biostudies-literatureMara PNational Science Foundation (NSF)National Science Foundation929https://www.ebi.ac.uk/biostudies/studies/S-EPMC11123730biostudies-literatureUnknown12(5)Plasmids are mobile genetic elements known to carry secondary metabolic genes that affect the fitness and survival of microbes in the environment. Well-studied cases of plasmid-encoded secondary metabolic genes in marine habitats include toxin/antitoxin and antibiotic biosynthesis/resistance genes. Here, we examine metagenome-assembled genomes (MAGs) from the permanently-stratified water column of the Cariaco Basin for integrated plasmids that encode biosynthetic gene clusters of secondary metabolites (smBGCs). We identify 16 plasmid-borne smBGCs in MAGs associated primarily with Planctomycetota and Pseudomonadota that encode terpene-synthesizing genes, and genes for production of ribosomal and non-ribosomal peptides. These identified genes encode for secondary metabolites that are mainly MicroorganismsPlasmid-Borne Biosynthetic Gene Clusters within a Permanently Stratified Marine Water Column.PMC11123730OCE-1259110OCE-1336082 To Virginia EdgcombOCE-1335436OCE-1335436 and OCE-1259110 to Gordon T TaylorOCE-1336082Mara PPachiadaki MGSuter EGeller-McGrath DTaylor GTEdgcomb VPfalsePlasmid-Borne Biosynthetic Gene Clusters within a Permanently Stratified Marine Water Column.Plasmids are mobile genetic elements known to carry secondary metabolic genes that affect the fitness and survival of microbes in the environment. Well-studied cases of plasmid-encoded secondary metabolic genes in marine habitats include toxin/antitoxin and antibiotic biosynthesis/resistance genes. Here, we examine metagenome-assembled genomes (MAGs) from the permanently-stratified water column of the Cariaco Basin for integrated plasmids that encode biosynthetic gene clusters of secondary metabolites (smBGCs). We identify 16 plasmid-borne smBGCs in MAGs associated primarily with Planctomycetota and Pseudomonadota that encode terpene-synthesizing genes, and genes for production of ribosomal and non-ribosomal peptides. These identified genes encode for secondary metabolites that are mainly 2024-01-01T00:00:00Z2024 May2026-06-28T03:09:33.825Z2026-06-28T03:05:14.875ZS-EPMC111237303879275910.3390/microorganisms12050929