Background/Question/Methods Plant microbiomes comprise various microorganisms, including prokaryotes, eukaryotes, and viruses. They have been shown to be the key determinant for the wellness of plant hosts. However, little is known about how interactions, especially the trophic interactions, between microbes from different domains modify the importance of microbiomes for plant hosts. Using duckweed Lemna minor and its microbiomes, I experimentally examined the influences of host-parasite and predator-prey interactions within the microbiomes on the growth and ecosystem functioning of L. minor populations. I prepared two axenic L. minor lineages, using two randomly selected clones. I respectively extracted two bacterial and bacteriophage communities from two L. minor’s natural microbiomes. I also prepared an axenic culture of Tetrahymena pyriformis, a common bacterivorous protist in freshwater ponds. Bacteriophages served as the parasites to the bacteria, while T. pyriformis as the predator. The experiment was replicated with four L. minor-microbiome combinations, and the presence/absence of parasitism or predation was manipulated. I performed the experiment with aqueous microcosms. After 35 days (~ten generations of L. minor), I measured L. minor abundance for its growth and total phosphorus (TP) removal as the ecosystem function. Results/Conclusions My results showed that parasitism and predation in microbiomes strongly influenced host growth and ecosystem functioning. Bacterial inoculation had only a moderate effect on L. minor abundance or TP when compared to the axenic control. However, the presence of parasites significantly reduced host growth and TP removal rate, whereas the predator promoted host growth and TP removal. Bacterial community 16S rRNA sequencing suggested that parasitism and predation drove changes in microbiome species richness and relative abundance, which might cause the differentiated microbiome effects on L. minor. These results demonstrate trophic interactions in microbiomes have strong influences on their hosts.