1887

Abstract

Three bacterial isolates, designated W44, W15 and W11, were isolated from the root of Oryza officinalis grown in Wuzhou, China. These isolates were Gram-negative, aerobic, motile and rod-shaped; demonstrated cellulase and urea activities; and formed cream-coloured colonies. The 16S rRNA gene sequence analysis indicated that the similarities between strain W44 and strains W15 and W11 were 100 %; all of them belonged to the genus Rhizobium and had the highest sequence similarity to Rhizobium rosettiformans W3 (98.7 %), followed by Rhizobium ipomoeae shin9-1 (98.2 %). Sequencing of housekeeping genes (recA, atpD, rpoB and glnA) of the novel isolates revealed similarities to members of established Rhizobium species to be less than 94.3 %. The values of DNA–DNA hybridization between strain W44 and the reference strains ( R. rosettiformans W3 and R. ipomoeae shin9-1) were 41.3 and 29.2 %, respectively. The major cellular fatty acid of strain W44 was summed feature 8 (C18 : 1ω9t and/or C18 : 1ω9c and/or C18 : 1ω7c). The polar lipid profile of strain W44 consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified lipids and two unidentified aminophospholipids. The G+C content of strain W44 was 62.4 mol%. In nodulation tests, none of the three strains could induce nodule formation in Glycine max, Phaseolus vulgaris or Medicago sativa. The nodulation gene (nodA), nitrogenase reductase gene (nifH) and virulence gene (virC) were not detected by PCR in these strains. Based on the above results and phenotypic features, a novel species, Rhizobium wuzhouense sp. nov., is proposed, with strain W44 (=CCTCC AB 2017179=GDMCC 1.1257=KCTC 62194) as the type strain.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002921
2018-07-20
2019-12-12
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/9/2918.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002921&mimeType=html&fmt=ahah

References

  1. Lindström K, Amsalu AA, Mousavi SA. Evolution and taxonomy of nitrogen-fixing organisms with emphasis on rhizobia. In de Bruijn FJ. (editor) Biological Nitrogen Fixation Hoboken, NJ: John Wiley & Sons; 2015; pp.21–38
    [Google Scholar]
  2. Lindström K, Mousavi SA. Rhizobium and other N-fixing symbioses. In Encyclopedia of Life Science (ELS) Chichester: John Wiley & Sons; 2010
    [Google Scholar]
  3. Frank B. Üeber die Pilzsymbiose der Leguminosen. Ber Dtsch Bot Ges 1889;7:332–346
    [Google Scholar]
  4. Yanni YG, Rizk RY, Corich V, Squartini A, Ninke K et al. Natural endophytic association between Rhizobium leguminosarum bv. trifolli and rice roots and assessment of its potential to promote rice growth. Plant Soil 1997;194:99–114 [CrossRef]
    [Google Scholar]
  5. Sheu SY, Chen ZH, Young CC, Chen WM. Rhizobium ipomoeae sp. nov., isolated from a water convolvulus field. Int J Syst Evol Microbiol 2016;66:1633–1640 [CrossRef][PubMed]
    [Google Scholar]
  6. Panday D, Schumann P, Das SK. Rhizobium pusense sp. nov., isolated from the rhizosphere of chickpea (Cicer arietinum L.). Int J Syst Evol Microbiol 2011;61:2632–2639 [CrossRef][PubMed]
    [Google Scholar]
  7. Zhang XX, Gao JS, Cao YH, Sheirdil RA, Wang XC et al. Rhizobium oryzicola sp. nov., potential plant-growth-promoting endophytic bacteria isolated from rice roots. Int J Syst Evol Microbiol 2015;65:2931–2936 [CrossRef][PubMed]
    [Google Scholar]
  8. Zhao JJ, Zhang J, Sun L, Zhang RJ, Zhang CW et al. Rhizobium oryziradicis sp. nov., isolated from rice roots. Int J Syst Evol Microbiol 2017;67:963–968 [CrossRef][PubMed]
    [Google Scholar]
  9. Gao JL, Sun P, Wang XM, Lv FY, Mao XJ et al. Rhizobium wenxiniae sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2017;67:2798–2803 [CrossRef][PubMed]
    [Google Scholar]
  10. Celador-Lera L, Menéndez E, Peix A, Igual JM, Velázquez E et al. Rhizobium zeae sp. nov., isolated from maize (Zea mays L.) roots. Int J Syst Evol Microbiol 2017;67:2306–2311 [CrossRef][PubMed]
    [Google Scholar]
  11. Chaudhary HJ, Peng G, Hu M, He Y, Yang L et al. Genetic diversity of endophytic diazotrophs of the wild rice, Oryza alta and identification of the new diazotroph, Acinetobacter oryzae sp. nov. Microb Ecol 2012;63:813–821 [CrossRef][PubMed]
    [Google Scholar]
  12. Peng GX, Chen WX, Tan ZY. Identification and phylogenetic analysis of closely related Rhizobium species by rRNA gene intergenic spacer sequence. J South China Agric Univ 2004;23:58–62
    [Google Scholar]
  13. Tan ZY, Xu XD, Wang ET, Gao JL, Martinez-Romero E et al. Phylogenetic and genetic relationships of Mesorhizobium tianshanense and related rhizobia. Int J Syst Bacteriol 1997;47:874–879 [CrossRef][PubMed]
    [Google Scholar]
  14. Mousavi SA, Österman J, Wahlberg N, Nesme X, Lavire C et al. Phylogeny of the Rhizobium-Allorhizobium-Agrobacterium clade supports the delineation of Neorhizobium gen. nov. Syst Appl Microbiol 2014;37:208–215 [CrossRef][PubMed]
    [Google Scholar]
  15. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  16. 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]
  17. Versalovic J, Koeuth T, Lupski JR. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 1991;19:6823–6831 [CrossRef][PubMed]
    [Google Scholar]
  18. Tan Z, Hurek T, Gyaneshwar P, Ladha JK, Reinhold-Hurek B. Novel endophytes of rice form a taxonomically distinct subgroup of Serratia marcescens. Syst Appl Microbiol 2001;24:245–251 [CrossRef][PubMed]
    [Google Scholar]
  19. Sasser M. Bacterial Identification by Gas Chromatographic Analysis of Fatty Acids Methyl Esters (GC-FAME), MIDI Technical Note 101. Newark, DE: MIDI Inc; 2006
    [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 [CrossRef]
    [Google Scholar]
  21. Graham PH, Sadowsky MJ, Keyser HH, Barnet YM, Bradley RS et al. Proposed minimal standards for the description of new genera and species of root- and stem-nodulating bacteria. Int J Syst Bacteriol 1991;41:582–587 [CrossRef]
    [Google Scholar]
  22. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018;68:461–466 [CrossRef][PubMed]
    [Google Scholar]
  23. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961;3:208–218 [CrossRef]
    [Google Scholar]
  24. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016;66:1100–1103 [CrossRef][PubMed]
    [Google Scholar]
  25. De Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970;12:133–142 [CrossRef][PubMed]
    [Google Scholar]
  26. 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 [CrossRef]
    [Google Scholar]
  27. Kuykendall LD, Young JM, Martínez-Romero E, Kerr A, Sawada H et al. Rhizobium. In Bergey's Manual of Systematics of Archaea and Bacteria New York, NY: John Wiley & Sons; 2015; pp.1–36
    [Google Scholar]
  28. Zehr JP, McReynolds LA. Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol 1989;55:2522–2526[PubMed]
    [Google Scholar]
  29. Haukka K, Lindström K, Young JP. Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America. Appl Environ Microbiol 1998;64:419–426[PubMed]
    [Google Scholar]
  30. Sawada H, Ieki H, Matsuda I. PCR detection of Ti and Ri plasmids from phytopathogenic Agrobacterium strains. Appl Environ Microbiol 1995;61:828–831[PubMed]
    [Google Scholar]
  31. Vincent JM. A manual for the practical study of the root-nodule bacteria. In International Biological Program Oxford: Blackwell Scientific; 1970; pp.1–13
    [Google Scholar]
  32. Gao JL, Sun JG, Li Y, Wang ET, Chen WX. Numerical taxonomy and DNA relatedness of tropical rhizobia isolated from Hainan Province, China. Int J Syst Bacteriol 1994;44:151–158 [CrossRef]
    [Google Scholar]
  33. García-Fraile P, Rivas R, Willems A, Peix A, Martens M et al. Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba. Int J Syst Evol Microbiol 2007;57:844–848 [CrossRef][PubMed]
    [Google Scholar]
  34. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002921
Loading
/content/journal/ijsem/10.1099/ijsem.0.002921
Loading

Data & Media loading...

Supplements

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