOX elements in diverse bacteria. . Genome Res 5:, 408–418. [CrossRef] [PubMed]
    [Google Scholar]
  22. Kuklinsky-Sobral J. , Araújo W. L. , Mendes R. , Geraldi I. O. , Pizzirani-Kleiner A. A. , Azevedo J. L. . ( 2004; ). Isolation and characterization of soybean-associated bacteria and their potential for plant growth promotion. . Environ Microbiol 6:, 1244–1251. [CrossRef] [PubMed]
    [Google Scholar]
  23. Laguerre G. , Nour S. M. , Macheret V. , Sanjuan J. , Drouin P. , Amarger N. . ( 2001; ). Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. . Microbiology 147:, 981–993.[PubMed]
    [Google Scholar]
  24. Mesbah M. , Premachandran U. , Whitman W. B. . ( 1989; ). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. . Int J Syst Bacteriol 39:, 159–167. [CrossRef]
    [Google Scholar]
  25. Miller L. T. . ( 1982; ). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. . J Clin Microbiol 16:, 584–586.[PubMed]
    [Google Scholar]
  26. Minnikin D. E. , O’Donnell A. G. , Goodfellow M. , Alderson G. , Athalye M. , Schaal K. , Parlett J. H. . ( 1984; ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2:, 233–241. [CrossRef]
    [Google Scholar]
  27. Mousavi S. A. , Österman J. , Wahlberg N. , Nesme X. , Lavire C. , Vial L. , Paulin L. , de Lajudie P. , Lindström K. . ( 2014; ). Phylogeny of the RhizobiumAllorhizobiumAgrobacterium clade supports the delineation of Neorhizobium gen. nov.. Syst Appl Microbiol 37:, 208–215. [CrossRef] [PubMed]
    [Google Scholar]
  28. Murray R. G. E. , Doetsch R. N. , Robinow C. F. . ( 1994; ). Determinative and cytological light microscopy. . In Methods for General and Molecular Bacteriology, pp. 31–32. Edited by Gerhardt P. , Murray R. G. E. , Wood W. A. , Krieg N. R. . . Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  29. Nick G. , Lindstrom K. . ( 1994; ). Use of repetitive sequences and the polymerase chain reaction to fingerprint the genomic DNA of Rhizobium galegae strains and to identify the DNA obtained by sonicating the liquid cultures and root nodules. . Syst Appl Microbiol 17:, 265–273. [CrossRef]
    [Google Scholar]
  30. Nick G. , Jussila M. , Hoste B. , Niemi R. M. , Kaijalainen S. , de Lajudie P. , Gillis M. , de Bruijn F. J. , Lindström K. . ( 1999; ). Rhizobia isolated from root nodules of tropical leguminous trees characterized using DNA-DNA dot-blot hybridisation and rep-PCR genomic fingerprinting. . Syst Appl Microbiol 22:, 287–299. [CrossRef]
    [Google Scholar]
  31. Paisley R. . ( 1996; ). MIS Whole Cell Fatty Acid Analysis by Gas Chromatography Training Manual. Newark, DE:: MIDI;.
    [Google Scholar]
  32. Peng G. X. , Yuan Q. H. , Li H. X. , Zhang W. , Tan Z. Y. . ( 2008; ). Rhizobium oryzae sp. nov., isolated from the wild rice Oryza alta . . Int J Syst Evol Microbiol 58:, 2158–2163. [CrossRef] [PubMed]
    [Google Scholar]
  33. Poly F. , Monrozier L. J. , Bally R. . ( 2001; ). Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. . Res Microbiol 152:, 95–103. [CrossRef] [PubMed]
    [Google Scholar]
  34. Quan Z. X. , Bae H. S. , Baek J. H. , Chen W. F. , Im W. T. , Lee S. T. . ( 2005; ). Rhizobium daejeonense sp. nov. isolated from a cyanide treatment bioreactor. . Int J Syst Evol Microbiol 55:, 2543–2549. [CrossRef] [PubMed]
    [Google Scholar]
  35. Saitou N. , Nei M. . ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4:, 406–425.[PubMed]
    [Google Scholar]
  36. Sarita S. , Sharma P. K. , Priefer U. B. , Prell J. . ( 2005; ). Direct amplification of rhizobial nodC sequences from soil total DNA and comparison to nodC diversity of root nodule isolates. . FEMS Microbiol Ecol 54:, 1–11. [CrossRef] [PubMed]
    [Google Scholar]
  37. Sasser M. . ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE:: MIDI Inc;.
    [Google Scholar]
  38. Scherer P. , Kneifel H. . ( 1983; ). Distribution of polyamines in methanogenic bacteria. . J Bacteriol 154:, 1315–1322.[PubMed]
    [Google Scholar]
  39. Schloter M. , Wiehe W. , Assmus B. , Steindl H. , Becke H. , Höflich G. , Hartmann A. . ( 1997; ). Root colonization of different plants by plant-growth-promoting Rhizobium leguminosarum bv. trifolii R39 studied with monospecific polyclonal antisera. . Appl Environ Microbiol 63:, 2038–2046.[PubMed]
    [Google Scholar]
  40. Segovia L. , Piñero D. , Palacios R. , Martínez-Romero E. . ( 1991; ). Genetic structure of a soil population of nonsymbiotic Rhizobium leguminosarum . . Appl Environ Microbiol 57:, 426–433.[PubMed]
    [Google Scholar]
  41. Seldin L. , Dubnau D. . ( 1985; ). Deoxyribonucleic acid homology among Bacillus polymyxa, Bacillus macerans, Bacillus azotofixans, and other nitrogen-fixing Bacillus strains. . Int J Syst Bacteriol 35:, 151–154. [CrossRef]
    [Google Scholar]
  42. Stackebrandt E. , Goebel B. M. . ( 1994; ). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44:, 846–849. [CrossRef]
    [Google Scholar]
  43. Sullivan J. T. , Eardly B. D. , van Berkum P. , Ronson C. W. . ( 1996; ). Four unnamed species of nonsymbiotic rhizobia isolated from the rhizosphere of Lotus corniculatus . . Appl Environ Microbiol 62:, 2818–2825.[PubMed]
    [Google Scholar]
  44. Tamura K. , Stecher G. , Peterson D. , Filipski A. , Kumar S. . ( 2013; ). mega6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol 30:, 2725–2729. [CrossRef] [PubMed]
    [Google Scholar]
  45. Thompson J. D. , Gibson T. J. , Plewniak F. , Jeanmougin F. , Higgins D. G. . ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. . Nucleic Acids Res 25:, 4876–4882. [CrossRef] [PubMed]
    [Google Scholar]
  46. Turdahon M. , Osman G. , Hamdun M. , Yusuf K. , Abdurehim Z. , Abaydulla G. , Abdukerim M. , Fang C. , Rahman E. . ( 2013; ). Rhizobium tarimense sp. nov., isolated from soil in the ancient Khiyik River. . Int J Syst Evol Microbiol 63:, 2424–2429.[CrossRef]
    [Google Scholar]
  47. Vincent J. M. . ( 1970a; ). A Manual for the Practical Study of the Root-Nodule Bacteria. Oxford:: Blackwell Scientific;.
    [Google Scholar]
  48. Vincent J. M. . ( 1970b; ). The cultivation, isolation and maintenance of rhizobia. . In A Manual for the Practical Study of the Root-Nodule Bacteria, pp. 1–13. Edited by Vincent J. M. . . Oxford:: Blackwell Scientific;.
    [Google Scholar]
  49. Wayne L. G. , Brenner D. J. , Colwell R. R. , Grimont P. A. D. , Kandler O. , Krichevsky M. I. , Moore L. H. , Moore W. E. C. , Murray R. G. E. . & other authors ( 1987; ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37:, 463–464. [CrossRef]
    [Google Scholar]
  50. Young J. M. , Kuykendall L. D. , Martínez-Romero E. , Kerr A. , Sawada H. . ( 2001; ). A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis . . Int J Syst Evol Microbiol 51:, 89–103.[PubMed] [CrossRef]
    [Google Scholar]
  51. Zehr J. P. , Jenkins B. D. , Short S. M. , Steward G. F. . ( 2003; ). Nitrogenase gene diversity and microbial community structure: a cross-system comparison. . Environ Microbiol 5:, 539–554. [CrossRef] [PubMed]
    [Google Scholar]
  52. Zhang X.-X. , Sun L. , Ma X.-T. , Sui X.-H. , Jiang R. . ( 2011; ). Rhizobium pseudoryzae sp. nov., isolated from the rhizosphere of rice. . Int J Syst Evol Microbiol 61:, 2425–2429. [CrossRef] [PubMed]
    [Google Scholar]
  53. Zhang X.-X. , Tang X. , Sheirdil R. A. , Sun L. , Ma X.-T. . ( 2014; ). Rhizobium rhizoryzae sp. nov., isolated from rice roots. . Int J Syst Evol Microbiol 64:, 1373–1377. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.062117-0
Loading
/content/journal/ijsem/10.1099/ijs.0.062117-0
Loading

Data & Media loading...

Supplements

Supplementary Material 

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