Advertisement

Archives of Microbiology

, Volume 198, Issue 2, pp 171–179 | Cite as

Ochrobactrum endophyticum sp. nov., isolated from roots of Glycyrrhiza uralensis

  • Li Li
  • Yan-Qiong Li
  • Zhao Jiang
  • Rui Gao
  • Salam Nimaichand
  • Yan-Qing Duan
  • Dilfuza Egamberdieva
  • Wei ChenEmail author
  • Wen-Jun LiEmail author
Original Paper

Abstract

A novel Gram-staining negative, motile, rod-shaped and aerobic bacterial strain, designated EGI 60010T, was isolated from healthy roots of Glycyrrhiza uralensis F. collected from Yili County, Xinjiang Province, North-West China. The 16S rRNA gene sequence of strain EGI 60010T showed 97.2 % sequence similarities with Ochrobactrum anthropi ATCC 49188T and Ochrobactrum cytisi ESC1T, and 97.1 % with Ochrobactrum lupini LUP21T. The phylogenetic analysis based on 16S rRNA gene sequences showed that the new isolate clustered with members of the genera Ochrobactrum, and formed a distinct clade in the neighbour-joining tree. Q-10 was identified as the respiratory quinone for strain EGI 60010T. The major fatty acids were summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), C19:0 cyclo ω8c, summed feature 4 (C17:1 iso I/anteiso B) and C16:0. The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol and phosphatidylcholine. The DNA G+C content of strain EGI 60010T was determined to be 60.4 mol%. The genomic DNA relatedness values determined between strain EGI 60010T and the closely related strains O. anthropi JCM 21032T, O. cytisi CCTCC AB2014258T and O. lupini NBRC 102587T were 50.3, 50.0 and 41.6 %, respectively. Based on the results of the molecular studies supported by its differentiating phenotypic characteristics, strain EGI 60010T was considered to represent a novel species within the genus Ochrobactrum, for which the name Ochrobactrum endophyticum sp. nov., is proposed. The type strain is EGI 60010T (=CGMCC 1.15082T = KCTC 42485T = DSM 29930T).

Keywords

Ochrobactrum endophyticum sp. nov. Endophytic bacteria Glycyrrhiza uralensis F. 

Notes

Acknowledgments

The authors are grateful to Prof. Dr. Takuji Kudo (JCM, Japan), Dr. Tomohiko Tamura (NBRC, Japan) and Dr. Fang Peng (CCTCC, China) for kindly providing the reference type strains. This research was supported by the National Natural Science Foundation of China (No. 31200008), West Light Foundation of the Chinese Academy of Sciences (XBBS201305), Projects of China Tobacco Yunnan Industrial Co. Ltd. (Nos. 2014YL01 and 2015CP01), the Hundred Talents Program of Chinese Academy of Sciences and the High-level Talents Program of Xinjiang Autonomous Region. W-J Li was also supported by Guangdong Province Higher Vocational Colleges and Schools Pearl River Scholar Funded Scheme (2014).

Supplementary material

203_2015_1170_MOESM1_ESM.doc (4.2 mb)
Supplementary material 1 (DOC 4283 kb)

References

  1. Cappuccino JG, Sherman N (2002) Microbiology: a laboratory manual, 6th edn. Benjamin/Cummings, Menlo ParkGoogle Scholar
  2. Cerny G (1978) Studies on aminopeptidase for the distinction of Gram-negative from Gram-positive bacteria. Appl Microbiol Biotechnol 5:113–122CrossRefGoogle Scholar
  3. Christensen H, Angen O, Mutters R, Olsen JE, Bisgaard M (2000) DNA–DNA hybridization determined in microwells using covalent attachment of DNA. Int J Syst Evol Microbiol 50:1095–1102CrossRefPubMedGoogle Scholar
  4. Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2,4-diaminobutyric acid. Appl Bacteriol 48:459–470CrossRefGoogle Scholar
  5. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230CrossRefPubMedGoogle Scholar
  6. Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229CrossRefGoogle Scholar
  7. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefPubMedGoogle Scholar
  8. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  9. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  10. He L, Li W, Huang Y, Wang LM, Liu ZH, Lanoot BJ, Vancanneyt M, Swings J (2005) Streptomyces jietaisiensis sp. nov., isolated from soil in northern China. Int J Syst Evol Microbiol 55:1939–1944CrossRefPubMedGoogle Scholar
  11. Holmes B, Popoff M, Kiredjian M, Kersters K (1988) Ochrobactrum anthropi gen. nov., sp. nov. from human clinical specimens and previously known as group Vd. Int J Syst Bacteriol 38:406–416CrossRefGoogle Scholar
  12. Huber B, Scholz HC, Kámpfer P, Falsen E, Langer S, Busse HJ (2010) Ochrobactrum pituitosum sp. nov., isolated from an industrial environment. Int J Syst Evol Microbiol 60:321–326CrossRefPubMedGoogle Scholar
  13. Imran A, Hafeez FY, Frühling A, Schumann P, Malik KA, Stackebrandt E (2010) Ochrobactrum ciceri sp. nov., isolated from nodules of Cicer arietinum. Int J Syst Evol Microbiol 60:1548–1553CrossRefPubMedGoogle Scholar
  14. Kämpfer P, Buczolits S, Albrecht A, Busse HJ, Stackebrandt E (2003) Towards a standardized format for the description of a novel species (of an established genus): Ochrobactrum gallinifaecis sp. nov. Int J Syst Evol Microbiol 53:893–896CrossRefPubMedGoogle Scholar
  15. Kämpfer P, Scholz HC, Huber B, Falsen E, Busse HJ (2007) Ochrobactrum haematophilum sp. nov. and Ochrobactrum pseudogrignonense sp. nov., isolated from human clinical specimens. Int J Syst Evol Microbiol 57:2513–2518CrossRefPubMedGoogle Scholar
  16. Kämpfer P, Sessitsch A, Schloter M, Huber B, Busse HJ, Scholz HC (2008) Ochrobactrum rhizosphaerae sp. nov. and Ochrobactrum thiophenivorans sp. nov., isolated from the environment. Int J Syst Evol Microbiol 58:1426–1431CrossRefPubMedGoogle Scholar
  17. Kämpfer P, Huber B, Busse HJ, Scholz HC, Tomaso H, Hotzel H, Melzer F (2011) Ochrobactrum pecoris sp. nov., isolated from farm animals. Int J Syst Evol Microbiol 61:2278–2283CrossRefPubMedGoogle Scholar
  18. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon Y, 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 62:716–721CrossRefPubMedGoogle Scholar
  19. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefPubMedGoogle Scholar
  20. 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 5:2359–2387CrossRefGoogle Scholar
  21. Lebuhn M, Achouak W, Schloter M, Berge O, Meier H, Barakat M, Hartmann A, Heulin T (2000) Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots, and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov. Int J Syst Evol Microbiol 50:2207–2223CrossRefPubMedGoogle Scholar
  22. Leifson E (1960) Atlas of bacterial flagellation. Academic Press, LondonCrossRefGoogle Scholar
  23. 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 57:1424–1428CrossRefPubMedGoogle Scholar
  24. 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 39:159–167CrossRefGoogle Scholar
  25. Ming H, Nie GX, Jiang HC, Yu TT, Zhou EM, Feng HG, Tang SK, Li WJ (2012) Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China. Antonie Van Leeuwenhoek 102:297–305CrossRefPubMedGoogle Scholar
  26. 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 47:87–95CrossRefGoogle Scholar
  27. Parte AC (2014) LPSN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42(D1):D613–D616PubMedCentralCrossRefPubMedGoogle Scholar
  28. Qin S, Li J, Chen HH, Zhao GZ, Zhu WY, Jiang CL, Xu LH, Li WJ (2009) Isolation, diversity, and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rain forests in Xishuangbanna, China. Appl Environ Microbiol 75:6176–6186PubMedCentralCrossRefPubMedGoogle Scholar
  29. Reddy GSN, Garcia-Pichel F (2005) Dyadobacter crusticola sp. nov., from Biological Soil Crusts in the Colorado Plateau, USA and emended description of the genus Dyadobacter Chelius and Tripplett 2000. Int J Syst Evol Microbiol 55:1295–1299CrossRefPubMedGoogle Scholar
  30. Reddy GSN, Nagy M, Garcia-Pichel F (2006) Belnapia moabensisgen nov., sp. nov., an a proteobacterium from biological soil crusts in the Colorado Plateau, USA. Int J SystEvol Microbiol 56:51–58CrossRefGoogle Scholar
  31. Rivas R, Velázquez E, Palomo J, Mateos PF, García-Benavides P, Martínez-Molina E (2002) Rapid identification of Clavibacter michiganensis subspecies sepedonicus using two primers random amplified polymorphic DNA (TP-RAPD) fingerprints. Eur J Plant Pathol 108:179–184CrossRefGoogle Scholar
  32. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  33. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc., NewarkGoogle Scholar
  34. 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 28:2731–2739PubMedCentralCrossRefPubMedGoogle Scholar
  35. Teyssier C, Marchandin H, Jean-Pierre H, Masnou A, Dusart G, Jumas-Bilak E (2007) Ochrobactrum pseudintermedium sp. nov., a novel member of the family Brucellaceae, isolated from human clinical samples. Int J Syst Evol Microbiol 57:1007–1013CrossRefPubMedGoogle Scholar
  36. 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. Nucleic Acids Res 25:4876–4882PubMedCentralCrossRefPubMedGoogle Scholar
  37. Tripathi AK, Verma SC, Chowdhury SP, Lebuhn M, Gattinger A, Schloter M (2006) Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India. Int J Syst Evol Microbiol 56:1677–1680CrossRefPubMedGoogle Scholar
  38. Trujillo ME, Willems A, Abril A, Planchuelo AM, Rivas R, Ludeña D, Mateos PF, Martinez-Molina E, Velázquez E (2005) Nodulation of Lupinus albus by strains of Ochrobactrum lupini sp. nov. Appl Environ Microbiol 71:1318–1327PubMedCentralCrossRefPubMedGoogle Scholar
  39. Velasco J, Romero C, López-Goñi I, Leiva J, Díaz R, Moriyón I (1998) Evaluation of the relatedness of Brucella spp. and Ochrobactrum anthropi and description of Ochrobactrum intermedium and description of Ochrobactrum intermedium sp. nov., a new species with a closer relationship to Brucella spp. Int J Syst Bacteriol 48:759–768CrossRefPubMedGoogle Scholar
  40. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464CrossRefGoogle Scholar
  41. Woo SG, Ten LN, Park J, Lee J (2011) Ochrobactrum daejeonense sp. nov., a nitrate-reducing bacterium isolated from sludge of a leachate treatment plant. Int J Syst Evol Microbiol 61:2690–2696CrossRefPubMedGoogle Scholar
  42. 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 55:1149–1153CrossRefPubMedGoogle Scholar
  43. Zurdo-Piñeiro JL, Rivas R, Trujillo ME, Vizcaíno N, Carrasco JA, Chamber M, Palomares A, Mateos PF, Martínez-Molina E, Velázquez E (2007) Ochrobactrum cytisi sp. nov. isolated from nodules of Cytisus scoparius in Spain. Int J Syst Evol Microbiol 57:784–788CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Li Li
    • 1
  • Yan-Qiong Li
    • 2
  • Zhao Jiang
    • 3
  • Rui Gao
    • 4
  • Salam Nimaichand
    • 5
  • Yan-Qing Duan
    • 4
  • Dilfuza Egamberdieva
    • 6
  • Wei Chen
    • 4
    Email author
  • Wen-Jun Li
    • 1
    • 3
    • 5
    Email author
  1. 1.Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesÜrümqiPeople’s Republic of China
  2. 2.Kunming Medical University Haiyuan CollegeKunmingPeople’s Republic of China
  3. 3.Yunnan Institute of MicrobiologyYunnan UniversityKunmingPeople’s Republic of China
  4. 4.China Tobacco Yunnan Industrial Co. Ltd.KunmingPeople’s Republic of China
  5. 5.State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and EvolutionSun Yat-Sen UniversityGuangzhouPeople’s Republic of China
  6. 6.Department of Biotechnology and Microbiology, Faculty of Biology and Soil ScienceNational University of UzbekistanTashkentRepublic of Uzbekistan

Personalised recommendations