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Background  The plant growth-promoting rhizobacteria (PGPR) strain  Bacillus amyloliquefaciens  SQR9, isolated from the cucumber rhizosphere, protects the host plant from pathogen invasion and promotes plant growth through efficient root colonization. The phytohormone indole-3-acetic acid (IAA) has been suggested to contribute to the plant-growth-promoting effect of  Bacillus  strains. The possible IAA synthetic pathways in  B .  amyloliquefaciens  SQR9 were investigated in this study, using a combination of chemical and genetic analysis.    Results  Gene candidates involved in tryptophan-dependent IAA synthesis were identified through tryptophan response transcriptional analysis, and inactivation of genes  ysnE ,  dhaS ,  yclC , and  yhcX  in SQR9 led to 86, 77, 55, and 24 % reductions of the IAA production, respectively. The genes  patB  (encoding a conserved hypothetical protein predicted to be an aminotransferase),  yclC  (encoding a UbiD family decarboxylase), and  dhaS  (encoding indole 3-acetaldehyde dehydrogenase), which were proposed to constitute the indole-3-pyruvic acid (IPyA) pathway for IAA biosynthesis, were separately expressed in SQR9 or co-expressed as an entire IAA synthesis pathway cluster in SQR9 and  B. subtilis  168, all these recombinants showed increased IAA production. These results suggested that gene products of  dhaS ,  patB ,  yclB ,  yclC ,  yhcX  and  ysnE  were involved in IAA biosynthesis. Genes  patB ,  yclC  and  dhaS  constitute a potential complete IPyA pathway of IAA biosynthesis in SQR9.    Conclusions  In conclusion, biosynthesis of IAA in  B. amyloliquefaciens  SQR9 occurs through multiple pathways.    Electronic supplementary material  The online version of this article (doi:10.1186/s12934-015-0323-4) contains supplementary material, which is available to authorized users.

Analysis and cloning of the synthetic pathway of the phytohormone indole-3-acetic acid in the plant-beneficial Bacillus amyloliquefaciens SQR9