Biotic interactions between eukaryotes and their associated bacterial communities are extremely widespread and often have profound effects on host health and fitness. Despite the relevance of such interactions, we do not yet understand the ecological and evolutionary implications related to symbiont acquisition in diverse microbiomes. Making use of the siphonous green alga Bryopsis plumosa, we will link the mode of acquisition, either vertical or horizontal, of the (endo)symbiotic bacterial community to the coevolutionary dynamics between bacteria and their host. Bacterial transmission through the different reproductive strategies of Bryopsis will be studied by means of high throughput 16S amplicon sequencing and fluorescence in situ hybridisation. In addition, the potential to acquire new bacteria during protoplast formation, a wounding response which simultaneously functions as a method of propagation, will be tested by tracing different fluorescently tagged bacteria during this process. The metagenome-assembled genomes of Bryopsis associated bacteria will be used to infer selection and drift effects on the bacteria and to identify the functional relevance of these bacteria for the host. By relating mode of transmission and partner fidelity to bacterial genome attributes, the underlying ecological and evolutionary processes regulating the interactions within this system will be identified.