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Changes in phytoplankton composition from large diatoms to small cryptophytes and their implications to the food web have been previously associated with rapid warming of surface waters in the western Antarctic Peninsula (WAP).However, ecological and physiological attributes that favor dominance of these flagellates in the region have not been fully explored. The overall aim of this work was to characterize the phytoplankton pigments and assemblages in relation to environmental conditions during three successive summer cruises (2013, 2014 and 2015) in the Gerlache Strait − a coastal area in the northern WAP. Data on phytoplankton (through HPLC/CHEMTAX pigment analysis) and associated physical (water column structure) and chemical (macronutrients) parameters were determined. Cryptophytes were conspicuously found in shallow mixed layers, under stratified conditions, as the main contributors to total phytoplankton biomass. Their greatest contributions were associated with warmer surface waters at the northwestern sector of the strait. Other phytoplankton groups (Phaeocystis antarctica in 2013 and small diatoms in both 2014 and 2015) were also important components. Photoprotective carotenoids (mainly alloxanthin), with an important role in preventing photodamage caused by excess light, were closely linked with the dominance of cryptophytes at surface layers. The results of this study suggest that the prevalence of cryptophytes in WAP coastal waters can be, to a great extent, due to a particular ability of those small flagellates to successfully grow in highly illuminated conditions in shallow upper mixed layers and strong water column stratification.

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Diatoms are considered the main base of the Southern Ocean food web as they are responsible for more than 85% of its annual primary production and play a crucial role in the Antarctic trophic structure and in the biogeochemical cycles. Within this context, an intense diatom bloom reaching > 45 mg m−3 of chlorophyll a was registered in the Northern Antarctic Peninsula (NAP) during a late summer study in February 2016. Given that nutrient concentrations and grazing activities were not identified here as limiting factors on the bloom development, the aim of this study was to evaluate the effect of water column structure (stability and upper mixed layer depth) on the phytoplankton biomass and composition in the NAP. The diatom bloom, mainly composed by the large centric Odontella weissflogii (mostly > 70 μm in length), was associated with a local ocean carbon dioxide uptake that reached values greater than −60 mmol m−2 d−1. We hypothesize that the presence of a vertically large water column stability barrier, just below the pycnocline, was the main driver allowing for the development of the intense diatom bloom, particularly in the Gerlache Strait. Contrarily, a shift from diatoms to dinoflagellates (mainly Gymnodiniales < 20 μm) was observed associated with conditions of a highly stable thin layer. The results suggest that a large fraction of this intense diatom bloom is in fast sinking process, associated with low grazing pressure, showing a crucial role of diatoms for the efficiency of the biological carbon pump in this region.