Skip to main content

Variovorax guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere

Antonie van Leeuwenhoek volume 107, pages 65–72 (2015)Cite this article

Abstract

A 1-aminocyclopropane-1-carboxylate deaminase producing bacterium, designated GXGD002T, was isolated from the rhizosphere of banana plants cultivated in Guangxi province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain GXGD002T is a member of the genus Variovorax. High levels of 16S rRNA gene sequence similarity are found between strain GXGD002T and Variovorax paradoxus DSM 30034T (99.4 %), Variovorax ginsengisoli KCTC 12583T (99.1 %), Variovorax boronicumulans KCTC 22010T (99.0 %), Variovorax soli DSM18216T (98.7 %), Variovorax defluvii DSM 27259T (98.1 %) and Variovorax dokdonensis KCTC 12544T (97.4 %) respectively. However, the DNA–DNA hybridization values between strain GXGD002T and its closely related species V. paradoxus DSM 30034T, V. ginsengisoli KCTC 12583T and V. boronicumulans KCTC 22010T were found to be 40.7, 30.9 and 23.7 %, respectively. The DNA G + C content of strain GXGD002T was found to be 67.8 mol%. The major fatty acids of strain GXGD002T are C16:0 (20.3 %), C10:0 3OH (18.4 %), C17:0 cyclo (18.9 %), C18:1w7c (12.3 %) and summed feature 3 (13.9 %). The predominant respiratory quinone was identified as ubiquinone-8 (Q-8) and the major polar lipids as phosphatidylethanolamine and phosphatidylglycerol. The results of polyphasic taxonomic study including physiological and biochemical tests, whole-cell SDS-PAGE profiles and chemotaxonomic analysis allowed a clear differentiation of strain GXGD002T from the other species in the genus Variovorax. Based on these results, a new species, Variovorax guangxiensis, is proposed. The type strain is GXGD002T (=DSM 27352T = ACCC 05911T).

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2

References

  • Abeles FB, Morgan PW, Saltveit ME Jr (1992) Ethylene in Plant Biology, 2nd edn. Academic Press, New York, p 414

    Google Scholar 

  • Anzai Y, Kim H, Park JY, Wakabayashi H, Oyaizu H (2000) Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50:1563–1589

    CAS  PubMed  Article  Google Scholar 

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

    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

    CAS  PubMed  Article  Google Scholar 

  • De Ley J (1970) Reexamination of the association between melting point, buoyant density, and chemical base composition of deoxyribonucleic acid. J Bacteriol 101:738–754

    PubMed Central  PubMed  Google Scholar 

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

    CAS  PubMed  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 

  • Glick BR (2014) Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol Res 169:30–39

    CAS  PubMed  Article  Google Scholar 

  • Im W-T, Liu Q-M, Lee K-J, Kim S-Y, Lee S-T, Yi TH (2010) Variovorax ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field. Int J Syst Evol Microbiol 60:1565–1569

    CAS  PubMed  Article  Google Scholar 

  • Jin L, Kim KK, Ahn C-Y, Oh H-M (2012) Variovorax defluvii sp. nov., isolated from sewage. Int J Syst Evol Microbiol 62:1779–1783

    CAS  PubMed  Article  Google Scholar 

  • Kim B-Y, Weon H-Y, Yoo S-H, Lee S-Y, Kwon S-W, Go S-J, Stackebrandt E (2006) Variovorax soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 56:2899–2901

    CAS  PubMed  Article  Google Scholar 

  • Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M, Na H, Park S-C, Jeon Y S, Lee J-H & other authors (2012) Introducing EzTaxonETe: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

  • Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackerandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematic. Willey, Chichester, pp 115–175

    Google Scholar 

  • Marmur J (1961) A procedure for the isolation of DNA from micro-organism. J Mol Biol 3:208–218

    CAS  Article  Google Scholar 

  • Marmur J, Doty P (1962) Determination of base composition of deoxyribonucleic acid from its denaturation temperature. J Mol Biol 5:109–118

    CAS  PubMed  Article  Google Scholar 

  • Miller JH (1972) Experiments in molecular genetics. Cold Spring Harbour, Cold Spring Harbour Laboratory Press, NY

  • Minnikin D, O’Donnell A, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett J (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    CAS  Article  Google Scholar 

  • Miwa H, Ahmed I, Yoon J, Yokota A, Fujiwara T (2008) Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil. Int J Syst Evol Microbiol 58:286–289

    CAS  PubMed  Article  Google Scholar 

  • Onofre-Lemus J, Hernández-Lucas I, Girard L, Caballero-Mellado J (2009) ACC (1-aminocyclopropane-1-carboxylate) deaminase activity, a widespread trait in Burkholderia species, and its growth-promoting effect on tomato plants. Appl Environ Microbiol 75(20):6581–6590

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Penrose DM, Glick BR (2003) Methods for isolating and characterizing ACC deaminase containing plant growth promoting rhizobacteria. Physiol Plant 118(1):10–15

    CAS  PubMed  Article  Google Scholar 

  • Reasoner DJ, Geldreich EE (1985) A new medium for the enumeration and subculture of bacteria from potable water. Appl Environ Microbiol 49:1–7

    CAS  PubMed Central  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Shah S, Li J, Moffatt BA, Glick BR (1998) Isolation and characterization of ACC deaminase genes from two different plant growth-promoting rhizobacteria. Can J Microbiol 44:833–843

    CAS  PubMed  Article  Google Scholar 

  • Tan ZY, Xu XD, Wang ET, Gao JL, Chen WX, Martı´nez-Romero E (1997) Phylogenetic and genetic relationships of Mesorhizobium tianshanense and related rhizobia. Int J Syst Bacteriol 47:874–879

    CAS  PubMed  Article  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. Nucleic Acids Res 25:4876–4882

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Todorovic B, Glick BR (2008) The interconversion of ACC deaminase and d-cysteine desulfhydrase by directed mutagenesis. Planta 229:193–205

    CAS  PubMed  Article  Google Scholar 

  • Vauterin L, Vauterin P (1992) Computer-aided objective comparison of electrophoresis patterns for grouping and identification of microorganisms. Eur Microbiol 1:37–41

    Google Scholar 

  • Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, other authors (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

  • Willems A, De Ley J, Gillis M, Kersters K (1991) Comamonadaceae, a new family encompassing the Acidovorans rRNA complex, including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969). Int J Syst Bacteriol 41:445–450

    Article  Google Scholar 

  • Yoon J-H, Kang S-J, Oh T-K (2006) Variovorax dokdonensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 56: 811–814 Contains 17:1 ISO I/ANTEI B

Download references

Acknowledgments

This work was supported by “Special Fund for Agro-scientific Research in the Public Interest” (201203045) .The GenBank accession number for the 16S rRNA gene sequence of strain GXGD002T is JF495126.

Author information

Authors and Affiliations

  1. Beijing Agro- Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Science/Beijing Municipal Key Laboratory of Agricultural Gene Resources and Biotechnology, Beijing, 100097, People’s Republic of China

    Jun-lian Gao, Xu-ming Wang, Tian-lei Qiu, Ji-wei Li, Xiu-ai Li & Jian Chen

  2. Key Laboratory of Microbial Resources, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People’s Republic of China

    Mei Yuan & Jian-guang Sun

  3. China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People’s Republic of China

    Hong-can Liu

Authors
  1. Jun-lian Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mei Yuan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xu-ming Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tian-lei Qiu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ji-wei Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hong-can Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Xiu-ai Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Jian Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Jian-guang Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jian-guang Sun.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Gao, Jl., Yuan, M., Wang, Xm. et al. Variovorax guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere. Antonie van Leeuwenhoek 107, 65–72 (2015). https://doi.org/10.1007/s10482-014-0304-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-014-0304-3

Keywords

  • Variovorax guangxiensis sp. nov.
  • Taxonomy
  • 1-Aminocyclopropane-1-carboxylate deaminase
  • Banana rhizosphere