High‐throughput sequencing reveals neustonic and planktonic microbial eukaryote diversity in coastal waters

<jats:p>Neustonic organisms inhabit the sea surface microlayer (<jats:styled-content style="fixed-case">SML</jats:styled-content>) and have important roles in marine ecosystem functioning. Here, we use high‐throughput 18S <jats:styled-content style="fixed-case">rRNA</jats:styled-content> gene sequencing to characterize protist and fungal diversity in the <jats:styled-content style="fixed-case">SML</jats:styled-content> at a coastal time‐series station and compare with underlying plankton assemblages. Protist diversity was higher in <jats:styled-content style="fixed-case">F</jats:styled-content>ebruary (pre‐bloom) compared to <jats:styled-content style="fixed-case">A</jats:styled-content>pril (spring bloom), and was lower in the neuston than in the plankton. Major protist groups, including <jats:styled-content style="fixed-case">S</jats:styled-content>tramenopiles and <jats:styled-content style="fixed-case">A</jats:styled-content>lveolata, dominated both neuston and plankton assemblages. Chrysophytes and diatoms were enriched in the neuston in <jats:styled-content style="fixed-case">A</jats:styled-content>pril, with diatoms showing distinct changes in community composition between the sampling periods. Pezizomycetes dominated planktonic fungi assemblages, whereas fungal diversity in the neuston was more varied. This is the first study to utilize a molecular‐based approach to characterize neustonic protist and fungal assemblages, and provides the most comprehensive diversity assessment to date of this ecosystem. Variability in the <jats:styled-content style="fixed-case">SML</jats:styled-content> microeukaryote assemblage structure has potential implications for biogeochemical and food web processes at the air‐sea interface.</jats:p>