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Changes to the hydrologic cycle and anthropogenic disturbances have the potential to alter these poorly described communities. Here, we aimed to assess the variation within the viral and bacterial communities of one of the world's largest hypersaline estuaries over 13\u2009months. Using metagenomics, we identified viruses associated with two different salinity regimes, and we showed how viruses responded to pulse disturbances including freshwater inundation and freeze events. We identified 17, 324 viral species, of which 12,132 were found in only one of the salinity regimes. Our results demonstrate a potential association between freshwater pulses throughout June 2021 and shifts in viral community composition. Freeze events showed a greater propensity to alter the auxiliary metabolic genes (AMGs), or genes carried by viruses to alter host metabolism during infection. Viruses associated with low temperatures led to higher incidences of AMGs associated with sulfur cycling and oxidative phosphorylation as opposed to photosynthesis with freshwater inundation and no extreme weather. The contrasting responses to different pulse disturbances make evident the need to better understand how different types of disturbances alter viral communities and their potential to modulate important biogeochemical cycles.<\/jats:p>","DOI":"10.1111\/1758-2229.70354","type":"journal-article","created":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T12:01:46Z","timestamp":1778241706000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Viral Assemblages of a Hypersaline Estuary Show Divergent Responses to Freshwater and Temperature Disturbances"],"prefix":"10.1111","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9945-1017","authenticated-orcid":false,"given":"Jordan R.","family":"Walker","sequence":"first","affiliation":[{"name":"Department of Marine Biology Texas A&amp;M University at Galveston  Galveston Texas USA"},{"name":"Department of Biology University of Miami  Coral Gables Florida USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paxton T.","family":"Bachand","sequence":"additional","affiliation":[{"name":"Department of Life Sciences Texas A&amp;M University\u2010Corpus Christi  Corpus Christi Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9726-8649","authenticated-orcid":false,"given":"Jeffrey W.","family":"Turner","sequence":"additional","affiliation":[{"name":"Department of Life Sciences Texas A&amp;M University\u2010Corpus Christi  Corpus Christi Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0236-7634","authenticated-orcid":false,"given":"Jessica M.","family":"Labont\u00e9","sequence":"additional","affiliation":[{"name":"Department of Marine Biology Texas A&amp;M University at Galveston  Galveston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,5,8]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1029\/2019RG000683"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10661\u2010005\u20109031\u20106"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574\u20106941.2011.01054.x"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462\u20102920.2006.01137.x"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.3354\/ame041247"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010021\u201001101\u2010x"},{"key":"e_1_2_11_8_1","doi-asserted-by":"crossref","unstructured":"Bushnell B. 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