DNA-based stable isotope probing enables the identification of active bacterial endophytes in potatoes

Abstract

• A 13CO2 (99 atom-%, 350 ppm) incubation experiment was performed to identify active bacterial endophytes in two cultivars of Solanum tuberosum, cultivars Desirée and Merkur. We showed that after the assimilation and photosynthetic transformation of 13CO2 into 13C-labeled metabolites by the plant, the most directly active, cultivar-specific heterotrophic endophytic bacteria that consume these labeled metabolites can be identified by DNA stable isotope probing (DNA-SIP). • Density-resolved DNA fractions obtained from SIP were subjected to 16S rRNA gene-based community analysis using terminal restriction fragment length polymorphism analysis and sequencing of generated gene libraries. • Community profiling revealed community compositions that were dominated by plant chloroplast and mitochondrial 16S rRNA genes for the 'light' fractions of 13CO2-incubated potato cultivars and of potato cultivars not incubated with 13CO2. In the 'heavy' fractions of the 13CO2-incubated endophyte DNA, a bacterial 492-bp terminal restriction fragment became abundant, which could be clearly identified as Acinetobacter and Acidovorax spp. in cultivars Merkur and Desirée, respectively, indicating cultivar-dependent distinctions in 13C-label flow. These two species represent two common potato endophytes with known plant-beneficial activities. • The approach demonstrated the successful detection of active bacterial endophytes in potato. DNA-SIP therefore offers new opportunities for exploring the complex nature of plant-microbe interactions and plant-dependent microbial metabolisms within the endosphere. © The Authors (2008).