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Yet, the microbial controls on N\u2010cycling within these groundwater\u2013seawater mixing zones remain poorly understood. We investigated the spatio\u2010temporal variations in microbial communities and their N\u2010cycling potential within an alluvial Mediterranean STE with high N concentration. We explored changes in microbial abundance, heterotrophic activity, taxonomic composition, and the abundance of N\u2010cycling genes across groundwater samples collected at several depths and distances from the shoreline in winter and summer. Microbial abundance, activity, and diversity varied strongly across hydrochemical zones according to physicochemistry and aquifer depth but showed limited seasonality. Functional predictions suggested a complex, spatially structured suite of N pathways encoded by diverse taxa occupying different STE zones, and quantitative\u2010PCR revealed niche partitioning between ammonia\u2010oxidizing archaea, prevalent in fresh\u2010groundwater, and bacterial denitrifiers enriched in deep\u2010saline layers. Multiple linear model predictions showed a stronger fit for NO\n                    <jats:sub>2<\/jats:sub>\n                    <jats:sup>\u2212<\/jats:sup>\n                    and NH\n                    <jats:sub>4<\/jats:sub>\n                    <jats:sup>+<\/jats:sup>\n                    concentrations when using microbial properties than when using environmental variables, highlighting their importance for understanding N cycling in STEs. Our results suggest that the functional potential of the STE microbiome is complex and spatially structured across hydrochemical zones, explaining spatial variations in STE N\u2010cycling.\n                  <\/jats:p>","DOI":"10.1111\/1462-2920.70400","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T08:27:40Z","timestamp":1786523260000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Spatial Partitioning of Microbial Functional Potential Suggests Complex Nitrogen Cycling in a Subterranean Estuary"],"prefix":"10.1111","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2630-9316","authenticated-orcid":false,"given":"Daniel","family":"Romano\u2010Gude","sequence":"first","affiliation":[{"name":"Institut de Ci\u00e8ncies del Mar (ICM\u2010CSIC)  Barcelona Spain"},{"name":"Departament de Gen\u00e8tica i de Microbiologia Universitat Aut\u00f2noma de Barcelona  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