Resilience of blue carbon microbiomes in response to ecological and anthropogenic filtering

Global change is threatening the microbial consortia that sustain the services and functions of blue carbon ecosystems (BCEs), but little is known about how the composition and functioning of these consortia will respond to ecological and anthropogenic stressors. Here, we construct a continental-scale microbial genome catalog from 116 representative habitats, including mangrove forests, saltmarshes, and seagrass meadows, and recover 1954 non-redundant metagenome-assembled genomes (MAGs). We find that BCE microbiomes are taxonomically distinct from terrestrial, marine, and marginal sea ecosystems, with ecosystem type and spatial distribution further differentiating community composition. Environmental filtering constrains taxonomic composition, yet functional composition is largely invariant to taxonomic turnover. Specialist KEGG orthologues underpin over 90% of metabolic functions conserved across all BCEs. Notably, for carbon fixation, phylogenetically divergent functional lineages provide functional redundancy that can mitigate the effects of species replacement. Collectively, our study quantifies the vulnerability of BCEs to future species loss while providing a scientific basis for confidence that blue carbon ecosystems, supported by phylogenetic redundancy, may sustain functional stability despite environmental change.