Effects of in vitro culture, transformation, and RNA interference on foliar fungal microbiomes in poplar

Plant transformation is a common means for gene insertion and editing during scientificresearch and biotechnology; however, its effects on plant microbiomes are unknown. Weused ITS metabarcoding to evaluate the effects of transformation includingorganogenesis, propagation, and field acclimation on the foliar fungal microbiome inpoplar trees and at a field site over two growing seasons. Sterile, micropropagation-derived trees grown in a greenhouse were largely uncolonized after 50 days. Onceestablished in the field, fungal communities were nearly as diverse as in well-establishedtrees of the same genotype after one season of growth. We did not detect effects ofmicropropagation, or the use of antibiotic selection and organogenesis, on subsequentfoliar fungal communities. The expression of gene silencing-inducing constructs directedagainst the Septoria canker fungus also had no detectable effect on non-targetcommunities. Our results suggest that micropropagation, genetic transformation andassociated antibiotic selection and organogenesis, and the expression of antifungal RNAi,had minimal, if any, impacts on subsequent foliar microbiomes of field-grown Populus.