Decoding a Microbial Community for Healthy Kelp: 403 MAGs from the World’s Largest Kelp Farming Region

Kelp is economically and ecologically significant, with its organic nutrient-rich aquaculture water harboring diverse microbial communities that critically influence kelp health and productivity. To characterize these communities, we collected ten water samples from major kelp farming areas and reconstructed 403 medium- to high-quality Metagenome-Assembled Genomes (MAGs). Of these, 110 (27.3%) met high-quality criteria (completeness >90%, contamination <5%). Phylogenomic analysis classified these MAGs into 21 archaeal and 382 bacterial species across 19 phyla, with Pseudomonadota (n = 217), Bacteroidota (n = 74), and Patescibacteria (n = 24) as the dominant groups. UpSet plot analysis revealed the presence of a core set of 30 MAGs across all sampling sites. Notably, diseased samples exhibited a marked increase in Pseudomonadota MAGs, suggesting their potential as biomarkers for disease monitoring. Together, these findings provide foundational insights into the microbial ecology of kelp aquaculture systems, supporting improved disease management and sustainable practices.