Endophytic bacterial communities of field-grown Nicotiana attenuata plants are influenced by tissues and independent of ontogeny and JA-signaling capacities

Jasmonic acid (JA) mediates defense responses against herbivores and necrotrophic pathogens; does it influence recruitment of endophytic bacterial? We conducted a field experiment with transformed isogenic Nicotiana attenuata plants deficient in jasmonate biosynthesis (irAOC) and empty vector controls (EV), and used combination of culture-dependent and independent (454 pyrosequencing) techniques, statistical analyses and diversity indices to characterize root and leaf endophytic bacterial communities over five developmental stages, from rosette through flowering. In Pyrosequencing approach we found that endophytic bacterial communities in EV and irAOC plants are independent of developmental stages and phytohormone JA but not tissues. Both alpha and beta diversity differ significantly among irAOC, EV leaves and roots but not among genotypes. The non-metric MDS plot confirmed that bacterial endophytes are shaped by tissues but not by genotypes and ontogeny. In culture-dependent approach low species coverage and high variability among samples obscured consistent patterns in community composition that might have occurred over development stages, tissues and genotypes. Bacterial taxa from culture-dependent approaches were tentatively categorized as putative specialists and generalists based on their isolation from only one or both plant genotypes, respectively. Furthermore, we tested 18 EV and irAOC putative specialist and generalist taxa for their plant-growth promoting effects (PGP) and endophytic colonization specificity to EV and irAOC and found strong PGP-effect for three isolates which represented both specialist and generalist taxa. No alterations in elicited phytohormone levels were observed, consistent with the field results that JA-signaling does not shape endophyte communities. We infer that endophytic community’s differences among tissues might be due to the local soil community, which determine the root endophytic bacterial communities.