1887

Abstract

A Gram-positive-staining, aerobic, non-endospore-forming bacterial strain (JJ-59), isolated from a field-grown maize plant in Dunbar, Nebraska in 2014 was studied by a polyphasic approach. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-59 was shown to be a member of the genus Paenibacillus , most closely related to the type strains of Paenibacillus aceris (98.6 % 16S rRNA gene sequence similarity) and Paenibacillus chondroitinus (97.8 %). For all other type strains of species of the genus Paenibacillus lower 16S rRNA gene sequence similarities were obtained. DNA–DNA hybridization values of strain JJ-59 to the type strains of P. aceris and P. chondroitinus were 26 % (reciprocal, 59 %) and 52 % (reciprocal, 59 %), respectively. Chemotaxonomic characteristics such as the presence of meso-diaminopimelic acid in the peptidoglycan, the major quinone MK-7 and spermidine as the major polyamine were in agreement with the characteristics of the genus Paenibacillus . Strain JJ-59 shared with its next related species P. aceris the major lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminophospholipid, but the presence/absence of certain lipids was clearly distinguishable. Major fatty acids of strain JJ-59 were anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0, and the genomic G+C content is 47.2 mol%. Physiological and biochemical characteristics of strain JJ-59 were clearly different from the most closely related species of the genus Paenibacillus . Thus, strain JJ-59 represents a novel species of the genus Paenibacillus , for which the name Paenibacillus nebraskensis sp. nov. is proposed, with JJ-59 (=DSM 103623=CIP 111179=LMG 29764) as the type strain.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002357
2017-10-23
2019-10-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/12/4956.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002357&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. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
  12. Hwang YJ, Ghim SY. Paenibacillus aceris sp. nov., an isolate from the rhizosphere of Acer okamotoanum, a plant native to Ulleungdo Island, Republic of Korea. Int J Syst Evol Microbiol 2017; 67: 1039– 1045 [CrossRef] [PubMed]
    [Google Scholar]
  13. Kämpfer P, Busse HJ, Mcinroy JA, Hu CH, Kloepper JW et al. Paenibacillus rhizoplanae sp. nov., isolated from the rhizosphere of Zea mays. Int J Syst Evol Microbiol 2017; 67: 1058– 1063 [CrossRef] [PubMed]
    [Google Scholar]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. Lai WA, Hameed A, Lin SY, Hung MH, Hsu YH et al. Paenibacillus medicaginis sp. nov. a chitinolytic endophyte isolated from a root nodule of alfalfa (Medicago sativa L.). Int J Syst Evol Microbiol 2015; 65: 3853– 3860 [CrossRef] [PubMed]
    [Google Scholar]
  19. Kittiwongwattana T, 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]
  20. 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]
  21. 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]
  22. Gerhardt P, Murray RGE, Wood WA, Krieg NR. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  23. 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]
  24. Kämpfer P, Steiof M, Dott W. Microbiological characterization of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 1991; 21: 227– 251 [CrossRef] [PubMed]
    [Google Scholar]
  25. Kämpfer P. Evaluation of the Titertek-enterobac-automated system (TTE-AS) for identification of members of the family Enterobacteriaceae. Zentralbl Bakteriol 1990; 273: 164– 172 [CrossRef] [PubMed]
    [Google Scholar]
  26. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991; pp. 125– 175
    [Google Scholar]
  27. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 1978; 75: 4801– 4805 [CrossRef] [PubMed]
    [Google Scholar]
  28. 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 [CrossRef] [PubMed]
    [Google Scholar]
  29. 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]
  30. 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]
  31. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28: 1823– 1829 [CrossRef] [PubMed]
    [Google Scholar]
  32. 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]
  33. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. (editor) Mammalian Protein Metabolism New York, NY: Academic Press; 1969; pp. 21– 132 [Crossref]
    [Google Scholar]
  34. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  35. 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]
  36. 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]
  37. 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]
  38. Nakamura LK. Bacillus alginolyticus sp. nov. and Bacillus chondroitinus sp. nov., two alginate-degrading species. Int J Syst Bacteriol 1987; 37: 284– 286 [CrossRef]
    [Google Scholar]
  39. 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]
  40. 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]
  41. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66: 199– 202 [CrossRef]
    [Google Scholar]
  42. 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]
  43. Schumann P. Peptidoglycan structure. In Rainey FA, Oren A. (editors) Methods in Microbiology (Taxonomy of Prokaryotes)vol. 38 2011; pp. 101– 129
    [Google Scholar]
  44. 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]
  45. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 1988; 11: 1– 8 [CrossRef]
    [Google Scholar]
  46. Busse H-J, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997; 47: 698– 708 [CrossRef]
    [Google Scholar]
  47. Stolz A, Busse HJ, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57: 572– 576 [CrossRef] [PubMed]
    [Google Scholar]
  48. Hamana K, Akiba T, Uchino F, Matsuzaki S. Distribution of spermine in bacilli and lactic acid bacteria. Can J Microbiol 1989; 35: 450– 455 [CrossRef] [PubMed]
    [Google Scholar]
  49. 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]
  50. Kämpfer P, Busse HJ, Kloepper JW, Hu CH, Mcinroy JA et al. Paenibacillus cucumis sp. nov. isolated from a Cucumber plant. Int J Syst Evol Microbiol 2016; 66: 2599– 2603 [CrossRef] [PubMed]
    [Google Scholar]
  51. 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]
  52. 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]
  53. 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]
  54. Cao Y, Chen F, Li Y, Wei S, Wang G. Paenibacillus ferrarius sp. nov., isolated from iron mineral soil. Int J Syst Evol Microbiol 2015; 65: 165– 170 [CrossRef] [PubMed]
    [Google Scholar]
  55. 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 [CrossRef] [PubMed]
    [Google Scholar]
  56. Baek SH, Yi TH, Lee ST, Im WT. Paenibacillus pocheonensis sp. nov., a facultative anaerobe isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2010; 60: 1163– 1167 [CrossRef] [PubMed]
    [Google Scholar]
  57. Ming H, Nie GX, Jiang HC, Yu TT, Zhou EM et al. Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China. Antonie van Leeuwenhoek 2012; 102: 297– 305 [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002357
Loading
/content/journal/ijsem/10.1099/ijsem.0.002357
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