An Atlas of Macroalgal Epiphytic Bacterial Genomes Reveals Broad Biosynthetic and Metabolic Potential

Abstract

Macroalgal surfaces harbor epiphytic bacterial communities with potential roles in host metabolism, stress tolerance, chemical defense, and ecological interactions, yet their genome-resolved diversity remains poorly characterized across major macroalgal lineages. Here, we reconstructed epiphytic bacterial metagenome-assembled genomes (MAGs) from 108 culture-derived macroalgal shotgun datasets originally generated for host genome sequencing, together with three additional macroalgal species with paired high-accuracy long-read and short-read data. Benchmarking of matched MAGs showed comparable assembly sizes and genome quality between sequencing strategies, supporting short-read-based MAG recovery from host-associated macroalgal datasets. Across all datasets, we recovered 3272 preliminary MAGs and retained 1915 non-redundant, quality-controlled MAGs, of which 1543 could not be assigned to species-level taxa by GTDB-Tk based on ANI. These genomes were dominated by Pseudomonadota, Bacteroidota, and Planctomycetota, which together represented 88.3% of the collection, and included many species-level unassigned genomes. Functional analyses identified 12,950 biosynthetic gene clusters grouped into 7985 gene cluster families, 20 biosynthetically rich MAGs, and 222 KEGG modules. This atlas provides a genome-resolved resource for studying macroalgal holobiont function and microbial natural product potential.