Abstract
Coral reefs face severe threats from human activity, resulting in drastic biodiversity loss. Despite the urgency of safeguarding these ecosystems, we know little about the ecological impacts of losing coral reef host-associated microbial communities (microbiomes). Here, we experimentally studied the microbiomes attached to or released from seven benthic reef hosts belonging to the functional groups of stony corals, soft corals, macroalgae, and sponges while manipulating the coral reef metacommunity to mimic biodiverse or degraded reef habitats. Developing an ecological framework, we found host species and functional groups to show distinct patterns of interacting with the environment (i.e. by exuding, maintaining, acquiring, or exchanging microbiome members), with habitat biodiversity primarily influencing microbial acquisition. In a degraded compared to a biodiverse habitat, the microbiomes of stony corals were less connected to soft corals and sponges, while those of soft corals, macroalgae, and sponges became more tightly linked. Our study demonstrates that a decline in metacommunity biodiversity is not merely associated with a proportional loss in microbial diversity; rather, it triggers complex changes in the microbial interactions among the persisting hosts with each other and the environment. These results emphasize the importance of conserving coral reef host biodiversity to preserve the intricately linked microbiomes-and with them the ecosystem functions and services coral reefs provide.