Bacterial Traits Involved in Colonization of Arabidopsis thaliana Roots by Bacillus amyloliquefaciens FZB42

  • Dietel, Kristin ;
  • Beator, Barbara ;
  • Budiharjo, Anto ;
  • Fan, Ben ;
  • Borriss, Rainer
  • Received : 2012.10.16
  • Accepted : 2012.11.27
  • Published : 2013.03.01


Colonization studies previously performed with a green-fluorescent-protein, GFP, labeled derivative of Bacillus amyloliquefaciens FZB42 revealed that the bacterium behaved different in colonizing surfaces of plant roots of different species (Fan et al., 2012). In order to extend these studies and to elucidate which genes are crucial for root colonization, we applied targeted mutant strains to Arabidopsis seedlings. The fates of root colonization in mutant strains impaired in synthesis of alternative sigma factors, non-ribosomal synthesis of lipopeptides and polyketides, biofilm formation, swarming motility, and plant growth promoting activity were analyzed by confocal laser scanning microscopy. Whilst the wild-type strain heavily colonized surfaces of root tips and lateral roots, the mutant strains were impaired in their ability to colonize root tips and most of them were unable to colonize lateral roots. Ability to colonize plant roots is not only dependent on the ability to form biofilms or swarming motility. Six mutants, deficient in abrB-, sigH-, sigD-, nrfA-, yusV and RBAM017410, but not affected in biofilm formation, displayed significantly reduced root colonization. The nrfA- and yusV-mutant strains colonized border cells and, partly, root surfaces but did not colonize root tips or lateral roots.


Arabidopsis thaliana;Bacillus amyloliquefaciens;biocontrol;plant growth promotion;root colonization


  1. Branda, S. S., González-Pastor, J. E., Ben-Yehuda, S., Losick, R. and Kolter, R. 2001. Fruiting body formation by Bacillus subtilis. Proc. Natl. Acad. Sci. USA 98:11621−11626.
  2. Fan, B., Chen, X. H., Budiharjo, A., Bleiss, W., Vater, J. and Borris, R. 2011. Efficient colonization of plant roots by the plant growth promoting bacterium Bacillus amyloliquefaciens FZB42, engineered to express green fluorescent protein. J. Biotechnol. 151:303−311.
  3. Idris, E. E., Iglesias, D. J., Talon, M. and Borris, R. 2007. Tryptophan-dependent production of indole-3-acetic acid (IAA) affects level of plant growth promotion by Bacillus amyloliquefaciens FZB42. Mol. Plant-Microbe Interact. 20:619−626.
  4. Idriss, E. E., Makarewicz, O., Farouk, A., Rosner, K., Greiner, R., Bochow, H., Richter, T. and Borris, R. 2002. Extracellular phytase activity of Bacillus amyloliquefaciens FZB45 contributes to its plant-growth-promoting effect. Microbiology 148:2097−2109.
  5. Koumoutsi, A., Chen, X. H., Henne, A., Liesegang, H., Hitzeroth, G., Franke, P., Vater, J. and Borris, R. 2004. Structural and functional characterization of gene clusters directing nonribosomal synthesis of bioactive cyclic lipopeptides in Bacillus amyloliquefaciens strain FZB42. J. Bacteriol. 186:1084−1096.
  6. Koumoutsi, A., Chen, X. H., Vater, J. and Borris, R. 2007. DegU and YczE positively regulate the synthesis of bacillomycin D by Bacillus amyloliquefaciens strain FZB42. Appl. Environ. Microbiol. 73:6953−6964.
  7. Le Breton, Y., Mohapatra, N. P. and Haldenwang, W. G. 2006. In vivo random mutagenesis of Bacillus subtilis by use of TnYLB-1, a mariner-based transposon. Appl. Environ. Microbiol. 72:327−333.
  8. Lugtenberg, B. and Kamilova, F. 2009. Plant-growth-promoting rhizobacteria. Annu. Rev. Microbiol. 63:541−556.
  9. Budiharjo, A. 2011. Plant-Bacteria Interactions: Molecular Mechanisms of Phytostimulation by Bacillus amyloliquefaciens FZB42. Bacterial Genetics. Berlin, Humboldt-University Berlin. PhD.
  10. Chen, X. H., Koumoutsi, A., Scholz, R., Eisenreich, A., Schneider, K., et al. 2007. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat. Biotechnol. 25:1007−1014.
  11. Chen, X. H., Koumoutsi, A., Scholz, R., Schneider, K., Vater, J., Süssmuth, R., Piel, R. and Borris, R. 2009a. Genome analysis of Bacillus amyloliquefaciens FZB42 reveals its potential for biocontrol of plant pathogens. J. Biotechnol. 140:27−37.
  12. Chen, X. H., Scholz, R., Borris, M., Junge, H., Mogel, G., Kunz, R. and Borris, R. 2009b. Difficidin and bacilysin produced by plant-associated Bacillus amyloliquefaciens are efficient in controlling fire blight disease. J. Biotechnol. 140:38−44.
  13. Chin-A-Woeng, T. F. C., Bloemberg, G. V., Mulders, I. H., Dekkers, L. C. and Lugtenberg, B. J. 2000. Root colonization by phenazine-1-carboxamide-producing bacterium Pseudomonas chlororaphis PCL1391 is essential for biocontrol of tomato foot and root rot. Mol. Plant-Microbe Interact. 13:1340−1345.
  14. Fan, B., Borriss, R., Bleiss, W. and Wu, X. 2012. Gram-positive rhizobacterium Bacillus amyloliquefaciens FZB42 colonizes three types of plants in different patterns. J. Microbiol. 50:38−44.
  15. Borriss, R., Chen, X. H., Ruecket, C., Blom, J., Becker, A., Baumgarth, B., Fan, B., Pukall, R., Schumann, P. Sproer, C., Junge, H., Vater, J., Pühler, A. and Klenk, H. P. 2011. Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons. Int. J. Syst. Evol. Microbiol. 61(Pt 8):1786−1801.
  16. Mariappan, A., Makarewicz, O., Chen, X. H. and Borris, R. 2012. Two-component response regulator DegU controls the expression of bacilysin in plant-growth-promoting bacterium Bacillus amyloliquefaciens FZB42. J. Mol. Microbiol. Biotechnol. 22:114−125.
  17. Scholz, R., Molohon, K. J., Nachtigall, J., Vater, J., Markley, A. L., Süssmuth, R. D., Mitchell, D. A. and Borris, R. 2011. Plantazolicin, a novel microcin B17/streptolysin S-like natural product from Bacillus amyloliquefaciens FZB42. J. Bacteriol. 193:215−224.

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