Plant and Soil

, Volume 405, Issue 1–2, pp 65–79 | Cite as

Kill or cure? The interaction between endophytic Paenibacillus and Serratia strains and the host plant is shaped by plant growth conditions

  • Daria Rybakova
  • Maria Schmuck
  • Ute Wetzlinger
  • Angela Varo-Suarez
  • Octavian Murgu
  • Henry Müller
  • Gabriele Berg
Regular Article



Verticillium wilt is difficult to suppress, and causes severe yield losses in a broad range of crops. Five Serratia and five Paenibacillus endophytic isolates showing antagonistic properties against fungal pathogens were compared for their plant growth-promoting (PGP) potential under different plant growth conditions with the objective of evaluating the PGP of endophytic strains in different ad planta systems.


Preselected isolates were applied to the surface-sterilized seeds of oilseed rape and cauliflower using bio-priming. The isolates’ PGP effect and root colonization capacities were compared under gnotobiotic conditions. One strain from each genus was selected and tested for its PGP qualities in sterile and non-sterile soil.


Serratia treatment resulted in different levels of PGP, while Paenibacillus strains damaged roots under gnotobiotic conditions. P. polymyxa Sb3-1 did not have a significant effect on plant growth in non-sterile soil; however it did promote plant growth in the sterile soil. S. plymuthica 3RP8 and P. polymyxa Sb3-1 were selected for further testing of their biocontrol effect under field conditions.


The choice of growth environments in the investigation of plant-bacterium interaction is crucial. Non-sterile soil is suggested as the ideal medium for use in studying the PGP effect.


Biocontrol Bio-priming Plant growth promotion PGP BIOCOMES Brassica Serratia Paenibacillus Verticillium wilt 



The authors would like to thank Timothy Mark (Graz) for English revision and discussion. This project was funded by the European Union in frame of FP7-KBBE-2013-7-single-stage (BIOCOMES; No. 612713) and by the Austrian Research Promotion Agency (FFG; No. 836466). The authors gratefully acknowledge support from NAWI Graz. We thank Christin Zachow (Graz) for her help regarding experimental questions and Anastasia Bragina (Graz) for help regarding statistical issues.


  1. Amman RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56:1919–1925Google Scholar
  2. Anand R, Paul L, Chanway C (2006) Research on endophytic bacteria: recent advances with forest trees. In: Schulz B, Boyle C, Sieber TN (eds) Microbial Root Endophytes. Springer, Berlin, pp 89–106CrossRefGoogle Scholar
  3. Berg G (2009) Plant–microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture. Appl Microbiol Biotechnol 84(1):11–18CrossRefPubMedGoogle Scholar
  4. Berg G, Roskot N, Steidle A, Eberl L, Zock A, Smalla K (2002) Plant-dependent genotypic and phenotypic diversity of antagonistic rhizobacteria isolated from different Verticillium host plants. Appl Environ Microbiol 68:3328–3338CrossRefPubMedPubMedCentralGoogle Scholar
  5. Berg G, Krechel A, Ditz M, Sikora RA, Ulrich A, Hallmann J (2005) Endophytic and ectophytic potato‐associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi. FEMS Microbiol Ecol 51:215–229CrossRefPubMedGoogle Scholar
  6. Berg G, Zachow C, Müller H, Philipps J, Tilcher R (2013) Next-generation bio-products sowing the seeds of success for sustainable agriculture. Agronomy 3(4):648–656CrossRefGoogle Scholar
  7. Bragina A, Berg C, Müller H, Moser D, Berg G (2013) Insights into functional bacterial diversity and its effects on Alpine bog ecosystem functioning. Scientific reports: 3Google Scholar
  8. Cabanás CGL, Schilirò E, Valverde-Corredor A, Mercado-Blanco J (2014) The biocontrol endophytic bacterium Pseudomonas fluorescens PICF7 induces systemic defense responses in aerial tissues upon colonization of olive roots. Front Microbiol 5Google Scholar
  9. Cardinale M, Vieira de Castro J, Müller H, Berg G, Grube M (2008) In situ analysis of the bacterial community associated with the reindeer lichen Cladonia arbuscula reveals predominance of Alphaproteobacteria. FEMS Microbiol Ecol 66(1):63–71CrossRefPubMedGoogle Scholar
  10. Carvalhais LC, Muzzi F, Tan CH, Hsien-Choo J, Schenk PM (2013) Plant growth in Arabidopsis is assisted by compost soil-derived microbial communities. Front Plant Sci 4Google Scholar
  11. Cernava T, Mueller H, Aschenbrenner IA, Grube M,  Berg, G (2015) Analyzing the antagonistic potential of the lichen microbiome against pathogens by bridging metagenomic with culture studies. Front Microbiol 6:620Google Scholar
  12. D’aes J, Hua GKH, De Maeyer K, Pannecoucque J, Forrez I, Ongena M, Dietrich LEP, Thomashow LS, Mavrodi DV, Höfte M (2011) Biological control of Rhizoctonia root rot on bean by phenazine-and cyclic lipopeptide-producing Pseudomonas CMR12a. Phytopathol 101(8):996–1004CrossRefGoogle Scholar
  13. Daims H, Brühl A, Amann R, Schleifer KH, Wagner M (1999) The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22:434–444CrossRefPubMedGoogle Scholar
  14. Debode J, Declercq B, Höfte M (2005) Identification of cauliflower cultivars that differ in susceptibility to Verticillium longisporum using different inoculation methods. J Phytopathol 153(5):257–263CrossRefGoogle Scholar
  15. Dunker S, Keunecke H, Steinbach P, von Tiedemann A (2008) Impact of Verticillium longisporum on yield and morphology of winter oilseed rape (Brassica napus) in relation to systemic spread in the plant. J Phytopathol 156:698–707CrossRefGoogle Scholar
  16. Emmert EA, Handelsman J (1999) Biocontrol of plant disease: a (Gram‐) positive perspective. FEMS Microbiol Lett 171(1):1–9CrossRefPubMedGoogle Scholar
  17. Erlacher A, Cardinale M, Grosch R, Grube M, Berg G (2014) The impact of the pathogen Rhizoctonia solani and its beneficial counterpart Bacillus amyloliquefaciens on the indigenous lettuce microbiome. Front Microbiol 5Google Scholar
  18. Fürnkranz M, Lukesch B, Müller H, Huss H, Grube M, Berg G (2012) Microbial diversity inside pumpkins: microhabitat-specific communities display a high antagonistic potential against phytopathogens. Microb Ecol 63:418–428CrossRefPubMedGoogle Scholar
  19. Gasser I, Cardinale M, Müller H, Heller S, Eberl L, Lindenkamp N, Kaddor C, Steinbüchel A, Berg G (2011) Analysis of the endophytic lifestyle and plant growth promotion of Burkholderia terricola ZR2-12. Plant Soil 347(1–2):125–136CrossRefGoogle Scholar
  20. Gray CD, Kinnear PR (2012) IBM SPSS statistics 19 made simple. Psychology PressGoogle Scholar
  21. Haagensen JA, Hansen SK, Johansen T, Molin S (2002) In situ detection of horizontal transfer of mobile genetic elements. FEMS Microbiol Ecol 42:261–268CrossRefPubMedGoogle Scholar
  22. Handelsman J, Stabb E (1996) Biocontrol of soilborne plant pathogens. Plant Cell 8(10):1855–1869CrossRefPubMedPubMedCentralGoogle Scholar
  23. Heale JB, Karapapa VK (1999) The Verticillium threat to Canada’s major oilseed crop: Canola. Can J Plant Pathol 21(1):1–7CrossRefGoogle Scholar
  24. Jiménez-Gasco M, Malcolm GM, Berbegal M, Armengol J, Jiménez-Díaz RM (2014) Complex molecular relationship between vegetative compatibility groups (VCGs) in Verticillium dahliae: VCGs do not always align with clonal lineages. Phytopathol 104:650–9CrossRefGoogle Scholar
  25. Kalbe C, Marten P, Berg G (1996) Members of the genus Serratia as beneficial rhizobacteria of oilseed rape. Microbiol Res 151:4433–4400CrossRefGoogle Scholar
  26. Karapapa VK, Bainbridge BW, Heale JB (1997) Morphological and molecular characterization of Verticillium longisporum comb. nov. pathogenic to oilseed rape. Mycol Res 101(11):1281–1294CrossRefGoogle Scholar
  27. Kloepper JW, Schroth KJW (1980) Plant growth-promoting rhizobacteria and plant growth under gnotobiotic conditions. Phytopathol 71:642–644CrossRefGoogle Scholar
  28. Köberl M, Ramadan EM, Adam M, Cardinale M, Hallmann J, Heuer H, Smalla K, Berg G (2013) Bacillus and Streptomyces were selected as broad-spectrum antagonists against soilborne pathogens from arid areas in Egypt. FEMS Microbiol Lett 342:168–178CrossRefPubMedGoogle Scholar
  29. Kurze S, Dahl R, Bahl H, Berg G (2001) Biological control of fungal strawberry diseases by Serratia plymuthica HRO-C48. Plant Dis 85:529–534CrossRefGoogle Scholar
  30. Lal S, Tabacchioni S (2009) Ecology and biotechnological potential of Paenibacillus polymyxa: a minireview. Indian J Microbiol 49:2–10CrossRefPubMedPubMedCentralGoogle Scholar
  31. Li J, Zhao GZ, Varma A, Qin S, Xiong Z, Huang HY, Zhu WY, Zhao LX, Xu LH, Li WJ (2012) An endophytic Pseudonocardia species induces the production of artemisinin in Artemisia. annua. PLoS One 7(12):e51410CrossRefPubMedPubMedCentralGoogle Scholar
  32. Liebminger S, Aichner M, Oberauner L, Fürnkranz M, Cardinale M, Berg G (2011) A new textile-based approach to assess the antimicrobial activity of volatiles. Text Res J. doi: 10.1177/0040517511429607 Google Scholar
  33. Ludwig-Müller J (2014) Auxin homeostasis, signaling and interaction with other growth hormones during the clubroot disease of Brassicaceae. Plant Signal Behav 9, e28593CrossRefPubMedCentralGoogle Scholar
  34. Meier H, Amann R, Ludwig W, Schleifer KH (1999) Specific oligonucleotide probes for in situ detection of a major group of gram-positive bacteria with low DNA G+ C content. Syst Appl Microbiol 22(2):186–196CrossRefPubMedGoogle Scholar
  35. Messner R, Schweigrofler W, Ibl M, Berg G, Prillinger H (1996) Molecular characterization of the plant pathogen Verticillium dahliae Kleb. using RAPD-PCR and sequencing of the 18S rRNA-gene. J Phytopathol 144:347–354CrossRefGoogle Scholar
  36. Müller H, Berg G (2008) Impact of formulation procedures on the effect of the biocontrol agent Serratia plymuthica HRO-C48 on Verticillium wilt in oilseed rape. BioControl 53:905–916CrossRefGoogle Scholar
  37. Petersen LM, Tisa LS (2013) Friend or foe? A review of the mechanisms that drive Serratia towards diverse lifestyles. Can J Microbiol 59(9):627–640CrossRefPubMedGoogle Scholar
  38. Phi QT, Park YM, Seul KJ, Ryu CM, Park SH, Kim JG, Ghim SY (2010) Assessment of root-associated Paenibacillus polymyxa groups on growth promotion and induced systemic resistance in pepper. J Microbiol Biotechnol 20(12):1605–1613PubMedGoogle Scholar
  39. Prieto P, Navarro-Raya C, Valverde-Corredor A, Amyotte SG, Dobinson KF, Mercado-Blanco J (2009) Colonization process of olive tissues by Verticillium dahliae and its in planta interaction with the biocontrol root endophyte Pseudomonas fluorescens PICF7. Microb Biotechnol 2(4):499–511CrossRefPubMedPubMedCentralGoogle Scholar
  40. Raza W, Yang W, Shen QR (2008) Paenibacillus polymyxa: antibiotics, hydrolytic enzymes and hazard assessment. J Plant Pathol 90:419–430Google Scholar
  41. Rybakova D, Cernava T, Köberl M, Liebminger S, Etemadi M, Berg G (2015) Endophytes-assisted biocontrol: novel insights in ecology and the mode of action of Paenibacillus. Plant and soil; acceptedGoogle Scholar
  42. Siebold M, Tiedemann AV (2012) Potential effects of global warming on oilseed rape pathogens in Northern Germany. Fungal Ecol 5(1):62–72CrossRefGoogle Scholar
  43. Timmusk S (2015) Sfp-type PPTase inactivation promotes bacterial biofilm formation and ability to enhance wheat drought tolerance. Front Microbiol 6:387CrossRefPubMedPubMedCentralGoogle Scholar
  44. Timmusk S, Wagner EGH (1999) The plant-growth-promoting rhizobacterium Paenibacillus polymyxa induces changes in Arabidopsis thaliana gene expression: a possible connection between biotic and abiotic stress responses. Mol Plant Microbe 12(11):951–959CrossRefGoogle Scholar
  45. Timmusk S, Grantcharova N, Wagner EGH (2005) Paenibacillus polymyxa invades plant roots and forms biofilms. Appl Environ Microbiol 71(11):7292–7300CrossRefPubMedPubMedCentralGoogle Scholar
  46. Tyvaert L, França SC, Debode J, Höfte M (2014) The endophyte Verticillium Vt305 protects cauliflower against Verticillium wilt. J Appl Microbiol 116(6):1563–71CrossRefPubMedGoogle Scholar
  47. Weller DM (1988) Biological control of soilborne plant pathogens in the rhizosphere with bacteria. Annu Rev Phytopathol 26:379–407CrossRefGoogle Scholar
  48. Zachow C, Fatehi J, Cardinale M, Tilcher R, Berg G (2010) Strain‐specific colonization pattern of Rhizoctonia antagonists in the root system of sugar beet. FEMS Microbiol Ecol 74(1):124–135CrossRefPubMedGoogle Scholar
  49. Zachow C, Müller H, Tilcher R, Donat C, Berg G (2013) Catch the best: novel screening strategy to select stress protecting agents for crop plants. Agronomy 3:794–815CrossRefGoogle Scholar
  50. Zeise K, Steinbach P (2004) Schwarze Rapswurzeln und der Vormarsch der Verticillium-Rapswelke. Raps 22:170–174Google Scholar
  51. Zhou L, Hu Q, Johansson A, Dixelius C (2006) Verticillium longisporum and V. dahliae: infection and disease in Brassica napus. Plant Pathol 55(1):137–144CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Daria Rybakova
    • 1
  • Maria Schmuck
    • 1
  • Ute Wetzlinger
    • 1
  • Angela Varo-Suarez
    • 2
  • Octavian Murgu
    • 1
  • Henry Müller
    • 1
  • Gabriele Berg
    • 1
  1. 1.Institute of Environmental BiotechnologyGraz University of TechnologyGrazAustria
  2. 2.Departamento de AgronomíaUniversity of CórdobaCórdobaSpain

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