Skip to main content
SpringerLink
Log in

Changes in Root Bacterial Communities Associated to Two Different Development Stages of Canola (Brassica napus L. var oleifera) Evaluated through Next-Generation Sequencing Technology

  • Environmental Microbiology
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Crop production may benefit from plant growth-promoting bacteria. The knowledge on bacterial communities is indispensable in agricultural systems that intend to apply beneficial bacteria to improve plant health and production of crops such as canola. In this work, the diversity of root bacterial communities associated to two different developmental phases of canola (Brassica napus L.) plants was assessed through the application of new generation sequencing technology. Total bacterial DNA was extracted from root samples from two different growth states of canola (rosette and flowering). It could be shown how bacterial communities inside the roots changed with the growing stage of the canola plants. There were differences in the abundance of the genera, family, and even the phyla identified for each sample. While in both root samples Proteobacteria was the most common phylum, at the rosette stage, the most common bacteria belonged to the family Pseudomonadaceae and the genus Pseudomonas, and in the flowering stage, the Xanthomonadaceae family and the genus Xanthomonas dominated the community. This implies in a switch in the predominant bacteria in the different developmental stages of the plant, suggesting that the plant itself interferes with the associated microbial community.

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
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Lynch JM (1990) Longevity of bacteria—considerations in environmental release. Curr Microbiol 20:387–389

    Article  Google Scholar 

  2. Roesch LF, Fulthorpe RR, Riva A, Casella G, Hadwin AKM et al (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290

    PubMed  CAS  Google Scholar 

  3. Torsvik V, Goksoyr J, Daae FL (1990) High diversity in DNA of soil bacteria. Appl Environ Microbiol 56:782–787

    PubMed  CAS  Google Scholar 

  4. Duineveld BM, Rosado AS, van Elsas JD, van Veen JA (1998) Analysis of the dynamics of bacterial communities in the rhizosphere of the chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns. Appl Environ Microbiol 64:4950–4957

    PubMed  CAS  Google Scholar 

  5. Hartmann A, Assmus B, Kirchhof G, Schloter M (1997) Direct approaches for studying soil microbes. In: van Elsas JD, Trevors JT, Wellington EMH (eds) Modern soil microbiology. Dekker, New York

    Google Scholar 

  6. Liesack W, Janssen PH, Rainey FA, Ward-Rainey NL, Stackebrandt E (1997) Microbial diversity in soil: the need for a combined approach using molecular and cultivation techniques. In: van Elsas JD, Trevors JT, Wellington EMH (eds) Modern soil microbiology. Dekker, New York

    Google Scholar 

  7. Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    PubMed  CAS  Google Scholar 

  8. Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M et al (1998) Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554–568

    Article  PubMed  CAS  Google Scholar 

  9. Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57:369–394

    Article  PubMed  CAS  Google Scholar 

  10. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM et al (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci U S A 103:12115–12120

    Article  PubMed  CAS  Google Scholar 

  11. Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6:e280

    Article  PubMed  Google Scholar 

  12. Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA, et al (2008) Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. Plos Genetics 4

  13. Huse SM, Huber JA, Morrison HG, Sogin ML, Mark Welch D (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biology 8

  14. Tomm GO (2000) Situação atual e perspectivas da canola no Brasil. Comunicado Técnico On-line, 58. Passo Fundo: Embrapa Trigo

  15. Germida JJ, Siciliano SD, de Freitas JR, Seib AM (1998) Diversity of root-associated bacteria associated with held-grown canola (Brassica napus L.) and wheat (Triticum aestivum L.). FEMS Microbiol Ecol 26:43–50

    Article  CAS  Google Scholar 

  16. Kloepper JW, Lifshitz R, Schroth MN (1988) Pseudomonas inoculants to benefit plant-production. Isi Atl Sci-Anim Pl Sci 1:60–64

    Google Scholar 

  17. Siciliano SD, Goldie H, Germida JJ (1998) Enzymatic activity in root exudates of Dahurian wild rye (Elymus dauricus) that degrades 2-chlorobenzoic acid. J Agric Food Chem 46:5–7

    Article  PubMed  CAS  Google Scholar 

  18. Dunfield KE, Germida JJ (2003) Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (Brassica napus). Appl Environ Microbiol 69:7310–7318

    Article  PubMed  CAS  Google Scholar 

  19. Farina R, Beneduzi A, Ambrosini A, de Campos SB, Lisboa BB et al (2012) Diversity of plant growth-promoting rhizobacteria communities associated with the stages of canola growth. Appl Soil Ecol 55:44–52

    Article  Google Scholar 

  20. Soares RA, Roesch LFW, Zanatta G, Camargo FAO, Passaglia LMP (2006) Occurrence and distribution of nitrogen fixing bacterial community associated with oat (Avena sativa) assessed by molecular and microbiological techniques. Appl Soil Ecol 33:14

    Article  Google Scholar 

  21. Felske A, Engelen B, Nubel U, Backhaus H (1996) Direct ribosome isolation from soil to extract bacterial rRNA for community analysis. Appl Environ Microbiol 62:4162–4167

    PubMed  CAS  Google Scholar 

  22. Brosius J, Palmer ML, Kennedy PJ, Noller HF (1978) Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A 75:4801–4805

    Article  PubMed  CAS  Google Scholar 

  23. Sun Y, Cai Y, Liu L, Yu F, Farrell ML et al (2009) ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37:e76

    Article  PubMed  Google Scholar 

  24. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267

    Article  PubMed  CAS  Google Scholar 

  25. Lancashire PD, Bleiholder H, Vandenboom T, Langeluddeke P, Stauss R et al (1991) A uniform decimal code for growth-stages of crops and weeds. Ann Appl Biol 119:561–601

    Article  Google Scholar 

  26. Costacurta A, Vanderleyden J (1995) Synthesis of phytohormones by plant-associated bacteria. Crit Rev Microbiol 21:1–18

    Article  PubMed  Google Scholar 

  27. Khalid A, Arshad M, Zahir ZA (2004) Screening plant growth-promoting rhizobacteria for improving growth and yield of wheat. J Appl Microbiol 96:473–480

    Article  PubMed  CAS  Google Scholar 

  28. Beneduzi A, Peres D, da Costa PB, Bodanese Zanettini MH, Passaglia LM (2008) Genetic and phenotypic diversity of plant-growth-promoting bacilli isolated from wheat fields in southern Brazil. Res Microbiol 159:244–250

    Article  PubMed  CAS  Google Scholar 

  29. Beneduzi A, Peres D, Vargas LK, Bodanese-Zanettini MH, Passaglia LMP (2008) Evaluation of genetic diversity and plant growth promoting activities of nitrogen-fixing bacilli isolated from rice fields in South Brazil. Appl Soil Ecol 39:311–320

    Article  Google Scholar 

  30. McClinchey SL, Kott LS (2008) Production of mutants with high cold tolerance in spring canola (Brassica napus). Euphytica 162:51–67

    Article  CAS  Google Scholar 

  31. Chavarria G, Tomm GO, Muller A, Mendonca HF, Mello N et al (2011) Leaf area index of canola under varying row spacing and plant density of sowing. Ciencia Rural 41:2084–2089

    Article  Google Scholar 

  32. Di Cello F, Bevivino A, Chiarini L, Fani R, Paffetti D et al (1997) Biodiversity of a Burkholderia cepacia population isolated from the maize rhizosphere at different plant growth stages. Appl Environ Microbiol 63:4485–4493

    PubMed  Google Scholar 

  33. Grayston SJ, Wang SQ, Campbell CD, Edwards AC (1998) Selective influence of plant species on microbial diversity in the rhizosphere. Soil Biol Biochem 30:369–378

    Article  CAS  Google Scholar 

  34. Kaiser O, Puhler A, Selbitschka W (2001) Phylogenetic analysis of microbial diversity in the rhizoplane of oilseed rape (Brassica napus cv. Westar) employing cultivation-dependent and cultivation-independent approaches. Microb Ecol 42:136–149

    PubMed  CAS  Google Scholar 

  35. Marschner P, Yang CH, Lieberei R, Crowley DE (2001) Soil and plant specific effects on bacterial community composition in the rhizosphere. Soil Biol Biochem 33:1437–1445

    Article  CAS  Google Scholar 

  36. Kowalchuk GA, Buma DS, de Boer W, Klinkhamer PG, van Veen JA (2002) Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie Van Leeuwenhoek 81:509–520

    Article  PubMed  Google Scholar 

  37. Mitchell RJ, Hester AJ, Campbell CD, Chapman SJ, Cameron CM et al (2010) Is vegetation composition or soil chemistry the best predictor of the soil microbial community? Plant Soil 333:417–430

    Article  CAS  Google Scholar 

  38. Smalla K, Wieland G, Buchner A, Zock A, Parzy J et al (2001) Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol 67:4742–4751

    Article  PubMed  CAS  Google Scholar 

  39. Miller HJ, Henken G, Vanveen JA (1989) Variation and composition of bacterial-populations in the rhizospheres of maize, wheat, and grass cultivars. Can J Microbiol 35:656–660

    Article  Google Scholar 

  40. Hozore E, Alexander M (1991) Bacterial characteristics important to rhizosphere competence. Soil Biol Biochem 23:717–723

    Article  Google Scholar 

  41. Kloepper JW (1993) Plant growth-promoting rhizobacteria as biological control agents. Marcel Dekker, New York

    Google Scholar 

  42. Francis I, Holsters M, Vereecke D (2010) The Gram-positive side of plant-microbe interactions. Environ Microbiol 12:1–12

    Article  PubMed  CAS  Google Scholar 

  43. Marilley L, Aragno M (1999) Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots. Appl Soil Ecol 13:127–136

    Article  Google Scholar 

Download references

Acknowledgments

We thank R. Luís Mayer Weber for his valuable scientific comments. The work from Brazilian side was financed by a grant and fellowships from the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, and Instituto Nacional de Ciência e Tecnologia da Fixação Biológica do Nitrogênio. Work in the lab of VFW was supported in part by grant BRA 09/008 from the IB-BMBF Germany.

Author information

Authors and Affiliations

  1. Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Prédio 43312, Sala 207b, Caixa Postal 15.053, Porto Alegre, Rio Grande do Sul, CEP 91501-970, Brazil

    Samanta B. de Campos, Roberto Farina & Luciane M. P. Passaglia

  2. Department of Genetics of Prokaryotes, Bielefeld University, Bielefeld, Germany

    Jung-Won Youn & Volker F. Wendisch

  3. Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

    Sebastian Jaenicke, Sebastian Jünemann, Rafael Szczepanowski, Alexander Goesmann & Volker F. Wendisch

  4. Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Porto Alegre, Rio Grande do Sul, Brazil

    Anelise Beneduzi & Luciano K. Vargas

Authors
  1. Samanta B. de Campos
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jung-Won Youn
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Roberto Farina
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sebastian Jaenicke
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sebastian Jünemann
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Rafael Szczepanowski
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Anelise Beneduzi
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Luciano K. Vargas
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Alexander Goesmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Volker F. Wendisch
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Luciane M. P. Passaglia
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Luciane M. P. Passaglia.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Table S1

Sequencing data for samples R1 and R2 (PDF 61 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

de Campos, S.B., Youn, JW., Farina, R. et al. Changes in Root Bacterial Communities Associated to Two Different Development Stages of Canola (Brassica napus L. var oleifera) Evaluated through Next-Generation Sequencing Technology. Microb Ecol 65, 593–601 (2013). https://doi.org/10.1007/s00248-012-0132-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-012-0132-9

Keywords

Search

Navigation