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Endophytes colonize an ecological niche similar to that of phytopathogens, which make them candidate for disease suppression. Anthracnose is a disease caused by  Colletotrichum  spp., a phytopathogen that can infect guarana ( Paullinia cupana ), an important commercial crop in the Brazilian Amazon. We investigated the diversity of endophytic bacteria inhabiting the phyllosphere of asymptomatic and symptomatic anthracnose guarana plants. The PCR-denaturation gradient gel electrophoresis (PCR-DGGE) fingerprints revealed differences in the structure of the evaluated communities. Detailed analysis of endophytic bacteria composition using culture-dependent and 16S rRNA clone libraries revealed the presence of  Firmicutes ,  Proteobacteria ,  Actinobacteria ,  Bacteroidetes , and  Acidobacteria  phyla . Firmicutes  comprised the majority of isolates in asymptomatic plants (2.40E −4 ). However, cloning and sequencing of 16S rRNA revealed differences at the genus level for  Neisseria  (1.4E −4 ),  Haemophilus  (2.1E −3 ) and  Arsenophonus  (3.6E −5 ) in asymptomatic plants,  Aquicella  (3.5E −3 ) in symptomatic anthracnose plants, and  Pseudomonas  (1.1E −3 ), which was mainly identified in asymptomatic plants. In cross-comparisons of the endophytic bacterial communities as a whole, symptomatic anthracnose plants contained higher diversity, as reflected in the Shannon–Weaver and Simpson indices estimation ( P  < 0.05). Similarly, comparisons using LIBSHUFF and heatmap analysis for the relative abundance of operational taxonomic units (OTUs) showed differences between endophytic bacterial communities. These data are in agreement with the NMSD and ANOSIM analysis of DGGE profiles. Our results suggest that anthracnose can restructure endophytic bacterial communities by selecting certain strains in the phyllosphere of  P. cupana . The understanding of these interactions is important for the development of strategies of biocontrol for  Colletotrichum .   Electronic supplementary material  The online version of this article (doi:10.1186/s40064-015-1037-0) contains supplementary material, which is available to authorized users.

Endophytic bacterial diversity in the phyllosphere of Amazon Paullinia cupana associated with asymptomatic and symptomatic anthracnose