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Here, we analyzed 319 medium- to high-quality metagenome-assembled genomes (MAGs) recovered from four Antarctic sites (Whalers Bay, Crater Lake, Fumarole Bay, and Hannah Point) to investigate the relationship between geochemical gradients, biosynthetic gene clusters (BGCs), and antimicrobial resistance genes (ARGs). Integrating genome-resolved metagenomics, biosynthetic mining, resistome profiling, and environmental analyses, we identified 1,197 BGCs, with terpene clusters representing more than 25% of the total. Several biosynthetic hotspots were detected, including an Acidobacteriota MAG harboring 62 BGCs. Resistome composition exhibited strong site-specific structuring and was significantly associated with geochemical variables, particularly cobalt, iron, organic carbon, and thermal variation. Network analyses revealed highly connected MAGs affiliated with Pseudomonadota and Actinomycetota, linking diverse BGC and ARG classes. At the same time, genomic co-localization of biosynthetic and resistance determinants suggests potential adaptive associations between secondary metabolism and self-resistance mechanisms. Together, these findings demonstrate that environmental filtering shapes both the taxonomic and functional organization of Antarctic microbiomes and highlight polar ecosystems as reservoirs of unexplored biosynthetic diversity with potential biotechnological relevance.<\/jats:p>","DOI":"10.1007\/s11274-026-05201-8","type":"journal-article","created":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T12:41:02Z","timestamp":1786711262000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Environmental filtering shapes biosynthetic potential and resistome of antarctic microbiomes"],"prefix":"10.1007","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1685-1171","authenticated-orcid":false,"given":"William B.","family":"Medeiros","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly J.","family":"Hidalgo-Martinez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel D. 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