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Volume 69, Issue 12

sp. nov., a nitrogen-fixing bacterium isolated from the rhizosphere of wheat ( L.) Free

Abstract

A novel Gram-stain-variable, endospore-forming, motile, rod-shaped, facultative aerobic bacterium, designated 7197, was isolated from rhizosphere soil of wheat ( L.) collected from Yakeshi County, Inner Mongolia, PR China. This isolate was found to have the highest 16S rRNA gene sequence similarity to T27 (98.0 %), followed by S27 (97.9 %) and T98 (97.7 %). To ascertain the genomic relatedness of this strain to its phylogenetic neighbours, its genome sequence was determined. The average nucleotide identity values of genome sequences between the novel isolate and the type strains of related species T27, S27 and T98 were 87.9 %, 85.8 and 83.9 %, respectively. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids and one unidentified aminolipid. The major cellular fatty acids were anteiso-C (56.3 %), C (15.7 %) and iso-C (14.1 %).The genome size of strain 7197 was 5.21 Mb, comprising 4879 predicted genes with a DNA G+C content of 51.9 mol%. Menaquinone-7 was reported as the major respiratory quinone. The diamino acid in the cell-wall peptidoglycan was found to be -diaminopimelic acid. Based on phylogenetic, genomic, chemotaxonomic and phenotypic characteristics, strain 7197 was classified as a novel species within the genus , for which the name sp. nov. is proposed. The type strain of is 7197 (=DSM 103168=CGMCC 1.15699).

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  • Accepted:
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Keyword(s): Paenibacillus rhizophilus sp. nov. , rhizosphere and wheat
© 2019 IUMS
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2019-12-01
2024-04-20
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References

  1. Euzéby J, de Vos P, Ludwig W, Schleifer KH, Whitman WB. Paenibacillaceae fam. nov. In List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2010; 60:469–472
     [Google Scholar]
  2. Ash C, Priest FG, Collins MD. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus . Antonie van Leeuwenhoek 1993; 64:253–260[PubMed]
     [Google Scholar]
  3. Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K. Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus . Int J Syst Bacteriol 1997; 47:289–298 [View Article][PubMed]
     [Google Scholar]
  4. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
     [Google Scholar]
  5. Park MJ, Kim HB, An DS, Yang HC, Oh ST et al. Paenibacillus soli sp. nov., a xylanolytic bacterium isolated from soil. Int J Syst Evol Microbiol 2007; 57:146–150 [View Article][PubMed]
     [Google Scholar]
  6. Lee J, Shin NR, Jung MJ, Roh SW, Kim MS et al. Paenibacillus oceanisediminis sp. nov. isolated from marine sediment. Int J Syst Evol Microbiol 2013; 63:428–434 [View Article][PubMed]
     [Google Scholar]
  7. Zhang L, Gao JS, Zhang S, Ali Sheirdil R, Wang XC et al. Paenibacillus rhizoryzae sp. nov., isolated from rice rhizosphere. Int J Syst Evol Microbiol 2015; 65:3053–3059 [View Article][PubMed]
     [Google Scholar]
  8. Scheldeman P, Goossens K, Rodriguez-Diaz M, Pil A, Goris J et al. Paenibacillus lactis sp. nov., isolated from raw and heat-treated milk. Int J Syst Evol Microbiol 2004; 54:885–891 [View Article][PubMed]
     [Google Scholar]
  9. Roux V, Raoult D. Paenibacillus massiliensis sp. nov., Paenibacillus sanguinis sp. nov. and Paenibacillus timonensis sp. nov., isolated from blood cultures. Int J Syst Evol Microbiol 2004; 54:1049–1054 [View Article][PubMed]
     [Google Scholar]
  10. Jin HJ, Lv J, Chen SF. Paenibacillus sophorae sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sophora japonica. Int J Syst Evol Microbiol 2011; 61:767–771 [View Article][PubMed]
     [Google Scholar]
  11. Jin HJ, Zhou YG, Liu HC, Chen SF. Paenibacillus jilunlii sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Begonia semperflorens . Int J Syst Evol Microbiol 2011; 61:1350–1355 [View Article][PubMed]
     [Google Scholar]
  12. Gao M, Zhou J-Jiao, Wang E-Tao, Chen Q, Xu J et al. Multiphasic characterization of a plant growth promoting bacterial strain, Burkholderia sp. 7016 and its effect on tomato growth in the field. J Integr Agric 2015; 14:1855–1863 [View Article]
     [Google Scholar]
  13. Reasoner DJ, Geldreich EE. A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 1985; 49:1–7[PubMed]
     [Google Scholar]
  14. Logan NA, Berge O, Bishop AH, Busse HJ, de Vos P et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 2009; 59:2114–2121 [View Article][PubMed]
     [Google Scholar]
  15. 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 [View Article][PubMed]
     [Google Scholar]
  16. Lane DJ. 16S/23S rRNA sequencing. In Stackerandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematic Chichester: Wiley; 1991 pp. 115–175
     [Google Scholar]
  17. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article][PubMed]
     [Google Scholar]
  18. 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]
  19. 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][PubMed]
     [Google Scholar]
  20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
     [Google Scholar]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  22. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:1–6 [View Article][PubMed]
     [Google Scholar]
  23. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D et al. Toward an online repository of standard operating procedures (SOPs) for (meta)genomic annotation. OMICS 2008; 12:137–141 [View Article][PubMed]
     [Google Scholar]
  24. 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][PubMed]
     [Google Scholar]
  25. 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 [View Article][PubMed]
     [Google Scholar]
  26. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article][PubMed]
     [Google Scholar]
  27. Beneduzi A, Campos S, Ambrosini A, de Souza R, Granada C et al. Genome sequence of the diazotrophic Gram-positive rhizobacterium Paenibacillus riograndensis SBR5(T). J Bacteriol 2011; 193:6391–6392 [View Article][PubMed]
     [Google Scholar]
  28. Hong Y, Ma Y, Wu L, Maki M, Qin W et al. Characterization and analysis of nifH genes from Paenibacillus sabinae T27. Microbiol Res 2012; 167:596–601 [View Article][PubMed]
     [Google Scholar]
  29. Zhuang J, Xin D, Zhang YQ, Guo J, Zhang J. Paenibacillus albidus sp. nov., isolated from grassland soil. Int J Syst Evol Microbiol 2017; 67:4685–4691 [View Article][PubMed]
     [Google Scholar]
  30. Ma Y, Xia Z, Liu X, Chen S. Paenibacillus sabinae sp. nov., a nitrogen-fixing species isolated from the rhizosphere soils of shrubs. Int J Syst Evol Microbiol 2007; 57:6–11 [View Article][PubMed]
     [Google Scholar]
  31. Ma YC, Chen SF. Paenibacillus forsythiae sp. nov., a nitrogen-fixing species isolated from rhizosphere soil of Forsythia mira . Int J Syst Evol Microbiol 2008; 58:319–323 [View Article][PubMed]
     [Google Scholar]
  32. Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995; 61:3756–3758[PubMed]
     [Google Scholar]
  33. Gao JL, Sun P, Wang XM, Qiu TL, Lv FY et al. Filimonas zeae sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2016; 66:2730–2734 [View Article][PubMed]
     [Google Scholar]
  34. Gao JL, Yuan M, Wang XM, Qiu TL, Lv FY et al. Paenibacillus radicis sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2016; 66:807–811 [View Article][PubMed]
     [Google Scholar]
  35. Gao JL, Sun P, Wang XM, Cheng S, Lv F et al. Sphingomonaszeicaulis sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 2016; 66:3755–3760 [View Article][PubMed]
     [Google Scholar]
  36. Schaeffer AB, Fulton MD. A simplified method of staining endospores. Science 1933; 77:194 [View Article][PubMed]
     [Google Scholar]
  37. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc 1990
     [Google Scholar]
  38. Gao JL, Sun P, Sun XH, Tong S, Yan H et al. Caulobacter zeae sp. nov. and Caulobacter radicis sp. nov., novel endophytic bacteria isolated from maize root (Zea mays L.). Syst Appl Microbiol 2018; 41:604–610 [View Article][PubMed]
     [Google Scholar]
  39. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
     [Google Scholar]
  40. Carro L, Flores-Félix JD, Ramírez-Bahena MH, García-Fraile P, Martínez-Hidalgo P et al. Paenibacillus lupini sp. nov., isolated from nodules of Lupinus albus . Int J Syst Evol Microbiol 2014; 64:3028–3033 [View Article][PubMed]
     [Google Scholar]
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Paenibacillus rhizophilus sp. nov., a nitrogen-fixing bacterium isolated from the rhizosphere of wheat (Triticum aestivum L.)
Int J Syst Evol Microbiol 69, 3689 (2019); https://doi.org/10.1099/ijsem.0.003472
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