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In the upside-down jellyfish Cassiopea xamachana, the polyp-to-medusa transition (strobilation) requires the establishment of symbiosis with Symbiodiniaceae algal partners, yet bacterial community dynamics during this developmental process remain unknown. Here, we experimentally induced symbiosis in aposymbiotic polyps using four algal treatments: xenic Symbiodinium microadriaticum (native symbiont), xenic Breviolum minutum, antibiotic-treated B. minutum, and a photosynthetically impaired B. minutum mutant. We combined 16S rRNA gene sequencing with measurements of photosynthetic efficiency, asexual budding, and algal surface N-glycan profiles to characterize holobiont assembly during symbiosis onset and strobilation. Algal treatment structured bacterial communities in both algal cultures and polyp tissues. Our analyses identified a set of amplicon sequence variants that consistently distinguished strobilating polyps from non-strobilating aposymbiotic and mutant polyps, in addition to potential bacterial biomarkers associated with successful metamorphosis. Strobilation was associated with the enrichment of bacterial communities putatively involved in sulfur and nitrogen cycling, whereas non-strobilating aposymbiotic and mutant polyps were characterized by opportunistic bacteria and increased community variability. Together, these results reveal coordinated changes in algal physiology, surface glycan profiles, and bacterial community structure associated with successful strobilation in C. xamachana and support a model in which tripartite host\u2013alga\u2013bacteria interactions influence cnidarian life stage transitions.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag147","type":"journal-article","created":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T11:41:50Z","timestamp":1780573310000},"source":"Crossref","is-referenced-by-count":0,"title":["Cnidarian\u2013algal partnerships structure bacterial communities during strobilation in\n                    <i>Cassiopea xamachana<\/i>"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6328-7596","authenticated-orcid":false,"given":"Federica","family":"Montesanto","sequence":"first","affiliation":[{"name":"Whitney Laboratory for Marine Bioscience, University of Florida , St. Augustine, FL 32080, \u00a0","place":["United 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Augustine, FL 32080, \u00a0","place":["United States"]},{"name":"Department of Biology, University of Florida , Gainesville, FL 32611, \u00a0","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7487-7225","authenticated-orcid":false,"given":"Bailey","family":"Steinworth","sequence":"additional","affiliation":[{"name":"Whitney Laboratory for Marine Bioscience, University of Florida , St. Augustine, FL 32080, \u00a0","place":["United States"]},{"name":"Department of Biology, University of Florida , Gainesville, FL 32611, \u00a0","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria","family":"Sharp","sequence":"additional","affiliation":[{"name":"Pennsylvania State University , State College, PA 16802, \u00a0","place":["United 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