Early life stages of macroalgae depend on microbial communities that mediate their settlement, development, and survival, yet the ecological processes structuring these communities still remain poorly understood. In particular, the role of microbial predators in structuring host-associated microbiomes has rarely been tested experimentally, despite the ubiquity of predators in natural systems.
Here, we disentangle bottom-up and top-down controls on early macroalgal holobiont assembly and host survival using replicated, closed microcosms of the model Rhodophyte seaweed Palmaria palmata. We manipulated settlement substrate type, and trophic structure by independently adding probiotic bacterial communities ('microbial priming'), bacterivorous protists and eukaryvorous protists prior to and during the initial colonisation and settlement of P. palmata spores, respectively. Community dynamics were tracked over ten weeks using 16S and 18S rRNA gene sequencing alongside measurements of host settlement, growth, and survival rates.
Trophic complexity fundamentally restructured microbiome assembly and host outcomes. Notably, substrate type influenced spore settlement density; and bacterivorous protists increased bacterial diversity and homogenised community composition, consistent with predator-mediated regulation of lower trophic levels. Whereas eukaryovorous protists enhanced early host survival, likely by suppressing bacterivores and stabilising beneficial bacterial assemblages.
Together, these results demonstrate that microbial predators play a central yet underappreciated role in shaping early holobiont assembly and host survival. Rather than destabilising microbiomes, trophic interactions can promote diversity and host survival by regulating microbial dominance. These findings highlight the importance of incorporating multi-trophic interactions into microbiome ecology and suggest that early predator-mediated processes can have lasting consequences for host recruitment and resilience.