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Molecular surveys have revealed each individual as a holobiont hosting dense, taxonomically structured microbiomes in the gut, on the cuticle, and within feeding structures. These microbial partners expand dietary breadth through carbohydrate\u2010active enzymes, supply limiting vitamins, detoxify xenobiotics, and may buffer thermal and oxidative stress, thereby influencing host fitness and the fate of particulate organic carbon. Experimental studies show intact microbiomes often enhance growth or fecundity, with effects amplified under vitamin limitation or toxin exposure. In contrast, gut and pellet\u2010associated respiration can substantially reduce the carbon content of pellets within hours to days, depending on temperature and microbial composition. Vertical migrators also transport live bacteria and viruses below the thermocline, potentially seeding mesopelagic niches and affecting remineralization patterns. Despite these influences, zooplankton holobionts remain largely absent from biogeochemical models. This minireview synthesises current understanding of microbiome assembly and plasticity, their contributions to host performance and carbon export, and their role in microbial dispersal, underscoring the need to integrate holobiont traits into Earth\u2010system models to better predict ecosystem responses to warming and deoxygenation.<\/jats:p>","DOI":"10.1111\/1462-2920.70271","type":"journal-article","created":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T01:24:27Z","timestamp":1775438667000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Gut Microbiomes of Marine Zooplankton: Consequences for Host Performance, the Biological Carbon Pump, and Prokaryote Biogeography"],"prefix":"10.1111","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1069-212X","authenticated-orcid":false,"given":"Albert","family":"Calbet","sequence":"first","affiliation":[{"name":"Institut de Ci\u00e8ncies del Mar, CSIC  Barcelona Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2026,4,5]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41561-018-0081-0"},{"key":"e_1_2_12_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s43705-022-00195-4"},{"key":"e_1_2_12_4_1","doi-asserted-by":"publisher","DOI":"10.4319\/lo.2001.46.7.1824"},{"key":"e_1_2_12_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2015.166"},{"key":"e_1_2_12_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.envpol.2023.122188"},{"key":"e_1_2_12_7_1","doi-asserted-by":"publisher","DOI":"10.5194\/bg\u201014\u2010177\u20102017"},{"key":"e_1_2_12_8_1","doi-asserted-by":"publisher","DOI":"10.3354\/ame01663"},{"key":"e_1_2_12_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.aquatox.2023.106546"},{"key":"e_1_2_12_10_1","doi-asserted-by":"publisher","DOI":"10.1002\/2014GB005037"},{"key":"e_1_2_12_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fiac082"},{"key":"e_1_2_12_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature04056"},{"key":"e_1_2_12_13_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2423680122"},{"key":"e_1_2_12_14_1","doi-asserted-by":"publisher","DOI":"10.1002\/lno.12588"},{"key":"e_1_2_12_15_1","article-title":"Active Microbial Communities on Copepod Fecal Pellets in the North Atlantic","volume":"93","author":"De Corte D.","year":"2017","journal-title":"FEMS Microbiology Ecology"},{"key":"e_1_2_12_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.13944"},{"key":"e_1_2_12_17_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.15815"},{"key":"e_1_2_12_18_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0033107"},{"key":"e_1_2_12_19_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmars.2020.00405"},{"key":"e_1_2_12_20_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2010.06.006"},{"key":"e_1_2_12_21_1","doi-asserted-by":"publisher","DOI":"10.3390\/w15244203"},{"key":"e_1_2_12_22_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.est.9b05305"},{"key":"e_1_2_12_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2014.09.031"},{"key":"e_1_2_12_24_1","doi-asserted-by":"publisher","DOI":"10.1080\/19420889.2015.1029210"},{"key":"e_1_2_12_25_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.589816"},{"key":"e_1_2_12_26_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0230310"},{"key":"e_1_2_12_27_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1000668107"},{"key":"e_1_2_12_28_1","doi-asserted-by":"publisher","DOI":"10.1029\/2023EF004375"},{"key":"e_1_2_12_29_1","first-page":"1699","article-title":"Drivers of Carbon Export Efficiency in the Global Ocean","volume":"19","author":"Henson S. 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