Planktonic protist diversity across contrasting Subtropical and Subantarctic waters of the southwest Pacific

Planktonic protists are an essential component of marine pelagic ecosystems where they mediate important trophic and biogeochemical functions. Although these functions are largely influenced by their taxonomic affiliation, the composition and spatial variability of planktonic protist communities remain poorly characterized in vast areas of the ocean. Here, we investigated the diversity of these communities in contrasting oceanographic conditions of the southwest Pacific sector (33-58{degrees}S) using DNA metabarcoding of the 18S rRNA gene. Seawater samples collected during twelve cruises (n = 482, 0-2000 m) conducted east of New Zealand were used to characterize protist communities in Subtropical (STW) and Subantarctic (SAW) water masses and the Subtropical Front (STF) that separates them. Diversity decreased with latitude and temperature but tended to be lowest in the STF. Sample ordination resulting from the abundance of amplicon single variants (ASVs) corresponded to the different water masses. Overall, Dinophyceae (34% of standardized total number of reads) and Chlorophyta (27%) co-dominated the euphotic zone, but their relative abundance and composition at class and lower taxonomic levels varied consistently between water masses. Among Chlorophyta, several picoplanktonic algae species of the Mamiellophyceae class including Ostreococcus lucimarinus dominated in STW, while the Chloropicophyceae species Chloroparvula pacifica was most abundant in SAW. Bacillariophyta (7%), Prymnesiophyceae (5%), and Pelagophyceae (3%) classes were less abundant but showed analogous water mass specificity at class and finer taxonomic levels. Protist community composition in the STF had mixed characteristics and showed regional differences with the southern STF (50{degrees}S) having more resemblance with subantarctic communities than the STF over the Chatham Rise region (42-44{degrees}S). Below the euphotic zone, Radiolaria sequences dominated the dataset (52%) followed by Dinophyceae (27%) and other heterotrophic groups like Marine Stramenopiles and ciliates (3%). Among Radiolaria, several unidentified ASVs assigned to Spumellarida were most abundant, but showed significantly different distribution between STW and SAW highlighting the need to further investigate the taxonomy and ecology of this group. This study represents a significant step forward towards characterizing protistan communities composition in relation to major water masses and fronts in the South Pacific providing new insights about the biogeography and ecological preferences of different taxa from class to species and genotypic level. HighlightsO_LIWater-mass preference of different taxa emerged at class, species and genotypic level. C_LIO_LIMamiellophyceae green algae dominated in subtropical waters. C_LIO_LIDinophyceae and Chloropicophyceae green algae dominated in subantarctic waters. C_LIO_LIA diverse assemblage of Radiolaria dominated the mesopelagic zone. C_LIO_LISmall rather than large taxa dominated phytoplankton blooms in subtropical waters. C_LI