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f Paenibacillus albidus sp. nov., isolated from grassland soil

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  • Authors: Junli Zhuang1​ ,  Di Xin1​ ,  Yu-Qin Zhang2​ ,  Jingnan Guo1​ , Jianli Zhang1​
    • VIEW AFFILIATIONS
    • 1​ 1​School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China 2​ 2​Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
  • *Correspondence: Jianli Zhang [email protected]
  • First Published Online: 27 September 2017, International Journal of Systematic and Evolutionary Microbiology 67: 4685-4691, doi: 10.1099/ijsem.0.002356
  • Subject: New taxa - Firmicutes and Related Organisms
  • Received:
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  • A novel bacterial strain, designed Q4-3, was isolated from a soil sample obtained from Qilian grassland, Qinghai, China. Phylogenetic, phenotypic, chemotaxonomic and molecular analyses were performed on the new isolate. Cells were Gram-stain-positive, facultatively anaerobic, spore-forming, motile rods with peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences placed strain Q4-3 in the genus Paenibacillus, and its closest relatives were Paenibacillus odorifer JCM 21743, Paenibacillus typhae DSM 25190, Paenibacillus borealis DSM 13188 and Paenibacillus etheri DSM 29760 with 16S rRNA gene sequence similarities of 98.12, 97.89, 97.63 and 97.6 %, respectively. The isolate grew at 4-37 °C (optimum 28-30 °C), at pH 6.0-10.0 (optimum pH 7.5) and with 0-3 %(w/v) NaCl (optimum 1 %). The DNA of strain Q4-3 was determined to be 48.6 mol%. The predominant menaquinone was MK-7 and the diamino acid in the cell-wall peptidoglycan was found to be meso-diaminopimelic acid. Anteiso-C15 : 0 (55.5 %), iso-C16 : 0 (14.5 %) and C16 : 0 (13.3 %) were the major fatty acids. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified aminophospholipids and one unidentified lipid. Based on these results, strain Q4-3 is considered to represent a novel of the genus Paenibacillus, for which the name Paenibacillus albidus nov. is proposed. The type strain is Q4-3 (=CGMCC 1.16134=KCTC 33911).

  • The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and nifH sequences of strain Q4-3 are KY674517 and KY800539, respectively.

  • Six supplementary figures are available with the online Supplementary Material.

© 2017 IUMS | Published by the Microbiology Society

  • 1. 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] [Crossref]
    [Google Scholar]
  • 2. 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]
  • 3. Stjohn FJ, Rice JD, Preston JF. Paenibacillus sp. strain JDR-2 and XynA1: a novel system for methylglucuronoxylan utilization. Appl Environ Microbiol 2006; 72: 1496– 1506 [CrossRef] [PubMed]
    [Google Scholar]
  • 4. Huang Z, Dai W, Zhou Z, Wang G, Lin G et al. Paenibacillus terreus sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66: 243– 247 [CrossRef] [PubMed]
    [Google Scholar]
  • 5. Lee JJ, Yang DH, Ko YS, Park JK, Im EY et al. Paenibacillus swuensis sp. nov., a bacterium isolated from soil. J Microbiol 2014; 52: 106– 110 [CrossRef] [PubMed]
    [Google Scholar]
  • 6. Baik KS, Choe HN, Park SC, Kim EM, Seong CN. Paenibacillus wooponensis sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 2011; 61: 2763– 2768 [CrossRef] [PubMed]
    [Google Scholar]
  • 7. Tang QY, Yang N, Wang J, Xie YQ, Ren B et al. Paenibacillus algorifonticola sp. nov., isolated from a cold spring. Int J Syst Evol Microbiol 2011; 61: 2167– 2172 [CrossRef] [PubMed]
    [Google Scholar]
  • 8. Moon JC, Jung YJ, Jung JH, Jung HS, Cheong YR et al. Paenibacillus sacheonensis sp. nov., a xylanolytic and cellulolytic bacterium isolated from tidal flat sediment. Int J Syst Evol Microbiol 2011; 61: 2753– 2757 [CrossRef] [PubMed]
    [Google Scholar]
  • 9. 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]
  • 10. 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]
  • 11. 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 [CrossRef] [PubMed]
    [Google Scholar]
  • 12. Ko KS, Kim YS, Lee MY, Shin SY, Jung DS et al. Paenibacillus konsidensis sp. nov., isolated from a patient. Int J Syst Evol Microbiol 2008; 58: 2164– 2168 [CrossRef] [PubMed]
    [Google Scholar]
  • 13. Roux V, Fenner L, Raoult D. Paenibacillus provencensis sp. nov., isolated from human cerebrospinal fluid, and Paenibacillus urinalis sp. nov., isolated from human urine. Int J Syst Evol Microbiol 2008; 58: 682– 687 [CrossRef] [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 [CrossRef] [PubMed]
    [Google Scholar]
  • 15. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57: 1424– 1428 [CrossRef] [PubMed]
    [Google Scholar]
  • 16. 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]
  • 17. Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA et al. CLUSTAL W and CLUSTAL X version 2.0. Bioinformatics 2007; 23: 2947– 2948 [CrossRef] [PubMed]
    [Google Scholar]
  • 18. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406– 425 [PubMed]
    [Google Scholar]
  • 19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368– 376 [PubMed] [Crossref]
    [Google Scholar]
  • 20. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20: 406– 416 [Crossref]
    [Google Scholar]
  • 21. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30: 2725– 2729 [CrossRef] [PubMed]
    [Google Scholar]
  • 22. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16: 111– 120 [PubMed] [Crossref]
    [Google Scholar]
  • 23. Ding Y, Wang J, Liu Y, Chen S. Isolation and identification of nitrogen-fixing bacilli from plant rhizospheres in Beijing region. J Appl Microbiol 2005; 99: 1271– 1281 [CrossRef] [PubMed]
    [Google Scholar]
  • 24. Berge O, Guinebretière MH, Achouak W, Normand P, Heulin T. Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food. Int J Syst Evol Microbiol 2002; 52: 607– 616 [CrossRef] [PubMed]
    [Google Scholar]
  • 25. 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 [CrossRef] [PubMed]
    [Google Scholar]
  • 26. Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
    [Google Scholar]
  • 27. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55: 1149– 1153 [CrossRef] [PubMed]
    [Google Scholar]
  • 28. Goldfine H, Bloch K. On the origin of unsaturated fatty acids in Clostridia. J Biol Chem 1961; 236: 2596– 2601 [PubMed]
    [Google Scholar]
  • 29. 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]
  • 30. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  • 31. Collins MD. Isoprenoid quinone analysis in classification and identification. In Goodfellow M. (editor) Chemical Methods in Bacterial Systematics London: Academic Press; 1985; pp. 267– 287
    [Google Scholar]
  • 32. Schumann P. Peptidoglycan structure. In Rainey F, Oren A. (editors) Methods Microbiol London: Academic Press; 2011; pp. 101– 129
    [Google Scholar]
  • 33. 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]
  • 34. 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 [CrossRef] [PubMed]
    [Google Scholar]
  • 35. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3: 208– 218 [CrossRef]
    [Google Scholar]
  • 36. 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]
  • 37. Wang L, Baek SH, Cui Y, Lee HG, Lee ST. Paenibacillus sediminis sp. nov., a xylanolytic bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2012; 62: 1284– 1288 [CrossRef] [PubMed]
    [Google Scholar]
  • 38. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983; 4: 184– 192 [CrossRef] [PubMed]
    [Google Scholar]
  • 39. de Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12: 133– 142 [PubMed] [Crossref]
    [Google Scholar]
  • 40. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002; 52: 1043– 1047 [CrossRef] [PubMed]
    [Google Scholar]
  • 41. Kong BH, Liu QF, Liu M, Liu Y, Liu L et al. Paenibacillus typhae sp. nov., isolated from roots of Typha angustifolia L. Int J Syst Evol Microbiol 2013; 63: 1037– 1044 [CrossRef] [PubMed]
    [Google Scholar]
  • 42. 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]
  • 43. Guisado IM, Purswani J, González-López J, Pozo C. Paenibacillus etheri sp. nov., able to grow on media supplemented with methyl tert-butyl ether (MTBE) and isolated from hydrocarbon-contaminated soil. Int J Syst Evol Microbiol 2016; 66: 862– 867 [CrossRef]
    [Google Scholar]
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