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Background  Despite all the benefits assigned to the genetically modified plants, there are still no sufficient data available in literature concerning the possible effects on the microbial communities associated with these plants. Therefore, this study was aimed at examining the effects of the genetic modifications of two transgenic maize genotypes (MON810 – expressing the insecticidal Bt-toxin and TC1507 – expressing the insecticidal Bt-toxin and the herbicide resistance PAT [phosphinothricin- N -acetyltransferase]) on their endophytic microbial communities, in comparison to the microbial community found in the near-isogenic non-transgenic maize (control).    Results  The structure of the endophytic communities (Bacteria, Archaea and fungi) and their composition (Bacteria) were evaluated by denaturing gradient gel electrophoresis (DGGE) and the construction of clone libraries, respectively. DGGE analysis and the clone libraries of the bacterial community showed that genotype TC1507 slightly differed from the other two genotypes. Genotype TC1507 showed a higher diversity within its endophytic bacterial community when compared to the other genotypes. Although some bacterial genera were found in all genotypes, such as the genera  Burkholderia ,  Achromobacer  and  Stenotrophomonas , some were unique to genotype TC1507. Moreover, OTUs associated with  Enterobacter  predominated only in TC1507 clone libraries.    Conclusion  The endophytic bacterial community of the maize genotype TC1507 differed from the communities of the maize genotype MON810 and of their near-isogenic parental genotypes (non-Bt or control). The differences observed among the maize genotypes studied may be associated with insertion of the gene coding for the protein PAT present only in the transgenic genotype TC1507.

Endophytic microbial community in two transgenic maize genotypes and in their near-isogenic non-transgenic maize genotype