Antibiotic treatment impaired growth of tobacco in vitro shoots is associated with oxidative injury and reduced microbiome diversity

Plant in vitro cultures initiated from surface-sterilized explants often harbor complex microbial community. Antibiotics are commonly used to decontaminate plant tissue culture or during genetic transformation, however, the effect of antibiotic treatment on the diversity of indigenous microbial population and consequences for performance of the tissue culture are not completely understood. Therefore, the aim of this study was to assess the effect of antibiotic treatment on the growth and stress level of tobacco (Nicotiana tabacum L.) in vitro shoots as well as the composition of plant-associated microbiome. The study revealed that shoot cultivation on medium supplemented with 250 mg L−1 timentin resulted in 29 ± 4% reduced biomass accumulation and 1.2–1.6 fold higher level of oxidative stress injury compared to control. Moreover, the growth properties of shoots were only partially restored after transfer to medium without antibiotic. Shoot microbiome analysis using multi-variable region-based 16S rRNA sequencing revealed abundant microbial community in the control tobacco shoots, including bacteria from 59 families, however, it was largely dominated by Mycobacteriaceae. The antibiotic treatment resulted in a decline of species richness (the number of families was reduced 4.5-fold) and increased domination by the Mycobacteriaceae family. The results imply that the diversity of plant-associated microbiome might represent a significant factor contributing to the efficient propagation of in vitro tissue culture.