Deciphering Macroalgal Microbiomes: Metagenomic Insights, Ecological Roles and Bioprospecting Potential

Macroalgae host complex microbial communities that influence surface colonization, development, nutrient transformation, carbohydrate turnover, environmental responses, and the production of potentially valuable metabolites. Advances in shotgun metagenomics and genome-resolved analysis have greatly expanded access to this functional diversity, but they have also increased the risk of conflating genomic potential with biological activity or host benefit. This narrative review evaluates the bacterial component of macroalgal microbiomes—the component for which mechanistic and experimentally validated evidence is most extensive—through a framework that separates what has been proven from what is merely predicted, distinguishing functional prediction from expression, biochemical activity, metabolite exchange, host response, and experimental causality. Particular attention is given to bacteria-dependent morphogenesis, metabolic complementarity, environmental acclimation, carbohydrate-active enzymes and polysaccharide-utilization loci, biosynthetic gene clusters, and the translational potential of seaweed-associated microorganisms. Comparative perspectives from microalgal and cyanobacterial systems are used to identify principles that generalize across algal microbiomes while emphasizing the distinctive spatial and chemical complexity of macroalgal surfaces. Invasive and bloom-forming macroalgae provide an additional ecological context in which microbial functional redundancy, recruitment flexibility, and dominant populations may shape whole-community profiles. An illustrative, hypothesis-generating taxon-attribution case study, based on single metagenomic datasets from Rugulopteryx okamurae and Sargassum sp. holobionts in the Azores, which confounds host identity with sampling location, time, and thallus condition, shows that the disproportionate genomic contribution of the genus Cobetia measurably alters the interpretation of a specific subset of community-level KEGG pathway contrasts, while the majority of pathway-level and taxon-specific signals discussed retain their direction after this taxon’s exclusion and residual-community renormalization. Together, these analyses argue that macroalgal microbiome research should move beyond inventories of predicted functions toward explicit taxonomic attribution, experimental validation, and ecological context. Such integration will be essential for establishing which microbial functions are ecologically consequential and which can be translated reproducibly into biotechnology.