Seagrasses host unique and vulnerable microbiomes, structured by inter-domain microbial interactions.

Seagrass meadows are vital for coastal ecosystems but are declining worldwide due to human impacts. Microbes play key roles in seagrass health, yet their diversity and functions remain poorly understood. We investigated prokaryotes and microbial eukaryotes associated with different seagrass species across multiple regions by analyzing leaves, roots, and surrounding sediments. Microbiome similarity was minimal among seagrass and sediments (<5% shared small subunit (SSU|)-rRNA amplicon sequence variants -ASVs), among species (<2%), and between leaves and roots within species (<12%). Seagrass species, rather than environmental factors, primarily shaped microbiome composition. Network analysis revealed all seagrass microbiomes as highly vulnerable to the loss of keystone microbes, including bacterial taxa potentially supporting seagrass health through nutrient supply and detoxification processes. Although microbial eukaryotes have been traditionally linked to seagrass diseases, we found mostly positive interactions with keystone bacteria, suggesting overlooked roles in holobiont stability. These findings provide a benchmark for integrating microbiomes into seagrass conservation.