Skip to main content
SpringerLink
Log in

Comparison of Rhizosphere Bacterial Communities in Arabidopsis thaliana Mutants for Systemic Acquired Resistance

  • Original Article
  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Systemic acquired resistance (SAR) is an inducible systemic plant defense against a broad spectrum of plant pathogens, with the potential to secrete antimicrobial compounds into the soil. However, its impact on rhizosphere bacteria is not known. In this study, we examined fingerprints of bacterial communities in the rhizosphere of the model plant Arabidopsis thaliana to determine the effect of SAR on bacterial community structure and diversity. We compared Arabidopsis mutants that are constitutive and non-inducible for SAR and verified SAR activation by measuring pathogenesis-related protein activity via a β-glucoronidase (GUS) reporter construct driven by the β-1-3 glucanase promoter. We used terminal restriction fragment length polymorphism (T-RFLP) analysis of MspI- and HaeIII-digested 16S rDNA to estimate bacterial rhizosphere community diversity, with Lactobacillus sp. added as internal controls. T-RFLP analysis showed a clear rhizosphere effect on community structure, and diversity analysis of both rhizosphere and bulk soil operational taxonomic units (as defined by terminal restriction fragments) using richness, Shannon–Weiner, and Simpson’s diversity indices and evenness confirmed that the presence of Arabidopsis roots significantly altered bacterial communities. This effect of altered soil microbial community structure by plants was also seen upon multivariate cluster analysis of the terminal restriction fragments. We also found visible differences in the rhizosphere community fingerprints of different Arabidopsis SAR mutants; however, there was no clear decrease of rhizosphere diversity because of constitutive SAR expression. Our study suggests that SAR can alter rhizosphere bacterial communities, opening the door to further understanding and application of inducible plant defense as a driving force in structuring soil bacterial assemblages.

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

Figure 1
Figure 2
Figure 3

Similar content being viewed by others

References

  1. Bankhead SB, Landa BB, Lutton E, Weller DM, McSpadden Gardener BB (2004) Minimal changes in rhizobacterial population structure following root colonization by wild type and transgenic biocontrol strains. FEMS Microbiol Ecol 49:307–318

    Article  CAS  Google Scholar 

  2. Baudoin E, Benizri E, Guckert A (2003) Impact of artificial root exudates on the bacterial community structure in bulk soil and maize rhizosphere. Soil Biol Biochem 35:1183–1192

    Article  CAS  Google Scholar 

  3. Becker S, Boger P, Oehlmann R, Ernst A (2000) PCR bias in ecological analysis: a case study for quantitative Taq nuclease assays in analyses of microbial communities. Appl Environ Microbiol 66:4945–4953

    Article  PubMed  CAS  Google Scholar 

  4. Bent SJ, Pierson JD, Forney LJ, Danovaro R, Luna GM, Dell’Anno A, Pietrangeli B (2007) Measuring species richness based on microbial community fingerprints: the emperor has no clothes. Appl Environ Microbiol 73:2399–2401

    Article  PubMed  CAS  Google Scholar 

  5. Blackwood CB, Marsh T, Kim S-H, Eldor P (2003) Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl Environ Microbiol 69:926–932

    Article  PubMed  CAS  Google Scholar 

  6. Bowling SA, Guo A, Cao H, Gordon SA, Klessig DF, Dong X (1994) A mutation in Arabidopsis that leads to constitutive expression of systemic acquired resistance. Plant Cell 6:1845–1857

    Article  PubMed  CAS  Google Scholar 

  7. Boyes DC, Zayed AM, Ascenzi R, McCaskill AJ, Hoffman NE, Davis KR, Gorlach J (2001) Growth stage-based phenotypic analysis of Arabidopsis: a model for high throughput functional genomics in plants. Plant Cell 13:1499–1510

    Article  PubMed  CAS  Google Scholar 

  8. Burketova L, Stillerova K, Feltlova M (2003) Immunohistological localization of chitinase and b-1,3-glucanase in rhizomania-diseased and benzothiadiazole treated sugar beet roots. Physiol Mol Plant Pathol 63:47–54

    Article  CAS  Google Scholar 

  9. Cameron RK, Paiva NL, Lamb CJ, Dixon RA (1999) Accumulation of salicylic acid and PR-1 gene transcripts in relation to the systemic acquired resistance (SAR) response induced by Pseudomonas syringae pv. tomato in Arabidopsis. Physiol Mol Plant Pathol 55:121–130

    Article  CAS  Google Scholar 

  10. Cao H, Bowling SA, Gordon SA, Dong X (1994) Characterization of an Arabidopsis mutant that is nonresponsive to inducers of systemic acquired resistance. Plant Cell 6:1583–1592

    Article  PubMed  CAS  Google Scholar 

  11. Conrath U, Zhixiang C, Ricigliano JR, Klessig DF (1995) Two inducers of plant defense responses, 2,6-dichloroisonicotinic acid and salicylic acid, inhibit catalase activity in tobacco. Proc Natl Acad Sci USA 92:7143–7147

    Article  PubMed  CAS  Google Scholar 

  12. Curl EA, Truelove B (1986) The Rhizosphere. Springer, Berlin

    Google Scholar 

  13. Devoto A, Turner JG (2003) Regulation of jasmonate-mediated plant responses in Arabidopsis. Ann Bot 92:329–337

    Article  PubMed  CAS  Google Scholar 

  14. Dong X (2004) NPR1, all things considered. Curr Opin Plant Biol 7:547–552

    Article  PubMed  CAS  Google Scholar 

  15. Dunbar JM, Ticknor LO, Kuske CR (2000) Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis. Appl Environ Microbiol 66:2943–2950

    Article  PubMed  CAS  Google Scholar 

  16. Dunbar JM, Ticknor LO, Kuske CR (2001) Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl Environ Microbiol 67:190–197

    Article  PubMed  CAS  Google Scholar 

  17. 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 

  18. Egert M, Friedrich MW (2003) Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure. Appl Environ Microbiol 69:2555–2562

    Article  PubMed  CAS  Google Scholar 

  19. Fierer N, Schimel JP, Holden PA (2003) Influence of drying-rewetting frequency on soil bacterial community structure. Microb Ecol 45:63–71

    Article  PubMed  CAS  Google Scholar 

  20. Friedrich L, Lawton K, Ruess W, Masner P, Specker N, Gut Rella M, Meier B, Dincher S, Staub T, Uknes S, Metraux JP, Kessman H, Ryals J (1996) A benzothiadiaxole derivative induces systemic acquired resistance in tobacco. Plant J 10:61–70

    Article  CAS  Google Scholar 

  21. Fromin N, Achouak W, Thiery JM, Heulin T (2001) The genotypic diversity of Pseudomonas brassicacearum populations isolated from roots of Arabidopsis thaliana: influence of plant genotype. FEMS Microbiol Ecol 37:21–29

    Article  CAS  Google Scholar 

  22. Gessler C, Kuc J (1982) Induction of resistance to Fusarium wilt in cucumber by root and foliar pathogens. Phytopathology 72:1439–1441

    Article  Google Scholar 

  23. Grant M, Lamb CJ (2006) Systemic immunity. Curr Opin Plant Biol 9:414–420

    Article  PubMed  CAS  Google Scholar 

  24. Griffiths BS, Ritz K, Ebblewhite N, Dobson G (1999) Soil microbial community structure: effects of substrate loading rates. Soil Biol Biochem 31:145–153

    Article  CAS  Google Scholar 

  25. Hackl E, Zechmeister-Boltenstern S, Bodrossy L, Sessitsch A (2004) Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils. Appl Environ Microbiol 70:5057–5065

    Article  PubMed  CAS  Google Scholar 

  26. Heidel AJ, Clarke J, Antonovics J, Dong X (2004) Fitness costs of mutations affecting the systemic acquired resistance pathway in Arabidopsis thaliana. Genetics 168:2197–2206

    Article  PubMed  CAS  Google Scholar 

  27. Heil M (1999) Systemic acquired resistance: available information and open ecological questions. J Ecol 87:341–346

    Article  Google Scholar 

  28. Heil M, Baldwin IT (2002) Fitness costs of induced resistance: emerging experimental support for a slippery concept. Trends Plant Sci 7:61–67

    Article  PubMed  CAS  Google Scholar 

  29. Heil M, Hilpert A, Kaiser W, Linsenmair KE (2000) Reduced growth and seed set following chemical induction of pathogen defense: does systemic acquired resistance (SAR) incur allocation costs? J Ecol 88:645–654

    Article  CAS  Google Scholar 

  30. Kerkhof L, Santoro M, Garland J (2000) Response of soybean rhizosphere communities to human hygiene water addition as determined by community level physiological profiling (CLPP) and terminal restriction fragment length polymorphism (TRFLP) analysis. FEMS Microbiol Lett 184:95–101

    Article  PubMed  CAS  Google Scholar 

  31. Kowalchuk GA, de Bruijn FJ, Head IM, Akkermans ADL, van Elsas JD (2004) Molecular Microbial Ecology Manual, 2nd edn., vols. 1 and 2. Kluwer, Dordrecht, The Netherlands

    Google Scholar 

  32. Kuske CR, Ticknor LO, Miller ME, Dunbar JM, Davis JA, Barns SM, Belnap J (2002) Comparison of soil bacterial communities in rhizospheres of three plant species and the interspaces in an arid grassland. Appl Environ Microbiol 68:1854–1863

    Article  PubMed  CAS  Google Scholar 

  33. Lukow T, Dunfield PF, Liesack W (2000) Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants. FEMS Microbiol Ecol 32:241–247

    Article  CAS  Google Scholar 

  34. Malamy J, Hennig J, Klessig DF (1992) Temperature-dependent induction of Salicylic acid and its conjugates during the resistance response to tobacco mosaic virus infection. Plant Cell 4:359–366

    Article  PubMed  CAS  Google Scholar 

  35. Marilley L, Vogt G, Blanc M, Aragno M (1998) Bacterial diversity in the bulk soil and rhizosphere fractions of Lolium perenne and Trifolium repens as revealed by PCR restriction analysis of 16S rDNA. Plant Soil 198:219–224

    Article  CAS  Google Scholar 

  36. Marschner P, Yang C-H, 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 

  37. Martin AP (2002) Phylogenetic apporaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68:3673–3682

    Article  PubMed  CAS  Google Scholar 

  38. Moeseneder MM, Arrieta JM, Muyzer G, Winter C, Herndl G (1999) Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl Environ Microbiol 65:3518–3525

    PubMed  CAS  Google Scholar 

  39. O’Donnell AG, Seasman M, Macrae A, Waite I, Davies JT (2001) Plants and fertilisers as drivers of change in microbial community structure and function in soils. Plant Soil 232:135–145

    Article  CAS  Google Scholar 

  40. Pieterse CMJ, van Loon LC (1999) Salicylic acid-independent plant defence pathways. Trends Plant Sci 4:52–58

    Article  PubMed  Google Scholar 

  41. Pieterse CMJ, van Wees SCM, van Pelt JA, Knoester M, Laan R, Gerrits H, Weisbeek PJ, van Loon LC (1998) A novel signaling pathway controlling induced systemic resistance in Arabidopsis. Plant Cell 10:1571–1580

    Article  PubMed  CAS  Google Scholar 

  42. Rees GN, Baldwin DS, Watson GO, Perryman S, Nielsen DL (2004) Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: application of multivariate statistics. Antonie van Leeuwenhoek 86:339–347

    Article  PubMed  Google Scholar 

  43. Ryals J, Uknes S, Ward E (1994) Systemic acquired resistance. Plant Physiol 104:1109–1112

    PubMed  CAS  Google Scholar 

  44. Santamaria M, Thomson CJ, Read ND, Loake GJ (2001) The promoter of a basic PR1-like gene, AtPRB1, from Arabidopsis establishes an organ-specific expression pattern and responsiveness to ethylene and methyl jasmonate. Plant Mol Biol 47:641–652

    Article  PubMed  CAS  Google Scholar 

  45. Sauerborn J, Buschmann K, Ghiasvand Ghiasi K, Kogel K-H (2002) Benzothiadiazole activates resistance in sunflower (Helianthus annuus) to the root-parasitic weed Orobanche cumana. Phytopathology 92:59–64

    Article  CAS  PubMed  Google Scholar 

  46. Schutter M, Dick R (2001) Shifts in substrate utilization potential and structure of soil microbial communities in response to carbon substrates. Soil Biol Biochem 33:1481–1491

    Article  CAS  Google Scholar 

  47. Sessitsch A, Reiter B, Berg G (2004) Endophytic bacterial communities of field-grown potato plants and their plant-growth-promoting and antagonistic abilities. Can J Microbiol 50:239–249

    Article  PubMed  CAS  Google Scholar 

  48. Sessitsch A, Weilharter A, Gerzabek MH, Kirchmann H, Kandeler E (2001) Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl Environ Microbiol 67:4215–4224

    Article  PubMed  CAS  Google Scholar 

  49. Shah J (2003) The salicylic acid loop in plant defense. Curr Opin Plant Biol 6:365–371

    Article  PubMed  CAS  Google Scholar 

  50. Sliwinski MK, Goodman RM (2004) Comparison of crenarchaeal consortia inhabiting the rhizosphere of diverse terrestrial plants with those in bulk soil in native environments. Appl Environ Microbiol 70:1821–1826

    Article  PubMed  CAS  Google Scholar 

  51. Smalla K, Wieland G, Buchner A, Zock A, Parzy J, Kaiser S, Roskot N, Heuer, H, Berg G. (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 

  52. Sticher L, Mauch-Mani B, Metraux JP (1997) Systemic acquired resistance. Ann Rev Phytopathol 35:235–270

    Article  CAS  Google Scholar 

  53. Stokes TL, Richards EJ (2002) Induced instability of two Arabidopsis constitutive pathogen-response alleles. Proc Natl Acad Sci USA 99:7792–7796

    Article  PubMed  CAS  Google Scholar 

  54. Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625–630

    PubMed  CAS  Google Scholar 

  55. Tahiri-Alaoui A, Dumas-Gaudot E, Gianinazzi S, Antoniw J (1993) Expression of the PR-bi gene in roots of two Nicotiana species and their amphidipioid hybrid infected with virulent and avirulent races of Chalara elegans. Plant Pathol 42:728–736

    Article  CAS  Google Scholar 

  56. Tebbe CC, Vahjen W (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl Environ Microbiol 59:2657–2665

    PubMed  CAS  Google Scholar 

  57. van Loon LC, van Strien EA (1999) The families of pathogenesis-related proteins, their activities, and comparative analysis of PR-1 type proteins. Physiol Mol Plant Pathol 55:85–97

    Article  Google Scholar 

  58. Walker T, Pal Bais H, Grotewold E, Vivanco JM (2003) Root exudation and rhizosphere biology. Plant Physiol 132:44–51

    Article  PubMed  CAS  Google Scholar 

  59. Walker T, Pal Bais H, Halligan KM, Stermitz FR, Vivanco JM (2003) Metabolic profiling of root exudates of Arabidopsis thaliana. J Agric Food Chem 51:2548–2554

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The seeds used in this project were kindly provided by Dr. X. Dong (Duke University). Mark Wilson (Humboldt State Univ.) gave advice on preparing T-RFLP samples. Alan Raetz (CSUC) wrote PERL programs that helped with initial data analysis. Larry Hanne and Nancy Carter (CSUC) gave helpful suggestions. The ABI 310 genetic analyzer was funded by NSF CCLI #DUE-0126618 to GW. GW and KB received funds for this project from a CSU Biotechnology consortium (CSUPERB) faculty seed grant, and JH received funding from the Sigma Xi Grants-in-Aid program.

Author information

Authors and Affiliations

  1. Department of Biological Sciences, California State University, Chico, CA, 95929-0515, USA

    John W. Hein, Gordon V. Wolfe & Kristopher A. Blee

Authors
  1. John W. Hein
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gordon V. Wolfe
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kristopher A. Blee
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gordon V. Wolfe.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hein, J.W., Wolfe, G.V. & Blee, K.A. Comparison of Rhizosphere Bacterial Communities in Arabidopsis thaliana Mutants for Systemic Acquired Resistance. Microb Ecol 55, 333–343 (2008). https://doi.org/10.1007/s00248-007-9279-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-007-9279-1

Keywords

Search

Navigation