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Biodiversity and food chain length each can strongly influence ecosystem functioning, yet their interactions rarely have been tested. We manipulated grazer diversity in seagrass mesocosms with and without a generalist predator and monitored community development. Changing food chain length altered biodiversity effects: higher grazer diversity enhanced secondary production, epiphyte grazing, and seagrass biomass only with predators present. Conversely, changing diversity altered top-down control: predator impacts on grazer and seagrass biomass were weaker in mixed-grazer assemblages. These interactions resulted in part from among-species trade-offs between predation resistance and competitive ability. Despite weak impact on grazer abundance at high diversity, predators nevertheless enhanced algal biomass through a behaviourally mediated trophic cascade. Moreover, predators influenced every measured variable except total plant biomass, suggesting that the latter is an insensitive metric of ecosystem functioning. Thus, biodiversity and trophic structure interactively influence ecosystem functioning, and neither factor’s impact is predictable in isolation.

High plant species richness can enhance primary production, animal diversity, and invasion resistance. Yet theory predicts that plant and herbivore diversity, which often covary in nature, should have countervailing effects on ecosystem properties. Supporting this, we show in a seagrass system that increasing grazer diversity reduced both algal biomass and total community diversity, and facilitated dominance of a grazer-resistant invertebrate. In parallel with previous plant results, however, grazer diversity enhanced secondary production, a critical determinant of fish yield. Although sampling explained some diversity effects, only the most diverse grazer assemblage maximized multiple ecosystem properties simultaneously, producing a distinct ecosystem state. Importantly, ecosystem responses at high grazer diversity often differed in magnitude and sign from those predicted from summed impacts of individual species. Thus, complex interactions, often opposing plant diversity effects, arose as emergent consequences of changing consumer diversity, advising caution in extrapolating conclusions from plant diversity experiments to food webs.