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monitoring by microscopy offers a long-term ecological perspective of plankton communities, but detection approaches are uniquely biased. Genetic identification of marine plankton has become standard but is still not used in routine monitoring. This study assesses the value that genetic methods bring to microscopic and flow cytometry monitoring methods in the Western (English) Channel. An 18S high throughput sequencing (HTS) diversity survey of plankton taxa was performed on samples collected from an automated Water and Microplankton Sampler (WaMS) deployed on the Continuous Plankton Recorder platform (CPR) from 2011\u20132012. This survey detected contrasting but complementary taxa assemblages to that of microscopic surveys, mostly composed of smaller or naked or thin-walled plankton taxa, with most phytoplankton being under 10 \u00b5m infrequently recorded by other surveys. Most genetically-detected taxa in the survey were mixotrophic or heterotrophic. In comparison with microscopic phytoplankton counts from the CPR survey and Western Channel Observatory station L4, only 8\u201312 taxonomic families were common to all three surveys, most of them dinoflagellates, with a bias towards larger diatoms and dinoflagellate taxa in microscopy surveys. Additional quantitative real-time PCR detection of two potentially harmful taxa, the pelagophyte, Aureococcus anophagefferens and four Pseudo-nitzschia from 2011\u20132013. This revealed that growth of A. anophagefferens was elevated in the summer of 2011, whilst the appearance of Pseudo-nitzschia delicatissima in February of that year contrasted with it\u2019s timing at a coastal station. Smaller phytoplankton measured by flow cytometry had distinct seasonality and abundance in the mid-Atlantic compared to coastal regions reflecting distinct conditions.<\/jats:p>","DOI":"10.3390\/jmse11030480","type":"journal-article","created":{"date-parts":[[2023,2,24]],"date-time":"2023-02-24T02:32:12Z","timestamp":1677205932000},"page":"480","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Composition and Patterns of Taxa Assemblages in the Western Channel Assessed by 18S Sequencing, Microscopy and Flow Cytometry"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7843-6678","authenticated-orcid":false,"given":"Rowena","family":"Stern","sequence":"first","affiliation":[{"name":"Marine Biological Association, Citadel Hill, Plymouth PL1 2PB, UK"}]},{"given":"Kathryn","family":"Picard","sequence":"additional","affiliation":[{"name":"National Museum of Natural History at the Smithsonian Institute, 1000 Madison Drive NW, Washington, DC 20560, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7145-9367","authenticated-orcid":false,"given":"Jessica","family":"Clarke","sequence":"additional","affiliation":[{"name":"School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8570-2399","authenticated-orcid":false,"given":"Charlotte E.","family":"Walker","sequence":"additional","affiliation":[{"name":"Department of Biology, University of York, York YO10 5DD, UK"}]},{"given":"Claudia","family":"Martins","sequence":"additional","affiliation":[{"name":"Marine Biological Association, Citadel Hill, Plymouth PL1 2PB, UK"}]},{"given":"Clare","family":"Marshall","sequence":"additional","affiliation":[{"name":"Marine Biological Association, Citadel Hill, Plymouth PL1 2PB, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9612-4280","authenticated-orcid":false,"given":"Ana","family":"Amorim","sequence":"additional","affiliation":[{"name":"MARE\u2014Marine and Environmental Sciences Centre\/ARNET\u2014Aquatic Research Network, Faculdade de Ci\u00eancias, Universidade de Lisboa, 1749-016 Lisboa, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7187-6689","authenticated-orcid":false,"given":"E. Malcolm S.","family":"Woodward","sequence":"additional","affiliation":[{"name":"Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK"}]},{"given":"Claire","family":"Widdicombe","sequence":"additional","affiliation":[{"name":"Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3695-5151","authenticated-orcid":false,"given":"Glen","family":"Tarran","sequence":"additional","affiliation":[{"name":"Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK"}]},{"given":"Martin","family":"Edwards","sequence":"additional","affiliation":[{"name":"Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK"}]}],"member":"1968","published-online":{"date-parts":[[2023,2,23]]},"reference":[{"key":"ref_1","unstructured":"Clementson, L.A., Eriksen, R.S., and Willis, A. (2022). Advances in Phytoplankton Ecology, Elsevier."},{"key":"ref_2","unstructured":"Falkowski, P.G., and Raven, J.A. (2013). 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