Evaluating host to host transplants as a method to study plant bacterial assembly

The ability to predict plant microbiome assembly will enable new bacterial-based technologies for agriculture. A major step towards this is quantifying the roles of ecological processes on community assembly. This is challenging, in part because individuals within a populations of host plants may be colonised by different assemblages of bacteria, simply because of variation in soil communities proximal to said plants. This creates uncertainty because it is difficult to estimate if the absence of a given species was a) because it was not present to colonise the plant or b) it went locally extinct from competition, predation or similar. To address this, the authors develop a mesocosm system to study bacterial communities of individual plants by replicated transplantation to a recipient host plant population, ensuring new hosts receive a homogenous species pool for colonisation. We sought to understand which factors affected the transplant and, what the main drivers of variation in the model communities were. A nested factorial design was used to investigate the transplantation of cultured or total, root or leaf associated bacterial communities from donor host species to surrogate host species. Specific metrics were developed to quantify colonisation efficiency of communities. The results show the root communities were more effectively transplanted than leaf communities, and a higher proportion of cultured communities were recovered than total communities. For root communities the strongest drivers of beta diversity was the donor host species, and for leaves it was the surrogate host species. Overall the results reveal that root, but not leaf communities are suited to this system reflecting their differing ecological drivers.