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Antarctic krill Euphausia superba are key components of Antarctic ecosystems, serving as the major prey item for most of the megafauna in the region. Coastal fjords along the West Antarctic Peninsula have been identified as biological hotspots, areas in which high biomasses of both E. superba and their megafauna predators are consistently observed. We investigated feeding by E. superba in fjords and adjacent open waters of the West Antarctic Peninsula. Next generation sequencing of stomach contents from 174 krill indicated a diverse diet, with broad patterns consistent with previous understanding of E. superba feeding. Diatom sequence reads were frequent and abundant, indicating a largely diatom-based diet, while the occasional presence of high abundances of copepod sequence reads suggests carnivory supplemented the diet. Striking differences were observed between the stomach contents of krill collected in fjords and those of krill collected in adjacent open waters. Chaetoceros spp. diatoms made up 71% of the stomach contents sequences of krill collected in fjords, but less than 10% of the stomach contents sequences of krill collected in open waters. These differences could not be explained by differences in the surface water phytoplankton communities, as in both open waters and fjords Chaetoceros spp. made up less than 10% of the surface water sequence read assemblages. These feeding differences highlight the importance of taking into account regional differences in krill feeding when considering E. superba’s roles in Southern Ocean ecosystems, and suggest krill in fjords may make use of vertical structure in phytoplankton assemblages.

Antarctic krill Euphausia superba are a key component of food webs in the maritime West Antarctic Peninsula, and their life history is tied to the seasonal cycles of sea ice and primary production in the region. Previous work has shown a general in-shore migration of krill in winter in this region; however, the very near-shore has not often been sampled as part of these surveys. We investigated distribution, abundance, and size structure of krill in 3 fjordic bays along the peninsula, and in the adjacent Gerlache Strait area using vertically stratified MOCNESS net tows and ADCP acoustic biomass estimates. Krill abundance was high within bays, with net estimated densities exceeding 60 krill m-3, while acoustic estimates were an order of magnitude higher. Krill within bays were larger than krill in the Gerlache Strait. Within bays, krill aggregations were observed near the seafloor during the day with aggregations extending to the sediment interface, and exhibited diel vertical migration higher into the water column at night. We suggest these high winter krill abundances within fjords are indicative of an active seasonal migration by krill in the peninsula region. Potential drivers for such a migration include reduced advective losses and costs, and availability of sediment food resources within fjords. Seasonally near-shore krill may also affect stock and recruitment assessments and may have implications for managing the krill fishery in this area. KEYWORDS: Euphausiid · Abundance · Diel vertical migration · DVM · WAP · Fjord.

ABSTRACT Understanding diet composition is essential for unravelling trophic interactions in aquatic ecosystems. DNA metabarcoding, utilising various variable regions of the 18S rRNA gene, is increasingly employed to investigate zooplankton diet composition. However, accurate results depend on rapid inactivation of digestive enzymes and DNA nucleases through proper sample processing and preservation. In this study, we compare the prey communities of Antarctic krill retrieved from the 18S variable regions V4 and V7 and assess how different processing treatments affect the detected prey composition of both krill and salps. Our findings highlight the critical importance of prompt sample processing for species with highly efficient digestive enzymes, such as krill, to preserve rapidly digested prey, including gelatinous plankton. Comparative analyses of the V4 and V7 regions revealed significantly different prey communities within the same krill samples, indicating that these regions may not be suitable for direct comparisons within or across studies. To complement molecular approaches, we also analyse fatty acids (FA) as trophic markers which provide insights into dietary habits over both short and long time scales. By comparing FA signals from stomach and tissue samples of the same krill and salp individuals, we identified significant differences in trophic markers representing different plankton groups. These findings emphasise the necessity of separating digestive tract from tissue to distinguish between short- and long-term diet signals. Furthermore, integrating FA analysis with metabarcoding offers valuable insights into zooplankton digestion efficiency across taxonomic levels. This combined approach enhances our understanding of zooplankton feeding ecology and trophic interactions in marine ecosystems.

Antarctic fur seal (Arctocephalus gazella) colonies are found on sub-Antarctic islands around the continent. These islands experience a range of conditions in terms of physical and biological habitat, creating a natural laboratory to investigate local genetic adaptation. One striking habitat difference is in the availability of Euphausia superba krill as prey, which has led to A. gazella exhibiting a range of diets. A. gazella in some colonies consume exclusively krill, while their conspecifics in other colonies feed mainly on fish and consume few to no krill. To investigate potential adaptations to these different prey fields, reduced representation genome sequencing was conducted on A. gazella from the 8 major colonies. Twenty-seven genomic regions exhibiting signatures of natural selection were identified. Two of these genomic regions were clearly associated with seals living in krill-dominated areas or those in fish-dominated areas. Twenty-two additional genomic regions under selection showed a pattern consistent with prey differences as the driver of selection after historical migrations from krill-dominated habitats where lineages evolved to present krill-poor habitat areas were taken into account. Only 1 of the genomic regions identified appeared to be explained by any other environmental variable analysed (depth). Genomic regions under prey-driven selection included genes associated with regulation of gene expression, skeletal development, and lipid metabolism. Adaptation to local prey has implications for spatial management of this species and for the potential impacts of climate- or harvest-driven reductions in krill abundance on these seals. KEY WORDS: Arctocephalus gazella · Double digest restriction-site associated DNA sequencing · ddRAD · Diet · Euphausia superba · Natural selection

Antarctic krill (Euphausia superba) are integral to Southern Ocean pelagic ecosystems. Winters with extensive sea ice have been linked to high post-larval krill recruitment the following spring, suggesting that sea ice plays a critical role in larval overwinter survival. As the ocean warms and sea ice declines under climate change, understanding the mechanisms linking sea ice and krill recruitment is increasingly urgent. To address this, we developed a qualitative network model (QNM) that integrates evidence-based and hypothesized interactions to explore larval overwinter survival and growth under future climate scenarios in the southwest Atlantic sector. Our model highlights habitat-specific impacts, with substantial declines predicted for the North Antarctic Peninsula continental shelf due to reduced autumn primary productivity and warming. In contrast, survival may improve in open-ocean habitats under cooler scenarios that enhance sea-ice-associated processes, such as food availability and refuge. The inclusion of hypothesized mechanisms, such as sea-ice terraces providing refuge from predation, strengthened these conclusions and highlighted critical uncertainties, including the influence of glacial melt on food web dynamics. These findings demonstrate the value of QNMs in complementing quantitative approaches, offering a framework for identifying critical mechanisms, addressing knowledge gaps, and guiding future field and laboratory studies to improve predictions of krill responses to climate change.