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SCTLD affects &amp;gt;30 coral species that differ in their associations with dinoflagellate endosymbionts (family Symbiodiniaceae), and symbiont lineage-level dynamics may underlie variation in holobiont disease response. We analyzed 491 apparently healthy and SCTLD-affected corals in Florida (USA) and the United States Virgin Islands, representing 9 coral species sampled in situ or during an SCTLD transmission experiment. Based on the internal transcribed spacer-2 (ITS-2) region of rDNA, we identified 114 Symbiodiniaceae ITS-2 type profiles spanning 6 genera. Symbiodiniaceae composition varied significantly by coral species, disease susceptibility group, tissue health state, and region. In the corals Orbicella annularis and Colpophyllia natans, lesion-adjacent tissues had enriched relative abundance of a Durusdinium lineage, whereas Symbiodinium and Cladocopium lineages were relatively more abundant in apparently healthy tissues. Accounting for biogeography and host identity, our results suggest that in corals harboring multiple Symbiodiniaceae lineages, more susceptible lineages are lost first, leaving relatively resistant lineages in lesion-adjacent tissue until sloughing occurs. These findings indicate SCTLD acts as a selective filter on coral symbiont assemblages. Our results provide the first multi-species, multi-region evidence of fine-scale associations between Symbiodiniaceae lineages and SCTLD, establishing a framework for testing lineage-specific disease susceptibility in future experiments.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag228","type":"journal-article","created":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T11:16:26Z","timestamp":1786101386000},"source":"Crossref","is-referenced-by-count":0,"title":["Key coral symbiont lineages (family Symbiodiniaceae) are differentially associated with stony coral tissue loss disease"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0408-0576","authenticated-orcid":false,"given":"Carly E","family":"Karrick","sequence":"first","affiliation":[{"name":"Department of Environmental Science, Policy, and Management, University of California , Berkeley, CA 94720,","place":["United States"]},{"name":"BioSciences Department, Rice University , Houston, TX 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Florida Fish and Wildlife Conservation Commission , Marathon, FL 33050,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0413-9408","authenticated-orcid":false,"given":"Lindsay K","family":"Huebner","sequence":"additional","affiliation":[{"name":"Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission , Saint Petersburg, FL 33701,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9933-833X","authenticated-orcid":false,"given":"Daniel M","family":"Holstein","sequence":"additional","affiliation":[{"name":"School of Marine and Atmospheric Sciences, Stony Brook University , Stony Brook, NY 11794,","place":["United States"]},{"name":"Department of Oceanography & Coastal Sciences, Louisiana State University , Baton Rouge, LA 70803,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8371-0766","authenticated-orcid":false,"given":"Laura","family":"Mydlarz","sequence":"additional","affiliation":[{"name":"Department of Biology, The University of Texas at Arlington , TX 76019,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8639-7851","authenticated-orcid":false,"given":"Marilyn","family":"Brandt","sequence":"additional","affiliation":[{"name":"Center for Marine and Environmental Studies, University of the Virgin Islands , USVI 00802,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4249-2977","authenticated-orcid":false,"given":"Amy","family":"Apprill","sequence":"additional","affiliation":[{"name":"Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution , Woods Hole, MA 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