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Phytoplankton are critical to the Antarctic marine food web and associated biological carbon pump, yet long-term shifts in their community composition are poorly understood. Here, using a machine learning framework and combining pigment samples and environmental samples from austral summertime 1997–2023, we show declines in diatoms and increases in haptophytes and cryptophytes across much of Antarctica’s continental shelf. These trends—which are linked to sea ice increases—reversed after 2016, with a rebound in diatoms and a large increase in cryptophytes, coinciding with the loss of sea ice. Significant changes (P < 0.05) across the 25-year dataset include diatom chlorophyll a (chl-a) declines of 0.32 mg chl-a m−3 (~33% of the climatology) and increases for haptophytes and cryptophytes of 0.08 and 0.23 mg chl-a m−3, respectively. The long-term shifts in phytoplankton assemblages could reduce the dominance of the krill-centric food web and diminish the biologically mediated export of carbon to depth, with implications for the global-ocean carbon sink.

The Southern Ocean contributes substantially to the global biological carbon pump (BCP). Salps in the Southern Ocean, in particular Salpa thompsoni, are important grazers that produce large, fast-sinking fecal pellets. Here, we quantify the salp bloom impacts on microbial dynamics and the BCP, by contrasting locations differing in salp bloom presence/absence. Salp blooms coincide with phytoplankton dominated by diatoms or prymnesiophytes, depending on water mass characteristics. Their grazing is comparable to microzooplankton during their early bloom, resulting in a decrease of ~1/3 of primary production, and negative phytoplankton rates of change are associated with all salp locations. Particle export in salp waters is always higher, ranging 2- to 8- fold (average 5-fold), compared to non-salp locations, exporting up to 46% of primary production out of the euphotic zone. BCP efficiency increases from 5 to 28% in salp areas, which is among the highest recorded in the global ocean.

This study was made possible by funding from the Ministry for Business, Innovation and Employment (MBIE) of New Zealand, NIWA Coast and Oceans Food Webs (COES) and Ocean Flows (COOF), and the Royal Society of New Zealand Marsden Fast-track award to MD, and by U.S. National Science Foundation awards OCE- 1756610 and 1756465 to MS and KES.

The combination of iron limitation and microzooplankton grazing controls phytoplankton productivity and taxonomic composition in high-nutrient low-chlorophyll (HNLC) regions. While increased productivity and diatom contribution triggered by iron enrichment support this view, direct measurements of underpinning group-specific growth and grazing rates are scarce for the Southern Ocean. To assess these rates, we conducted dilution experiments coupled to high-performance liquid chromatography and flow-cytometry in sub-Antarctic waters on and off Campbell Plateau, southeast of Aotearoa-New Zealand. Off the plateau, growth and grazing were closely balanced for all groups despite a two-fold difference between slow- and fast-growing groups. On Campbell Plateau, where HNLC conditions were alleviated, the balance was disrupted, mainly by the preferential growth of diatoms and green algae, which was stimulated beyond grazing. Our results expand the recognized ability of diatoms to escape grazing control to picoplanktonic green algae that also avoid grazing and contribute significantly to phytoplankton productivity and biomass accumulation.

According to modern oceanographic perspectives that emphasize microbial pathways, phagotrophic protists comprise one to several levels of intermediate consumers between phytoplankton and larger metazooplankton (copepods and krill). However, recent attempts to quantify pelagic trophic structure in the open ocean using nitrogen stable isotope techniques have brought into question whether such measurements adequately account for protistan trophic steps. Here, we use a two-stage chemostat system, with Dunaliella tertiolecta andOxyrrhis marina as a predator-prey model, to address this question experimentally. To investigate15N trophic discrimination under different conditions of nitrogen availability and recycling, Oxyrrhis was fed in the light and in the dark on phytoplankton provided with high and low nutrient ratios of N: P. We used both bulk and amino acids-compound specific isotopic analysis (AA-CSIA) to distinguish trophic fractionation from changes in the δ15N values of phytoplankton (isotopic baseline). Results demonstrate that protistan consumers are not, in fact, significantly enriched in 15N relative to their prey, a marked departure from the general findings for metazoan consumers. In addition, we show that changes in the isotopic baseline propagate rapidly through the protistan food chain, highlighting the need to account for this variability at ecologically relevant time scales. If protistan trophic steps are largely invisible or significantly underestimated using nitrogen isotope measurements, research that utilize such measurements in ecological, fisheries, and climate change studies may miss a large part of the ocean's variability in food-web structure and ecosystem function. © 2014, by the Association for the Sciences of Limnology and Oceanography, Inc.

Model code is available as a zip file (Supplementary Dataset 6) that includes a Matlab live script, which can be used to generate all figures and summary data in the manuscript. It is also available on GitHub: https://github.com/mstukel/SalpEcosystemEfficiency and on Zenodo: https://doi.org/10.5281/zenodo.12700512.

This paper has heavily relied on the extensive data collected from numerous voyages to the Southern Ocean over a span of 26 years. While it is challenging to individually acknowledge everyone involved, we would like to express our sincere gratitude to the scientific community as a whole. The unwavering dedication of scientists in sharing their data through online repositories showcases the remarkable commitment of the oceanographic community to unravelling the mysteries of intricately complex oceans. I would like to thank Dr. Thomas Ryan-Keogh, Dr. Sandy Thomalla and the SOCCO project for their contributions of pigment data and help. We acknowledge NIWA for providing funding through the NIWA PhD scholarship (CDPS2001) and the University of Otago (Department of Marine Science) for their support throughout the PhD programme. We are also grateful to the New Zealand MBIE Endeavour Programme C01X1710 (Ross-RAMP), Antarctic Science Platform, Project 3 (MBIE contract ANTA1801), MBIE NIWA SSIF (“Structure and function of marine ecosystems”) for financial support. We acknowledge the contribution to this work by the R open-source collective and R Studio.