Cryptomonadales have acquired their plastids by secondary endosymbiosis. A novel clade-CRY1-has been discovered at the base of the Cryptomonadales tree, but it remains unknown whether it contains plastids. Cryptomonadales are also an important component of phytoplankton assemblages. However, they cannot be readily identified in fixed samples, and knowledge on dynamics and distribution of specific taxa is scarce. We investigated the phenology of the CRY1 lineage, three cryptomonadales clades and a species Proteomonas sulcata in a brackish lagoon of the Baltic Sea (salinity 0.3-3.9) using fluorescence in situ hybridization. A newly design probe revealed that specimens of the CRY1 lineage were aplastidic. This adds evidence against the chromalveolate hypothesis, and suggests that the evolution of cryptomonadales' plastids might have been shorter than is currently assumed. The CRY1 lineage was the most abundant cryptomonad clade in the lagoon. All of the studied cryptomonads peaked in spring at the most freshwater station, except for P. sulcata that peaked in summer and autumn. Salinity and concentration of dissolved inorganic nitrogen most significantly affected their distribution and dynamics. Our findings contribute to the ecology and evolution of cryptomonads, and may advance understanding of evolutionary relationships within the eukaryotic tree of life.

Department of Fisheries Oceanography and Marine Ecology National Marine Fisheries Research Institute ul Kołłątaja 1 81 332 Gdynia Poland

Institute of Microbiology Czech Academy of Sciences Center Algatech ul Novohradska 237 37981 Třeboň Czech Republic Department of Fisheries Oceanography and Marine Ecology National Marine Fisheries Research Institute ul Kołłątaja 1 81 332 Gdynia Poland

Limnological Station Institute of Plant Biology University of Zurich Seestr 187 CH 8802 Kilchberg Switzerland

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