1887

Abstract

A Gram-stain-positive, aerobic, endospore-forming bacterial strain isolated from the rhizosphere of Zea mays was studied to determine its detailed taxonomic position. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-64 was shown to be a member of the genus Paenibacillus , most closely related to the type strains of Paenibacillus silagei (99 %) and Paenibacillus borealis (97.5 %). 16S rRNA gene sequence similarity to all other Paenibacillus species was ≤97.5 %. DNA–DNA hybridization values to the type strains of P. silagei and P. borealis were 51 % (reciprocal 25 %) and 31 % (reciprocal 37 %), respectively. The presence of meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan, the major quinone MK-7 and the polyamine pattern with spermidine as the major component were well in line with the characteristics of the genus Paenibacillus . Furthermore, the polar lipid profile of strain JJ-64 with the predominant lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and two unidentified aminophospholipids reflected the close phylogenetic relatedness to P. silagei . Major fatty acids were iso- and anteiso-branched components. Physiological and biochemical characteristics allowed the further phenotypic differentiation of strain JJ-64 from the most closely related species. Thus, strain JJ-64 represents a novel species of the genus Paenibacillus , for which the name Paenibacillus rhizoplanae sp. nov. is proposed. The type strain is JJ-64 (=LMG 29875=CCM 8725).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001779
2017-05-05
2019-10-21
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/4/1058.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001779&mimeType=html&fmt=ahah

References

  1. Ash C, Priest FG, Collins MD. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Antonie van Leeuwenhoek 1993;64:253–260[CrossRef]
    [Google Scholar]
  2. Carro L, Flores-Félix JD, Cerda-Castillo E, Ramírez-Bahena MH, Igual JM et al. Paenibacillus endophyticus sp. nov., isolated from nodules of Cicer arietinum. Int J Syst Evol Microbiol 2013;63:4433–4438 [CrossRef][PubMed]
    [Google Scholar]
  3. Lai W, Hameed A, Lin S, Hung M, Hsu Y et al. Paenibacillus medicaginis sp. nov. a chitinolytic endophyte isolated from the root nodule of alfalfa (Medicago sativa L.). Int J Syst Evol Microbiol 2015;65:3853–3860[CrossRef]
    [Google Scholar]
  4. Kittiwongwattana C, Thawai C. Paenibacillus lemnae sp. nov., an endophytic bacterium of duckweed (Lemna aequinoctialis). Int J Syst Evol Microbiol 2015;65:107–112 [CrossRef][PubMed]
    [Google Scholar]
  5. Gao JL, Lv FY, Wang XM, Qiu TL, Yuan M et al. Paenibacillus wenxiniae sp. nov., a nifH gene-harbouring endophytic bacterium isolated from maize. Antonie van Leeuwenhoek 2015;108:1015–1022 [CrossRef][PubMed]
    [Google Scholar]
  6. 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 [CrossRef][PubMed]
    [Google Scholar]
  7. Hong YY, Ma YC, Zhou YG, Gao F, Liu HC et al. Paenibacillus sonchi sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sonchus oleraceus. Int J Syst Evol Microbiol 2009;59:2656–2661 [CrossRef][PubMed]
    [Google Scholar]
  8. Beneduzi A, Costa PB, Parma M, Melo IS, Bodanese-Zanettini MH et al. Paenibacillus riograndensis sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Triticum aestivum. Int J Syst Evol Microbiol 2010;60:128–133 [CrossRef][PubMed]
    [Google Scholar]
  9. Zhang J, Wang ZT, Yu HM, Ma Y. Paenibacillus catalpae sp. nov., isolated from the rhizosphere soil of Catalpa speciosa. Int J Syst Evol Microbiol 2013;63:1776–1781 [CrossRef][PubMed]
    [Google Scholar]
  10. Kim BC, Lee KH, Kim MN, Kim EM, Min SR et al. Paenibacillus pini sp. nov., a cellulolytic bacterium isolated from the rhizosphere of pine tree. J Microbiol 2009;47:699–704 [CrossRef][PubMed]
    [Google Scholar]
  11. Kim BC, Lee KH, Kim MN, Kim EM, Rhee MS et al. Paenibacillus pinihumi sp. nov., a cellulolytic bacterium isolated from the rhizosphere of Pinus densiflora. J Microbiol 2009;47:530–535 [CrossRef][PubMed]
    [Google Scholar]
  12. 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 [CrossRef][PubMed]
    [Google Scholar]
  13. Wang DS, Jiang YY, Wei XM, Lai HX, Xue QH. Paenibacillus quercus sp. nov., isolated from rhizosphere of Quercus aliena var. acuteserrata. Antonie van Leeuwenhoek 2014;105:1173–1178 [CrossRef][PubMed]
    [Google Scholar]
  14. Son JS, Kang HU, Ghim SY. Paenibacillus dongdonensis sp. nov., isolated from rhizospheric soil of Elymus tsukushiensis. Int J Syst Evol Microbiol 2014;64:2865–2870 [CrossRef][PubMed]
    [Google Scholar]
  15. Han TY, Tong XM, Wang YW, Wang HM, Chen XR et al. Paenibacillus populi sp. nov., a novel bacterium isolated from the rhizosphere of Populus alba. Antonie van Leeuwenhoek 2015;108:659–666 [CrossRef][PubMed]
    [Google Scholar]
  16. Liu Y, Zhai L, Wang R, Zhao R, Zhang X et al. Paenibacillus zeae sp. nov., isolated from maize (Zea mays L.) seeds. Int J Syst Evol Microbiol 2015;65:4533–4538 [CrossRef][PubMed]
    [Google Scholar]
  17. Rivas R, Mateos PF, Martínez-Molina E, Velázquez E. Paenibacillus phyllosphaerae sp. nov., a xylanolytic bacterium isolated from the phyllosphere of Phoenix dactylifera. Int J Syst Evol Microbiol 2005;55:743–746 [CrossRef][PubMed]
    [Google Scholar]
  18. Rivas R, García-Fraile P, Mateos PF, Martínez-Molina E, Velázquez E. Paenibacillus cellulosilyticus sp. nov., a cellulolytic and xylanolytic bacterium isolated from the bract phyllosphere of Phoenix dactylifera. Int J Syst Evol Microbiol 2006;56:2777–2781 [CrossRef][PubMed]
    [Google Scholar]
  19. Grady EN, Macdonald J, Liu L, Richman A, Yuan ZC. Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact 2016;15:203 [CrossRef][PubMed]
    [Google Scholar]
  20. Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  21. Moaledj K. Comparison of Gram-staining and alternate methods, KOH test and aminopeptidase activity in aquatic bacteria: their application to numerical taxonomy. J Microbiol Methods 1986;5:303–310[CrossRef]
    [Google Scholar]
  22. Kämpfer P, Steiof M, Dott W. Microbiological characterisation of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microbiol Ecol 1991;21:227–243[CrossRef]
    [Google Scholar]
  23. Kämpfer P. Evaluation of the Titertek-Enterobac-Automated system (TTE-AS) for284 identification of Enterobacteriaceae. Zentbl Bakteriol 1990;273:164–172 [CrossRef]
    [Google Scholar]
  24. Christensen WB. Urea decomposition as a means of differentiating Proteus and paracolon cultures from each other and from salmonella and shigella types. J Bacteriol 1946;52:461–466[PubMed]
    [Google Scholar]
  25. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics United Kingdom: Wiley, Chichester; 1991; pp.115–175
    [Google Scholar]
  26. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci 1978;75:4801–4805 [CrossRef][PubMed]
    [Google Scholar]
  27. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004;32:1363–1371 [CrossRef][PubMed]
    [Google Scholar]
  28. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The All-Species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008;31:241–250 [CrossRef][PubMed]
    [Google Scholar]
  29. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007;35:7188–7196 [CrossRef][PubMed]
    [Google Scholar]
  30. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006;22:2688–2690 [CrossRef][PubMed]
    [Google Scholar]
  31. Felsenstein J. PHYLIP (Phylogeny Inference Package) Version 3.6 Distributed by the Author University of Washington, Seattle: Department of Genome Sciences; 2005
    [Google Scholar]
  32. Felsenstein J. Confidence limits of phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791[CrossRef]
    [Google Scholar]
  33. Gonzalez JM, Saiz-Jimenez C. A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature. Environ Microbiol 2002;4:770–773[PubMed][CrossRef]
    [Google Scholar]
  34. Glaeser SP, Falsen E, Martin K, Kämpfer P. Alicyclobacillus consociatus sp. nov., isolated from a human clinical specimen. Int J Syst Evol Microbiol 2013;63:3623–3627 [CrossRef][PubMed]
    [Google Scholar]
  35. Tohno M, Sakamoto M, Ohkuma M, Tajima K. Paenibacillus silagei sp. nov. isolated from corn silage. Int J Syst Evol Microbiol 2016;66:3873–3877 [CrossRef][PubMed]
    [Google Scholar]
  36. Elo S, Suominen I, Kämpfer P, Juhanoja J, Salkinoja-Salonen M et al. Paenibacillus borealis sp. nov., a nitrogen-fixing species isolated from spruce forest humus in Finland. Int J Syst Evol Microbiol 2001;51:535–545 [CrossRef][PubMed]
    [Google Scholar]
  37. Ziemke F, Höfle MG, Lalucat J, Rosselló-Mora R. Reclassification of Shewanella putrefaciens owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 1998;48:179–186 [CrossRef][PubMed]
    [Google Scholar]
  38. Pitcher DG, Saunders NA, Owen RJ. Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 1989;8:151–156[CrossRef]
    [Google Scholar]
  39. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990;13:128–130[CrossRef]
    [Google Scholar]
  40. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66:199–202[CrossRef]
    [Google Scholar]
  41. Altenburger P, Kämpfer P, Makristathis A, Lubitz W, Busse H-J. Classification of bacteria isolated from a medieval wall painting. J Biotechnol 1996;47:39–52[CrossRef]
    [Google Scholar]
  42. Schumann P. Peptidoglykan structure. In Rainey FA, Oren A. (editors) Methods in Microbiology (Taxonomy of Prokaryotes)vol.38 London: Academic Press; 2011; pp.101–129
    [Google Scholar]
  43. Kämpfer P, Rosselló-Mora R, Falsen E, Busse HJ, Tindall BJ. Cohnella thermotolerans gen. nov., sp. nov., and classification of 'Paenibacillus hongkongensis' as Cohnella hongkongensis sp. nov. Int J Syst Evol Microbiol 2006;56:781–786 [CrossRef][PubMed]
    [Google Scholar]
  44. Busse H-J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988;11:1–8[CrossRef]
    [Google Scholar]
  45. Altenburger P, Kämpfer P, Akimov VN, Lubitz W, Busse H-J. Polyamine distribution in actinomycetes with group B peptidoglycan and species of the genera Brevibacterium, Corynebacterium and Tsukamurella. Int J Syst Bacteriol 1997;47:270–277[CrossRef]
    [Google Scholar]
  46. Stolz A, Busse HJ, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007;57:572–576 [CrossRef][PubMed]
    [Google Scholar]
  47. Hamana K, Akiba T, Uchino F, Matsuzaki S. Distribution of spermine in bacilli and lactic acid bacteria. Can J Microbiol 1989;35:450–455[PubMed][CrossRef]
    [Google Scholar]
  48. Kämpfer P, Falsen E, Lodders N, Martin K, Kassmannhuber J et al. Paenibacillus chartarius sp. nov., isolated from a paper mill. Int J Syst Evol Microbiol 2012;62:1342–1347 [CrossRef][PubMed]
    [Google Scholar]
  49. Kämpfer P, Busse H-J, Kloepper JW, Hu C-H, Mcinroy JA et al. Paenibacillus cucumis sp. nov., isolated from a cucumber plant. Int J Syst Evol Microbiol 2016;66:2599–2603[CrossRef]
    [Google Scholar]
  50. Glaeser SP, Falsen E, Busse HJ, Kämpfer P. Paenibacillus vulneris sp. nov., isolated from a necrotic wound. Int J Syst Evol Microbiol 2013;63:777–782 [CrossRef][PubMed]
    [Google Scholar]
  51. 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]
  52. 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 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001779
Loading
/content/journal/ijsem/10.1099/ijsem.0.001779
Loading

Data & Media loading...

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