Functional partitioning among core and peripheral bacteria shapes the giant kelp holobiont

The giant kelp Macrocystis pyrifera hosts diverse microbial communities integral to its ecological function, yet the distribution of microbial functions across different holobionts remains poorly resolved. Here, we used genome-resolved metagenomics to examine how microbial occupancy shapes genomic strategies and functional traits within the M. pyrifera microbiome, analyzing kelp-associated bacteria from eight sites spanning ~ 1,000 km along the southeastern Pacific coast and reconstructing 214 metagenome-assembled genomes (MAGs). We identified a bacterial core that persists across sites with streamlined genomes enriched in photosynthetic and sulfur-cycling pathways, and peripheral bacteria with larger, more plastic genomes, specialized in nitrogen cycling and adaptive defense systems. Core taxa also exhibited enhanced polysaccharide degradation and complex quorum-sensing networks, while peripheral or restricted taxa showed greater environmental sensing and antibiotic resistance traits. These findings reveal a partitioning of microbial functions, highlighting complementary ecological roles among microbial partners hosted by the kelp across a broad spatial range.