Abstract
<title>Abstract</title> <p> <bold>Plasmids are key drivers of microbial evolution and horizontal gene transfer, yet their role in the sponge (</bold> <bold>Porifera</bold> <bold>) holobiont remains largely unclear. Here, we analyzed 526 marine sponge metagenomes worldwide and recovered 6,945 reference sponge plasmids, revealing a vast, largely uncharacterized genetic reservoir. Two-thirds of sponge plasmid-encoded protein families were absent from major reference databases. Plasmid abundance and diversity were significantly higher in high microbial-abundance (HMA) sponges than low microbial-abundance (LMA) sponges, and plasmid distributions largely segregated between the HMA-LMA dichotomy, indicating strong host-associated filtering. The most widespread and abundant plasmids were enriched in genes linked to plasmid stability and defense, including toxin-antitoxin and restriction-modification systems, suggesting adaptive advantages for prokaryotic hosts. Notably, some plasmids encoded putative enzymes involved in steroid biotransformation and secondary metabolites or antibiotic production, implicating plasmids in host hormone physiology and host-microbe interactions. Together, these findings reveal plasmids as major, previously overlooked contributors to sponge holobiont adaptation and functional plasticity</bold> . </p>