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In these environments, microbial communities play essential roles in ecosystem functioning, with temporal and depth\u2010related compositional shifts often linked to glacial meltwater input. In this study, we characterised microbial communities from southern Patagonia and the Drake Passage using high\u2010throughput 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\u2013abundance 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\u2010terminating glaciers displaying more hub microorganisms (highly connected bacteria and microbial eukaryotes) than water\u2010terminating glaciers. Short\u2010term analyses identified microbial taxa that varied significantly in abundance over a 10\u2010day period and were present in inter\u2010domain co\u2010occurrence networks. Together, these results identify a small set of abundant and well\u2010connected microorganisms that structure summer microbiomes in Patagonian fjords and may link glacial runoff regimes into distinct modes of community interactions.<\/jats:p>","DOI":"10.1111\/1758-2229.70412","type":"journal-article","created":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T05:17:31Z","timestamp":1788931051000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Stable Bacterial Cores and Patchy Eukaryotic Communities Shape the Summer Microbiomes of Patagonian Fjord Ecosystems Across Spatial, Functional and Temporal Gradients"],"prefix":"10.1111","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4388-6791","authenticated-orcid":false,"given":"Nicole","family":"Trefault","sequence":"first","affiliation":[{"name":"Centro GEMA\u2010Gen\u00f3mica, Ecolog\u00eda y Medio Ambiente Universidad Mayor  Santiago Chile"},{"name":"Millenium Nucleus in Marine Agronomy of Seaweed Holobionts (MASH)  Puerto Montt Chile"},{"name":"FONDAP Center IDEAL\u2010 Dynamics of High Latitude Marine Ecosystem  Valdivia Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-1531-6721","authenticated-orcid":false,"given":"Susana","family":"Rodr\u00edguez\u2010Marconi","sequence":"additional","affiliation":[{"name":"Centro GEMA\u2010Gen\u00f3mica, Ecolog\u00eda y Medio Ambiente Universidad Mayor  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0061-3355","authenticated-orcid":false,"given":"Mar\u00eda Fernanda","family":"Manrique\u2010de\u2010la\u2010Cuba","sequence":"additional","affiliation":[{"name":"Centro GEMA\u2010Gen\u00f3mica, Ecolog\u00eda y Medio Ambiente Universidad Mayor  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0602-2406","authenticated-orcid":false,"given":"Patricio","family":"Flores\u2010Herrera","sequence":"additional","affiliation":[{"name":"Centro GEMA\u2010Gen\u00f3mica, Ecolog\u00eda y Medio Ambiente Universidad Mayor  Santiago Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3808-197X","authenticated-orcid":false,"given":"Clara Natalia","family":"Rodr\u00edguez\u2010Fl\u00f3rez","sequence":"additional","affiliation":[{"name":"Secretariat of Environment and Sustainable Development of Boyac\u00e1  Concepci\u00f3n Colombia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4022-9101","authenticated-orcid":false,"given":"Bernd","family":"Krock","sequence":"additional","affiliation":[{"name":"Alfred Wegener Institut\u2010Helmholtz Zentrum f\u00fcr Polar\u2010und Meeresforschung  Bremerhaven Germany"},{"name":"Centro de Investigaci\u00f3n Oceanogr\u00e1fica COPAS COASTAL Universidad de Concepci\u00f3n  Concepci\u00f3n Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,8]]},"reference":[{"issue":"2","key":"e_1_2_10_2_1","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.seares.2011.03.005","article-title":"Seasonal Phytoplankton Dynamics in Extreme Southern South America (Beagle Channel, Argentina)","volume":"66","author":"Almandoz G. 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