Bacterial endophytes of sweet potato tuberous roots affected by the plant genotype and growth stage

• The bacterial endophytes in the tubers of sweet potato genotypes were studied.
• The endophytic bacterial communities were influenced by the plant growth stage.
• The sweet potato genotypes influenced the endophytes only at the first sampling.
• Bacteria from the Proteobacteria, Actinobacteria and Firmicutes phyla were found.

This study aimed to characterize the endophytic bacterial communities in the tuberous roots of three sweet potato genotypes, IPB-149, IPB-137 and IPB-052. The hypothesis is that plant genotype and growth stage influence bacterial composition. Using cultivation-independent (Polymerase chain reaction-denaturing gradient gel electrophoresis–PCR-DGGE–based on 16S rRNA gene fragments and DNA sequencing) and cultivation-dependent (bacterial isolation) methods it was shown that plant growth stage influenced the endophytic bacterial communities, and that plant genotypes also significantly influenced these communities, but only at the first sampling (three months after planting). A total of 93 strains were isolated from the roots of the different genotypes, and 59 groups were revealed by BOX-PCR. Bacteria from the Proteobacteria, Actinobacteria and Firmicutes phyla were found, and Bacillus strains predominated in the roots of IPB-052 and IPB-149 (72% and 79%, respectively). Almost half of the strains isolated from IPB-137 roots (47%) were Gammaproteobacteria. In addition, the isolates were tested for antimicrobial substance and indole acetic acid production, organic and inorganic phosphate solubilization, siderophore production and for the presence of nitrogenase gene. All isolates with antagonistic activity against the sweet potato-pathogenic fungus Plenodomus destruens belong to the genus Bacillus. Indole acetic acid production was predominantly found among the strains isolated from IPB-137; once again suggesting an influence of the sweet potato genotype on its endophytes.