Stable Bacterial Cores and Patchy Eukaryotic Communities Shape the Summer Microbiomes of Patagonian Fjord Ecosystems Across Spatial, Functional and Temporal Gradients

ABSTRACT Patagonian fjord ecosystems are shaped by a combination of glacial, oceanographic and climatic factors that generate physical and chemical gradients. In these environments, microbial communities play essential roles in ecosystem functioning, with temporal and depth‐related compositional shifts often linked to glacial meltwater input. In this study, we characterised microbial communities from southern Patagonia and the Drake Passage using high‐throughput sequencing of the 16S and 18S rRNA genes across seven study areas. We found that bacterial and eukaryotic communities differed across the sampling areas, with salinity showing the strongest association with community composition in both microbial domains. Bacterial core communities, defined here using a combined occupancy–abundance approach, were widespread throughout fjords and channels, whereas eukaryotic core communities were spatially restricted. Network analyses revealed contrasting modes of community organisation across these fjord systems, with land‐terminating glaciers displaying more hub microorganisms (highly connected bacteria and microbial eukaryotes) than water‐terminating glaciers. Short‐term analyses identified microbial taxa that varied significantly in abundance over a 10‐day period and were present in inter‐domain co‐occurrence networks. Together, these results identify a small set of abundant and well‐connected microorganisms that structure summer microbiomes in Patagonian fjords and may link glacial runoff regimes into distinct modes of community interactions.