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Many Antarctic perennially ice-covered lakes are density stratified, within which an oxygenated upper layer overlies deeper, darker anoxic waters. We carried out the first 16S and 18S rRNA gene high throughput sequencing of microplankton and benthic microbial mats in perennially ice-covered Lake Joyce, McMurdo Dry Valleys, Antarctica. We evaluated community composition and richness at different lake and water depths, and determined the level of connectivity of benthic and planktonic microbial communities. While some overlap between benthos and plankton was observed, the microbial communities were distinct in richness and community composition. The benthic communities comprised microbial mats, which were dominated by Cyanobacteria and Proteobacteria, whereas the planktonic community showed an increased contribution of Bacteroidota. A higher number of 16S rRNA gene ASVs were specific for the plankton than the mats, whereas more 18S rRNA gene ASVs were specific to the microbial mats than the plankton. The benthic eukaryotic community was dominated by ciliates and diatoms while Cryptophyceae were abundant in the plankton. These findings demonstrate that both benthic and planktonic communities need to be considered for census of taxonomic richness, productivity, and ecological processes occurring within Antarctic lakes.<\/jats:p>","DOI":"10.1093\/femsec\/fiag078","type":"journal-article","created":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T11:58:00Z","timestamp":1786017480000},"source":"Crossref","is-referenced-by-count":0,"title":["Distinct benthic and planktonic microbial communities within the stratified water column of the perennially ice-covered Lake Joyce, Antarctica"],"prefix":"10.1093","volume":"102","author":[{"given":"Carla","family":"Greco","sequence":"first","affiliation":[{"name":"Natural History Museum, Department of Sciences , London, SW7 5BD ,","place":["United Kingdom"]},{"name":"School of Biological Sciences, University of Bristol , Bristol, BS8 1TQ ,","place":["United 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