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Global threats to ocean biodiversity have generated a worldwide movement to take actions to improve conservation and management. Several international initiatives have recommended the adoption of marine protected areas (MPAs) in national and international waters. National governments and the Commission for the Conservation of Antarctic Marine Living Resources have successfully adopted multiple MPAs in the Southern Ocean despite the challenging nature of establishing MPAs in international waters. But are these MPAs representative of Southern Ocean biodiversity? Here we answer this question for both existing and proposed Antarctic MPAs, using benthic and pelagic regionalizations as a proxy for biodiversity. Currently about 11.98% of the Southern Ocean is protected in MPAs, with 4.61% being encompassed by no-take areas. While this is a relatively large proportion of protection when compared to other international waters, current Antarctic MPAs are not representative of the full range of benthic and pelagic ecoregions. Implementing additional protected areas, including those currently under negotiation, would encompass almost 22% of the Southern Ocean. It would also substantially improve representation with 17 benthic and pelagic ecoregions (out of 23 and 19, respectively) achieving at least 10% representation.

The Marine Biogeochemistry Library (MARBL) is a prognostic ocean biogeochemistry model that simulates marine ecosystem dynamics and the coupled cycles of carbon, nitrogen, phosphorus, iron, silicon, and oxygen. MARBL is a component of the Community Earth System Model (CESM); it supports flexible ecosystem configuration of multiple phytoplankton and zooplankton functional types; it is also portable, designed to interface with multiple ocean circulation models. Here, we present scientific documentation of MARBL, describe its configuration in CESM2 experiments included in the Coupled Model Intercomparison Project version 6 (CMIP6), and evaluate its performance against a number of observational data sets. The model simulates present‐day air‐sea CO2 flux and many aspects of the carbon cycle in good agreement with observations. However, the simulated integrated uptake of anthropogenic CO2 is weak, which we link to poor thermocline ventilation, a feature evident in simulated chlorofluorocarbon distributions. This also contributes to larger‐than‐observed oxygen minimum zones. Moreover, radiocarbon distributions show that the simulated circulation in the deep North Pacific is extremely sluggish, yielding extensive oxygen depletion and nutrient trapping at depth. Surface macronutrient biases are generally positive at low latitudes and negative at high latitudes. CESM2 simulates globally integrated net primary production (NPP) of 48 Pg C yr−1 and particulate export flux at 100 m of 7.1 Pg C yr−1. The impacts of climate change include an increase in globally integrated NPP, but substantial declines in the North Atlantic. Particulate export is projected to decline globally, attributable to decreasing export efficiency associated with changes in phytoplankton community composition. Plain Language Summary Numerical models of the ocean carbon cycle and biogeochemistry play a key role in understanding the fate of human carbon dioxide emissions and the magnitude of expected climate change over the next several decades to a century. Models are needed to quantify changes in the carbon reservoirs of the ocean and atmosphere and to explore interactions between climate change and carbon reservoirs that could amplify or damp future warming. This paper presents the Marine Biogeochemistry Library (MARBL), which is an ocean biogeochemistry model coupled to the Community Earth System Model (CESM). MARBL was designed to be compatible with multiple ocean models, a design motivated by an interest in building a diverse community of researchers around the development of MARBL. This paper presents a technical description of MARBL and an evaluation of the ocean biogeochemical simulation in CESM version 2. Overall, the model captures large‐scale biogeochemical distributions, though several important biases are highlighted, including those dependent on the representation of circulation. MARBL provides a robust platform for researchers to address critical questions related to the impacts of climate variability and change on marine ecosystems. Key Points MARBL is the ocean biogeochemistry component of the Community Earth System Model, version 2 (CESM2) MARBL is a flexible, plankton functional type model with a modular architecture supporting portability across ocean circulation models MARBL robustly represents key biogeochemical processes, but physical biases limit model fidelity

The Southern Ocean ecosystem has undergone extensive changes in the past two centuries driven by industrial sealing and whaling, climate change and commercial fishing. However, following the end of commercial whaling, some populations of whales in this region are recovering. Baleen whales are reliant on Antarctic krill, which is also the largest Southern Ocean fishery. Since 1993, krill catch has increased fourfold, buoyed by nutritional supplement and aquaculture industries. In this Perspective, we approximate baleen whale consumption of Antarctic krill before and after whaling to examine if the ecosystem can support both humans and whales as krill predators. Our back-of-the-envelope calculations suggest that current krill biomass cannot support both an expanding krill fishery and the recovery of whale populations to pre-whaling sizes, highlighting an emerging human-wildlife conflict. We then provide recommendations for enhancing sustainability in this region by reducing encounters with whales and bolstering the krill population. The Southern Ocean ecosystem is recovering from 20th-century industrial whaling, while the krill fishery in this region has grown rapidly and may expand further, driven by demand for supplements and aquaculture feed. This Perspective discusses how current krill biomass is unlikely to support both a growing krill fishery and rebounding whale populations in the Southern Ocean.

Climate change is rapidly altering the habitat of Antarctic krill ( Euphausia superba ), a key species of the Southern Ocean food web. Krill are a critical element of Southern Ocean ecosystems as well as biogeochemical cycles, while also supporting an international commercial fishery. In addition to trends forced by global-scale, human-driven warming, the Southern Ocean is highly dynamic, displaying large fluctuations in surface climate on interannual to decadal timescales. The dual roles of forced climate change and natural variability affecting Antarctic krill habitat, and therefore productivity, complicate interplay of observed trends and contribute to uncertainty in future projections. We use the Community Earth System Model Large Ensemble (CESM-LE) coupled with an empirically derived model of krill growth to detect and attribute trends associated with “forced,” human-driven climate change, distinguishing these from variability arising naturally. The forced trend in krill growth is characterized by a poleward contraction of optimal conditions and an overall reduction in Southern Ocean krill habitat. However, the amplitude of natural climate variability is relatively large, such that the forced trend cannot be formally distinguished from natural variability at local scales over much of the Southern Ocean by 2100. Our results illustrate how natural variability is an important driver of regional krill growth trends and can mask the forced trend until late in the 21st century. Given the ecological and commercial global importance of krill, this research helps inform current and future Southern Ocean krill management in the context of climate variability and change.

The Southern Ocean around Antarctica is one of the fastest changing regions on the planet and an emerging resource frontier for fisheries. Here, we present the Antarctic Ecosystem Value Index created by merging ecosystem information across food web trophic levels, from phytoplankton to fish and penguins, to quantify the ecological value of marine areas around the Antarctic continent. We find that coastal polynyas - areas of reduced sea-ice - have Index values 31–72% higher than surrounding areas, suggesting that these areas are biologically valuable hot spots for a number of ice-dependent Antarctic Species. Using output from an Earth system model to generate future projections of the Index, we find that high-value locations, often within polynyas, are likely to continue to be valuable throughout the 21st century despite environmental changes. The Antarctic Ecosystem Value Index indicates that penguins lose importance as their habitat becomes increasingly unsuitable, so protecting high-value habitat areas may be critical for these species. This study also shows that while many high-value Index areas are within existing or proposed Marine Protected Areas, there are several opportunities for adopting additional protection, particularly in East Antarctica and the Amundsen Sea. Here, the authors propose the Antarctic Ecosystem Value Index, an Earth systems model-based measure of marine ecological value. The index identifies potential present and future high-value locations, which often fall within coastal polynyas.

Southern Ocean phytoplankton production supports rich Antarctic marine ecosystems comprising copepods, krill, fish, seals, penguins, and whales. Anthropogenic climate change, however, is likely to drive rearrangements in phytoplankton community composition with potential ramifications for the whole ecosystem. In general, phytoplankton communities dominated by large phytoplankton, i.e., diatoms, yield shorter, more efficient food chains than ecosystems supported by small phytoplankton. Guided by a large ensemble of Earth system model simulations run under a high emission scenario (RCP8.5), we present hypotheses for how anthropogenic climate change may drive shifts in phytoplankton community structure in two regions of the Southern Ocean: the Antarctic Circumpolar Current (ACC) region and the sea ice zone (SIZ). Though both Southern Ocean regions experience warmer ocean temperatures and increased advective iron flux under 21st century climate warming, the model simulates a proliferation of diatoms at the expense of small phytoplankton in the ACC, while the opposite patterns are evident in the SIZ. The primary drivers of simulated diatom increases in the ACC region include warming, increased iron supply, and reduced light from increased cloudiness. In contrast, simulated reductions in ice cover yield greater light penetration in the SIZ, generating a phenological advance in the bloom accompanied by a shift to more small phytoplankton that effectively consume available iron; the result is an overall increase in net primary production, but a decreasing proportion of diatoms. Changes of this nature may promote more efficient trophic energy transfer via copepods or krill in the ACC region, while ecosystem transfer efficiency in the SIZ may decline as small phytoplankton grow in dominance, possibly impacting marine food webs sustaining Antarctic marine predators. Despite the simplistic ecosystem representation in our model, our results point to a potential shift in the relative success of contrasting phytoplankton ecological strategies in different regions of the Southern Ocean, with ramifications for higher trophic levels.

Understanding and managing the response of marine ecosystems to human pressures including climate change requires reliable large-scale and multi-decadal information on the state of key populations. These populations include the pelagic animals that support ecosystem services including carbon export and fisheries. The use of research vessels to collect information using scientific nets and acoustics is being replaced with technologies such as autonomous moorings, gliders, and meta-genetics. Paradoxically, these newer methods sample pelagic populations at ever-smaller spatial scales, and ecological change might go undetected in the time needed to build up large-scale, long time series. These global-scale issues are epitomised by Antarctic krill ( Euphausia superba ), which is concentrated in rapidly warming areas, exports substantial quantities of carbon and supports an expanding fishery, but opinion is divided on how resilient their stocks are to climatic change. Based on a workshop of 137 krill experts we identify the challenges of observing climate change impacts with shifting sampling methods and suggest three tractable solutions. These are to: improve overlap and calibration of new with traditional methods; improve communication to harmonise, link and scale up the capacity of new but localised sampling programs; and expand opportunities from other research platforms and data sources, including the fishing industry. Contrasting evidence for both change and stability in krill stocks illustrates how the risks of false negative and false positive diagnoses of change are related to the temporal and spatial scale of sampling. Given the uncertainty about how krill are responding to rapid warming we recommend a shift towards a fishery management approach that prioritises monitoring of stock status and can adapt to variability and change.

Antarctic coastal polynyas are persistent and recurrent regions of open water located between the coast and the drifting pack-ice. In spring, they are the first polar areas to be exposed to light, leading to the development of phytoplankton blooms, making polynyas potential ecological hotspots in sea-ice regions. Knowledge on polynya oceanography and ecology during winter is limited due to their inaccessibility. This study describes i) the first in situ chlorophyll fluorescence signal (a proxy for chlorophyll-a concentration and thus presence of phytoplankton) in polynyas between the end of summer and winter, ii) assesses whether the signal persists through time and iii) identifies its main oceanographic drivers. The dataset comprises 698 profiles of fluorescence, temperature and salinity recorded by southern elephant seals in 2011, 2019-2021 in the Cape-Darnley (CDP;67˚S-69˚E) and Shackleton (SP;66˚S-95˚E) polynyas between February and September. A significant fluorescence signal was observed until April in both polynyas. An additional signal occurring at 130m depth in August within CDP may result from in situ growth of phytoplankton due to potential adaptation to low irradiance or remnant chlorophyll-a that was advected into the polynya. The decrease and deepening of the fluorescence signal from February to August was accompanied by the deepening of the mixed layer depth and a cooling and salinification of the water column in both polynyas. Using Principal Component Analysis as an exploratory tool, we highlighted previously unsuspected drivers of the fluorescence signal within polynyas. CDP shows clear differences in biological and environmental conditions depending on topographic features with higher fluorescence in warmer and saltier waters on the shelf compared with the continental slope. In SP, near the ice-shelf, a significant fluorescence signal in April below the mixed layer (around 130m depth), was associated with fresher and warmer waters. We hypothesize that this signal could result from potential ice-shelf melting from warm water intrusions onto the shelf leading to iron supply necessary to fuel phytoplankton growth. This study supports that Antarctic coastal polynyas may have a key role for polar ecosystems as biologically active areas throughout the season within the sea-ice region despite inter and intra-polynya differences in environmental conditions.

We characterized five years of seasonal metabolic patterns in two tidal sloughs in Lower South San Francisco Bay, one surrounded by a broad tidal marsh and the other connected to restored salt ponds (ponds). Despite comparable seasonal dissolved oxygen (DO) patterns, the two sloughs exhibited markedly different seasonal metabolic rates. The in-depth analysis of these small intertidal systems reveals the complexity of processes at work in the fringing habitats of larger estuaries. In the marsh-connected slough, respiration rates peaked in summer (~10 g O2/m2/d), coincident with highly dynamic net ecosystem production rates (NEP). The peaks in DO consumption were correlated with temperature and tidal elevation. The most negative NEP rates were associated with the highest nighttime tides, when strong over-marsh respiration rates cannot be balanced by production. Thus, the combination of warmer water and the coincidence of higher-high tides with dark hours during summer may largely explain seasonal DO patterns in the marsh-connected slough. In the pond-connected slough, strong net heterotrophy (NEP < -20 g O2/m2/d) correlated with peak phytoplankton production and export from the adjacent ponds in spring, consistent with the hypothesis that organic matter exported from the pond exerts oxygen demand in the turbid slough. The impact of the elevated spring respiration rates appears to be offset by the super-oxygen-saturated water entering the slough from the highly productive pond. Oxygen minima in the slough (< 5 g/m3) occurred in summer when outflow from the pond was lower in DO, coinciding with weaker, but still very high, in-slough respiration (~ 10 g O2/m2/d).

The Antarctic sea ice zone is a dynamic and rapidly changing system, where physical and biological processes shape ecosystem structure and function. Antarctic krill (Euphausia superba) are a key species in Southern Ocean ecosystems, tightly linked to the physical environment through sea ice, ocean circulation, and primary production dynamics. Using three interdisciplinary modeling approaches, this work traces the interactions between large-scale climate and sea ice dynamics to their ecological impacts on krill habitat use. First, Earth System Model simulations indicate that ongoing sea ice loss will fundamentally alter net primary productivity, with polynyas and marginal ice zones remaining crucial productivity hotspots. Second, a qualitative network model highlights regional differences in autumn productivity and sea ice cover that affect larval krill overwinter survival under future climate scenarios. The model also suggests that sea ice terraces may serve as predator refuges, an emerging hypothesis requiring further investigation. Third, integrating the descent-ascent cycle of early-stage larval krill into a regional ocean modeling system reveals how physical and biological processes shape transport pathways and retention in nursery grounds. Results suggest that connectivity between spawning and nursery areas is influenced by biological variability, particularly in early life history traits. This dissertation offers complementary insights into climate variability, sea ice dynamics, and krill ecology, providing a multi-faceted perspective on how the Antarctic marine ecosystem responds to environmental change. By linking climate-driven shifts in sea ice and ocean circulation to krill habitat use, population connectivity, and recruitment processes, these findings advance climate-informed ecosystem modeling and support adaptive management strategies. More broadly, this research highlights the necessity of interdisciplinary approaches for forecasting the future of Antarctic ecosystems in a rapidly changing climate.