Skip to main content
SpringerLink
Log in

Rhizobium album sp. nov., isolated from a propanil-contaminated soil

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

A novel Gram-stain negative, facultatively anaerobic, non-spore-forming, motile and rod-shaped bacterium (NS-104T) was isolated from a propanil-contaminated soil in Nanjing, China. Growth occurred at pH 5.0–9.0 (optimum 6.0), 16–37 °C (optimum 30 °C) and in the presence of 0–2.0% (w/v) NaCl (optimum, without NaCl). Strain NS-104T showed high 16S rRNA gene sequence identity to Rhizobium azooxidifex DSM 100211T (96.7%). The phylogenetic analysis of the 16S rRNA gene as well as the housekeeping genes recA, atpD and glnA demonstrated that strain NS-104T belongs to the genus Rhizobium. Strain NS-104T did not form nodules on six different legumes, and the nodD, nodC and nifH genes were neither amplified by PCR nor found in the draft genome of strain NS-104T. The sole respiratory quinone was ubiquinone Q-10. The polar lipid profile included the major amounts phosphatidylmonomethylethanolamine, phosphatidylglycerol and moderate amounts of phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and unidentified aminolipids. The major cellular fatty acids were C18:1ω7c (39.6%), C19:0 cyclo ω8c (29.8%) and C16:0 (11.5%). The G + C content of strain NS-104T was 61.9 mol%. Strain NS-104T therefore represents a new species, for which the name Rhizobium album sp. nov. is proposed, with the type strain NS-104T (= KCTC 62327T = CCTCC AB 2017250T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Beveridge TJ, Lawrence JR, Murray RGE (2007) Sampling and staining for light microscopy. Methods Gen Mol Microbiol 3:19–33

    Google Scholar 

  • Breznak JA, Costilow RN (2007) Physicochemical factors in growth. Methods Gen Mol Bacteriol 3:309–329

    Google Scholar 

  • Chen WF (2016) Progress and perspective of systematics of rhizobia. Microbiology China 43(5):1095–1100

    Google Scholar 

  • Dall’Agnol RF, Ribeiro RA, Delamuta JR, Ormeño-Orrillo E, Rogel MA, Andrade DS, Matínez-Romero E, Hungria M (2014) Rhizobium paranaense sp. nov., an effective N2-fixing symbiont of common bean (Phaseolus vulgaris L.) with broad geographical distribution in Brazil. Int J Syst Evol Microbiol 64:3222–3229

    Article  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Frank B (1889) Über die Pilzsymbiose der Leguminosen. Ber Dtsch Bot Ges 7:332–346 (in German)

    Google Scholar 

  • Ghosh W, Roy P (2006) Mesorhizobium thiogangeticum sp. nov., a novel sulfur-oxidizing chemolithoautotroph from rhizosphere soil of an Indian tropical leguminous plant. Int J Syst Evol Microbiol 56(1):91–97

    Article  CAS  PubMed  Google Scholar 

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, 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  CAS  PubMed  Google Scholar 

  • Kluge AG, Farris JS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32

    Article  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Laguerre G, Nour SM, Macheret V, Sanjuan J, Drouin P, Amarger N (2001) Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. Microbiology 147:981–993

    Article  CAS  PubMed  Google Scholar 

  • Lane DL (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, New York, pp 115–175

    Google Scholar 

  • Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714

    Article  CAS  PubMed  Google Scholar 

  • Li R, Zhu H, Ruan J, Qian W, Fang XD, Shi ZB, Li YR, Li ST, Shan G, Kristiansen K, Li SG, Yang HM, Wang J, Wang J (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu TY, Li Y Jr, Liu XX, Sui XH, Zhang XX, Wang ET, Chen WX, Chen WF, Puławska J (2012) Rhizobium cauense sp. nov., isolated from root nodules of the herbaceous legume Kummerowia stipulacea grown in campus lawn soil. Syst Appl Microbiol 35(7):415–420

    Article  CAS  PubMed  Google Scholar 

  • Liu XM, Chen K, Meng C, Zhang L, Zhu JC, Huang X, Li SP, Jiang JD (2014) Pseudoxanthobacter liyangensis sp. nov., isolated from dichlorodiphenyltrichloroethane-contaminated soil. Int J Syst Evol Microbiol 64:3390–3394

    Article  CAS  PubMed  Google Scholar 

  • Martens M, Delaere M, Coopman R, De Vos P, Gillis M, Willems A (2007) Multilocus sequence analysis of Ensifer and related taxa. Int J Syst Evol Microbiol 57:489–503

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Parag B, Sasikala Ch, Ramana ChV (2013) Molecular and culture dependent characterization of endolithic bacteria in two beach sand samples and description of Rhizobium endolithicum sp. nov. Antonie Van Leeuwenhoek 104:1235–1244

    Article  CAS  PubMed  Google Scholar 

  • Ramírez-Bahena MH, García-Fraile P, Peix A, Valverde A, Rivas R, Igual JM, Mateos PF, Martínez-Molina E, Velázquez E (2008) Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain R. leguminosarum DSM 30132 (= NCIMB 11478) as Rhizobium pisi sp. nov. Int J Syst Evol Microbiol 58:2484–2490

    Article  CAS  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. Technical Note 101. Newark, DE: MIDI Inc

  • Tamaoka J, Katayama-Fujimura Y, Kuraishi H (1983) Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36

    Article  CAS  Google Scholar 

  • Tel-Zur N, Abbo S, Myslabodski D, Mizrahi Y (1999) Modified CTAB procedure for DNA isolation from epiphytic cacti of the genera Hylocereus and Selenicereus (Cactaceae). Plant Mol Biol Rep 17:249–254

    Article  CAS  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tighe SW, De Lajudie P, Dipietro K, Lindström K, Nick G, Jarvis BD (2000) Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the Sherlock Microbial Identification System. Int J Syst Evol Microbiol 50:787–801

    Article  CAS  PubMed  Google Scholar 

  • Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202

    Article  CAS  Google Scholar 

  • Tindall BJ, Sikorski J, Smibert RM, Kreig NR (2007) Phenotypic characterization and the principles of comparative systematics. Methods Gen Mol Microbiol 3:330–393

    Google Scholar 

  • Ueda T, Suga Y, Yahiro N, Matsuguchi T (1995) Remarkable N2-fixing bacterial diversity detected in rice roots by molecular evolutionary analysis of nifH gene sequences. J Bacteriol 177:1414–1417

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Undine B, Peter K, Stefanie P, Jürgen A, Andreas U (2016) Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov. Int J Syst Evol Microbiol 66:2354–2361

    Article  CAS  Google Scholar 

  • Vinuesa P, Silva C, Lorite MJ, Izaguirre-Mayoral ML, Bedmar EJ, Martínez-Romero E (2005) Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands. Syst Appl Microbiol 28:702–716

    Article  CAS  PubMed  Google Scholar 

  • Yoon JH, Kang SJ, Yi HS, Oh TK, Ryu CM (2010) Rhizobium soli sp.nov., isolated from soil. Int J Syst Evol Microbiol 60:1387–1393

    Article  CAS  PubMed  Google Scholar 

  • Zhang XX, Li BM, Wang HS, Sui XH, Ma XT, Hong Q, Jiang RB (2012) Rhizobium petrolearium sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 62:1871–1876

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Song M, Cao Q, Wu S, Zhao Y, Huang JW, Chen K, Li SP, Xia ZY, Jiang JD (2015a) Camelimonas fluminis sp. nov., a cyhalothrin-degrading bacterium isolated from river water. Int J Syst Evol Microbiol 65:3109–3114

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Song M, Chen XL, Xu RJ, Chen K, Li SP, Xia ZY, Jiang JD (2015b) Devosia honganensis sp. nov., isolated from the soil of a chemical factory. Antonie Van Leeuwenhoek 108:1301–1307

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was financially supported by Grants from the National Natural Science Foundation of China (31670111) and the National Key Research and Development Program of China (2016YFD0800203).

Author information

Authors and Affiliations

  1. Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

    Ping Hang, Long Zhang, Xi-Yi Zhou, Qiang Hu & Jian-Dong Jiang

Authors
  1. Ping Hang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Long Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xi-Yi Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Qiang Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jian-Dong Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jian-Dong Jiang.

Ethics declarations

Conflict of interest

The authors declare that there are no conflicts of interest.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 861 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hang, P., Zhang, L., Zhou, XY. et al. Rhizobium album sp. nov., isolated from a propanil-contaminated soil. Antonie van Leeuwenhoek 112, 319–327 (2019). https://doi.org/10.1007/s10482-018-1160-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-018-1160-3

Keywords

Search

Navigation