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Paenibacillus nicotianae sp. nov., isolated from a tobacco sample

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Abstract

A Gram-stain positive, facultative anaerobic endospore-forming bacterium, designated strain YIM h-19T, was isolated from a tobacco sample. Cells were observed to be motile rods by means of peritrichous flagella and colonies were observed to be convex, yellow, circular and showed catalase-positive and oxidase-negative reactions. Strain YIM h-19T was able to grow at 4–45 °C, pH 6.0–8.0 and 0–3 % NaCl (w/v). The predominant respiratory quinone was identified as MK-7. Major fatty acids were identified as anteiso-C15:0, anteiso-C17:0 and C16:0. The polar lipids were found to be phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unidentified polar lipids. The genomic DNA G+C content was determined to be 54 mol%. 16S rRNA gene sequence analysis showed the strain YIM h-19T was most closely related to Paenibacillus hordei RH-N24T and Paenibacillus hunanensis FeL05T with similarities of 98.30 and 94.64 % respectively. However, DNA–DNA hybridization data indicated that the isolate represented a novel genomic species with the genus Paenibacillus. All data from genotypic and phenotypic analyses support the conclusion that strain YIM h-19T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus nicotianae sp. nov. is proposed. The type strain is YIM h-19T (=CGMCC1.12819T = NRRL B-59112T).

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References

  • Ash C, Priest FG, Collins MD (1993) 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 64:253–260

    Article  PubMed  CAS  Google Scholar 

  • Cerny G (1978) Studies on aminopeptidase for the distinction of gram-negative from gram-positive bacteria. Appl Microbiol Biotechnol 5:113–122

    Article  CAS  Google Scholar 

  • Chou JH, Chou YJ, Lin KY, Sheu SY, Sheu DS, Arun AB, Young CC, Chen WM (2007) Paenibacillus fonticola sp. nov., isolated from a warm spring. Int J Syst Evol Microbiol 57:1346–1350

    Article  PubMed  CAS  Google Scholar 

  • Christensen H, Angen O, Mutters R, Olsen JE, Bisgaard M (2000) DNA–DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 50:1095–1102

    Article  PubMed  CAS  Google Scholar 

  • Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2, 4-diaminobutyric acid. Appl Bacteriol 48:459–470

    Article  CAS  Google Scholar 

  • Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    Article  PubMed  CAS  Google Scholar 

  • DeLey J, Caltoir H, Reeynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rate. Eur J Biochem 12:133–142

    Article  CAS  Google Scholar 

  • Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometr icdeoxyribonucleic acid-deoxyriboribonucleic acid hybridization in micro dilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229

    Article  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  PubMed  CAS  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Gonzalez C, Gutierrez C, Ramirez C (1978) Halobacterium vallismortis sp. nov., an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 24:710–715

    Article  PubMed  CAS  Google Scholar 

  • Groth I, Rodríguez C, Schütze B, Schmitz P, Leistner E, Goodfellow M (2004) Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K.nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov. Int J Syst Evol Microbiol 54:2121–2129

    Article  PubMed  CAS  Google Scholar 

  • Hugh R, Leifson E (1953) The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 66:24–26

    PubMed  CAS  PubMed Central  Google Scholar 

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park S-C, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    Article  PubMed  CAS  Google Scholar 

  • Kim MJ, Lee SH, Lee SH, Choi EJ, Jeon CO (2013) Paenibacillus hordei sp. nov., isolated from naked barley in Korea. Antonie Van Leeuwenhoek 103:3–9

    Article  PubMed  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  PubMed  CAS  Google Scholar 

  • Kovacs N (1956) Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 178:703–704

    Article  PubMed  CAS  Google Scholar 

  • Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2387

    Article  CAS  Google Scholar 

  • Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) 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 57:1424–1428

    Article  PubMed  Google Scholar 

  • Li J, Zhao GZ, Chen HH, Wang HB, Qin S, Zhu WY, Xu LH, Jiang CL, Li WJ (2008) Antitumour and antimicrobial activities of endophytic streptomycetes from pharmaceutical plants in rainforest. Lett Appl Microbiol 47:574–580

    Article  PubMed  CAS  Google Scholar 

  • Lim JM, Jeon CO, Lee JC, Xu LH, Jiang CL, Kim CJ (2006) Paenibacillus gansuensis sp. nov., isolated from desert soil of Gansu Province in China. Int J Syst Evol Microbiol 56:2131–2134

    Article  PubMed  CAS  Google Scholar 

  • Liu Y, Liu L, Qiu F, Schumann P, Shi Y, Zou Y, Zhang X, Song W (2010) Paenibacillus hunanensis sp. nov., isolated from rice seeds. Int J Syst Evol Microbiol 60:1266–1270

    Article  PubMed  CAS  Google Scholar 

  • Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    Article  CAS  Google Scholar 

  • Minnikin DE, Collins MD, Goodfellow M (1979) Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87–95

    Article  CAS  Google Scholar 

  • Montes MJ, Mercade E, Bozal N, Guinea J (2004) Paenibacillus antarcticus sp. nov., a novel psychrotolerant organism from the Antarctic environment. Int J Syst Evol Microbiol 54:1521–1522

    Article  PubMed  CAS  Google Scholar 

  • Rivas R, Mateos PF, Eustoquio M-M, Encarna V (2005a) Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium. Int J Syst Evol Microbiol 55:405–408

    Article  PubMed  CAS  Google Scholar 

  • Rivas R, Gutierrez C, Abril A, Mateos PF, Martinez-Molina E, Ventosa A, Velazquez E (2005b) Paenibacillus rhizosphaeraesp. nov., isolated from the rhizosphere of Cicer arietinum. Int J Syst Evol Microbiol 55:1305–1309

    Article  PubMed  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    PubMed  CAS  Google Scholar 

  • Sasser M (1990) Identification of Bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. MIDI Inc, Newwark

    Google Scholar 

  • Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K (1997) 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 47:289–298

    Article  PubMed  CAS  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876–4882

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Traiwan J, Park MH, Kim W (2011) Paenibacillus puldeungensis sp. nov., isolated from a grassy sandbank. Int J Syst Evol Mictobiol 61:670–673

    Article  CAS  Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler OK, Krichevsky MI, Moore LH, Moore WEC, Murray TGE et al (1987) International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • Williams S (1989) Genus Streptomyces waksman and henrici 1943. BERGEY’s Manual of Systematic Bacteriology 4:2452–2492

  • Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu LH, Jiang CL (2005) Naxibacter alkalitolerans gen. nov., sp nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We are grateful to Prof. Takuji Kudo (JCM, Japan) and Dr. Jung-Sook Lee (KCTC, Korea) for their kind providing the reference type strains, and Prof. Aharon Oren (The Hebrew University of Jerusalem, Israel) for his kind help with the Latin etymology for the new species. This work was funded jointly by projects of National Natural Science Foundation of China (No. 31160432), China tobacco Yunnan industrial Co. Lid. (No. 2011CP02), Department of Science and Technology of Yunnan Province (Nos. 2011FA002 and 2012BA015) and China National Tobacco Corporation (110201201009 BR-03). WNH and W-J L extend their appreciation to the Deanship of Scientific Research at King Saud University for funding the work through the research group Project No. RGP-205.

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Authors and Affiliations

  1. Life Science College, Yunnan Normal University, Kunming, 650500, People’s Republic of China

    Qing-Qing Li

  2. China Tobacco Yunnan Industrial Co., Ltd, Kunming, 650231, People’s Republic of China

    Xing-Kui Zhou, Li-Zhi Dang & Yan-Qing Duan

  3. Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People’s Republic of China

    Juan Cheng, Min-Jiao Liu & Wen-Jun Li

  4. Bioproducts Research Chair (BRC), Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia

    Wael N. Hozzein

  5. Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650500, People’s Republic of China

    Qing-Qing Li

  6. Yunnan Haoruo Institute of Biotechnology, Kunming, 650204, People’s Republic of China

    Qing-Qing Li & Qun Hu

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  1. Qing-Qing Li
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Correspondence to Wen-Jun Li or Yan-Qing Duan.

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Qing-Qing Li and Xing-Kui Zhou have contributed equally to this work.

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Li, QQ., Zhou, XK., Dang, LZ. et al. Paenibacillus nicotianae sp. nov., isolated from a tobacco sample. Antonie van Leeuwenhoek 106, 1199–1205 (2014). https://doi.org/10.1007/s10482-014-0289-y

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  • DOI: https://doi.org/10.1007/s10482-014-0289-y

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