Severe 21st-century ocean acidification in Antarctic Marine Protected Areas

Domain: earth_science
Published: 2024-01-04
Editorial outcome: major_revision

Abstract
Antarctic coastal waters are home to several established or proposed Marine Protected Areas (MPAs) supporting exceptional biodiversity. Despite being threatened by anthropogenic climate change, uncertainties remain surrounding the future ocean acidification (OA) of these waters. Here we present 21st-century projections of OA in Antarctic MPAs under four emissions scenarios using a high-resolution ocean–sea ice–biogeochemistry model with realistic ice-shelf geometry. By 2100, we project pH declines of up to 0.36 (total scale) for the top 200 m. Vigorous vertical mixing of anthropogenic carbon produces severe OA throughout the water column in coastal waters of proposed and existing MPAs. Consequently, end-of-century aragonite undersaturation is ubiquitous under the three highest emissions scenarios. Given the cumulative threat to marine ecosystems by environmental change and activities such as fishing, our findings call for strong emission-mitigation efforts and further management strategies to reduce pressures on ecosystems, such as the continuation and expansion of Antarctic MPAs.

Introduction
Ocean acidification (OA) is an environmental problem threatening marine biodiversity across the global oceans2–4. OA is caused by the invasion of anthropogenic carbon (C_anth) into the ocean, which results in a decline in pH and in the saturation states of the calcium carbonate minerals aragonite (Ω_arag) and calcite (Ω_calc). The Southern Ocean is especially sensitive to OA due to the prevalence of high CO2 concentrations in cold waters, the upwelling of carbon-rich deep waters with low pH values and a high Revelle factor1,2,5. Earth system model projections suggest that surface waters in the open Southern Ocean might become seasonally undersaturated with respect to the more soluble mineral aragonite (Ω_arag < 1) by 20352,6–8. Projections of OA on the Antarctic continental shelves have so far been elusive due to the inability of coarse-resolution models to realistically resolve physical and biogeochemical processes at high resolution and in ice-shelf cavities. Observations9–24 and regional models25,26 indicate that Antarctic shelf waters are a present-day sink for anthropogenic carbon (C_anth). This net sink is the result of strong biologically driven uptake in summer, while sea-ice cover typically prevents outgassing to the atmosphere in winter25. Shelf waters are especially prone to OA resulting from rising atmospheric CO2, reductions in sea-ice cover and enhanced freshwater input. Dense-water formation on these shelves implies that shelf OA signals can subsequently spread into the global abyssal ocean11,15,16,20,21,23.

Designed to protect the unique high-latitude Southern Ocean biodiversity27,28, a network of MPAs is being developed by the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR). MPAs have been established at the South Orkney Islands Southern Shelf and in the Ross Sea region, with three additional MPAs proposed in the Weddell Sea, East Antarctica and along the western Antarctic Peninsula (Fig. 1)29–31. If realized, this network of MPAs would protect ~60% of Antarctic shelf waters (outside of ice-shelf cavities). Key organisms in the high-latitude Southern Ocean ecosystem include primary producers such as diatoms and the haptophyte Phaeocystis32,33, mid-trophic level organisms such as Antarctic krill, foraminifera, pteropods and smaller fish (e.g., Antarctic silverfish)30,34–37 and upper-trophic level predators such as large fish (e.g., Antarctic toothfish), seabirds, seals, whales and penguins31,38–41. In addition, the benthic ecosystem is highly diverse, including sponges, bivalves and echinoderms (e.g., starfish and sea urchins; see Fig. 1)42–44. New species and habitats, such as icefish nesting grounds, continue to be discovered in remote Antarctic coastal waters45,46. By preserving genetic, species and ecosystem diversity through limitation or prohibition of human activities (e.g., fishing), the implementation of MPAs can increase resilience of marine ecosystems to environmental change, including those resulting from climate change47–49.

OA is one of many Southern Ocean ecosystem stressors arising from climate change, along with warming, deoxygenation and changes in sea-ice cover and circulation. As such, a change in each of these factors individually or in a multitude of factors combined directly impacts the fitness of marine organisms and ecosystem functioning29,50–52. A large number of studies suggest that physiological processes are negatively impacted by OA, with the severity of the impact varying across organisms and life stages. Due to a higher metabolic demand under OA, phytoplankton gross primary production is reduced at pCO2 >800 μatm, though species-specific differences, species interactions and potential adaptation are not yet well understood3,53–60. An >80% reduction in egg hatch rates and thus recruitment of Antarctic krill has been reported at pCO2 >1500 μatm61, while adult krill appear to be resilient to elevated pCO2 62,63. Calcium carbonate shell dissolution in undersaturated waters (Ω < 1) has been reported for benthic organisms4, foraminifera4 and pteropods64,65. Juvenile pteropods exhibit increased resting metabolic rates at pCO2 >900 μatm66 and egg development is delayed at pH < 7.867. In contrast, the development of juvenile dragonfish accelerates at pH < 7.8, but their mortality is highest when exposed to both OA and warming68. Juvenile Antarctic emerald rockcod and black rockcod show reduced metabolic capacity to adapt to warming when exposed to pH < 7.769,70. Benthic bivalve and sea urchin larvae are increasingly malformed and damaged at pH < 7.8, possibly compromising their survival4,71. Altogether, acknowledging knowledge gaps on direct OA impacts for important species in the Southern Ocean food web (e.g., Antarctic silverfish and upper-trophic level organisms), even small impacts of OA on individual species can accumulate through the food web, as shifts in development can cause predator-prey mismatches62,67,68. While the overall number of available studies is low and inter-species variability is potentially high3,55,72, OA is among the cumulative threats to marine food webs that along with other direct threats, such as potential overfishing, stand to disrupt marine food webs in these sensitive Antarctic waters.

Here, we use a global ocean–sea ice–biogeochemistry model with eddy-permitting grid resolution on the Antarctic continental shelves and a representation of ice-shelf cavities to project twenty-first-century OA in the regions encompassed by the five adopted and proposed Antarctic MPAs under four “shared socioeconomic pathways" (SSP) emission scenarios73,74. The four SSP scenarios represent different pathways of societal development, ranging from SSP1 assuming an increasing importance of sustainable practices to the fossil-fuel intensive SSP575. By the year 2100, the atmospheric forcing applied in this study corresponds to an increase in global 2 m air temperatures relative to the 1990s of 1.2 °C (SSP1-2.6), 2.3 °C (SSP2-4.5), 3.4 °C (SSP3-7.0) and 4.2 °C (SSP5-8.5)76. Atmospheric CO2 levels in these scenarios will have increased to 446, 603, 867, and 1135 ppm75 by the year 2100, respectively. Our results suggest a dramatic increase in the volume of calcium carbonate undersaturated MPA waters by 2100. Furthermore, we show that C_anth mixes into shelf waters more readily than open-ocean waters, resulting in more severe OA on the continental shelves, where OA-sensitive ecosystems reside4,44.

Results
More severe ocean acidification on continental shelves than in the open ocean under high-emission scenarios
Simulated C_anth concentrations averaged over the top 200 m of the water column are similar in magnitude on the continental shelves and in the open ocean under present-day conditions throughout the Antarctic (Fig. 2a). In contrast, future top 200 m C_anth concentrations and those at the seafloor are at least two times higher on the continental shelves than in the open ocean for the high-emission scenario SSP5-8.5 (Fig. 2b–d). In the open ocean, bottom C_anth concentrations are elevated in the main dense-water formation regions in the Weddell Sea and the Ross Sea and downstream of these regions (up to 4 and 70 μmol kg–1 in some places for the 1990s and 2090s, respectively), whereas C_anth concentrations on the continental shelves exceed 10 and 120 μmol kg–1 in many places around the Antarctic continent (Fig. 2b, d). This shelf–open ocean gradient is in general agreement with observations, which indicate present-day shelf C_anth concentrations of up to 50 μmol kg–116,21,22,24 (observations taken between 2003 and 2014) and bottom concentrations of up to 25 μmol kg–1 in the Ross Sea region MPA16,21,24 (2003–2014) and 16 μmol kg–1 in the Weddell Sea MPA9,17,18 (1988–2008).

The difference in average C_anth concentrations between the continental shelves and the open ocean is caused by enhanced vertical mixing of C_anth in Antarctic shelf waters77, as illustrated by steeper slopes of the C_anth isolines in Fig. 2e–i (continental shelves) than in Fig. 2j–n (open ocean). This enhanced vertical mixing is a signature of dense-water formation on the continental shelves, which readily transports C_anth from the surface to depth11,15,16,20,21,23. Consequently, by 2100, C_anth concentrations in the top 750 m exceed 50 μmol kg–1 on all continental shelves in the high-emission scenario, while waters with such high concentrations are restricted to the top ~200 m in the open ocean. Given that the South Orkney Islands Southern Shelf MPA only encompasses waters that are deeper than 2000 m, it is unsurprising that C_anth penetration in this region is confined to shallower depths than in all other MPAs. The strong vertical mixing on the shelves (where most of the MPA area is located, Fig. 1) is the ultimate cause of severe OA on continental shelves and in the MPAs studied.

In the 1990s, waters on the continental shelves had a higher pH compared to the average over the regions encompassed by the whole MPA (dashed black lines on top and to the right of the solid black lines in Figs. 3 and 4, respectively). Averaged over the top 200 m, the pH in Antarctic coastal waters was up to 0.05 higher in the 1990s than in the regions encompassed by the whole MPAs (with a maximum for the East Antarctic MPA), while this difference amounts to up to 0.1 for bottom pH (Weddell Sea and East Antarctic MPA; Fig. 1). Over the twenty-first century, this shelf–open ocean gradient is sustained for the lower-emission scenarios, but it reverses for the two highest-emission scenarios in the regions encompassed by the Weddell Sea, East Antarctic and Ross Sea region MPAs (dashed colored lines below and to the left of the solid colored lines in Figs. 3 and 4, respectively). By 2100, the average pH on the continental shelves is up to 0.01 (top 200 m) and 0.04 (bottom) lower than in the area of the whole MPA, again demonstrating the overall stronger acidification in the shallow continental shelf seas than in the open ocean (Fig. 1; note that the region of the South Orkney Islands Southern Shelf MPA is exclusively “open ocean"; see Methods). Expressed as an increase in hydrogen ion concentration by the 2090s relative to the 1990s, the acidity on the continental shelves increases by up to 144% (top 200 m; Weddell Sea) and 130% (bottom; Weddell Sea), which is substantially more than for the whole-MPA averages (up to 131% and 80%; see numbers printed into panels in Fig. 3).

Over the twenty-first century, both the magnitude and sign of the vertical pH gradient in the adopted and proposed MPAs are altered due to OA. Surface waters in all MPAs have a higher pH than waters at depth in the 1990s, with the pH difference between the surface and 1500 m ranging from 0.23 in the Ross Sea region MPA to 0.27 in the South Orkney Islands Southern Shelf MPA (black lines in Fig. 4). Yet, by the 2090s, surface waters are more acidic than waters at depth for the two highest-emission scenarios, with a reversed vertical pH gradient ranging from -0.01 in the Ross Sea region MPA to -0.07 in the East Antarctic MPA for the SSP5-8.5 scenario. This is caused by a pH decline that is up to five times stronger at the surface than at 1500 m across all MPAs for all except the lowest-emission scenario, for which the acidification at the surface and at depth are similar (solid lines in Fig. 4; same for Ω_arag; see Supplementary Fig. 1 for Ω_calc). Notably, this change in vertical gradient is less pronounced on the continental shelves in the Ross Sea region MPA and Weddell Sea MPA (dashed lines), reflecting the more efficient downward transfer of the OA signal where dense waters are formed and highlighting the key role of vertical mixing.

Drastic twenty-first-century increase in calcium carbonate undersaturation
By 2100, the saturation state of aragonite and calcite decreases substantially in the Antarctic MPAs. While the depth of the aragonite saturation horizon, i.e., the depth at which Ω_arag = 1, ranges from 351 to 678 m across the MPAs in the 1990s (deepest in the Weddell Sea), it is projected to rise to the surface in all MPAs by 2100 for the two highest-emission scenarios and to 40 to 70 m and 80 to 253 m for the lower-emission scenarios SSP2-4.5 and SSP1-2.6, respectively (see circles on the y-axis of all Ω_arag panels in Fig. 4). In the 1990s, 51–84% of waters in the upper 2000 m across all MPAs are undersaturated with respect to aragonite (Ω_arag < 1), whereas only 18–51% of continental shelf waters experience undersaturation (Fig. 5). Furthermore, all waters in the MPAs are supersaturated with respect to calcite in the top 2000 m (see also Supplementary Fig. 2). However, by 2100, 17–63% of waters across all MPAs and 60–75% of all shelf waters are undersaturated with respect to calcite in the highest-emission scenario. More critically, virtually all (>95%) waters in the MPAs are undersaturated with respect to aragonite for the three highest-emission scenarios, with this ubiquitous undersaturation only being avoidable for the lowest-emission scenario SSP1-2.6 (see also Fig. 6). While 30–65% remain supersaturated for the shelves in this scenario, the undersaturated conditions in the whole MPAs are widespread even under strong climate-change mitigation (>20% supersaturation only for the proposed Weddell Sea and Antarctic Peninsula MPAs but <10% for all others).

The onset of undersaturated conditions with respect to aragonite varies with depth and across seasons, scenarios and to some extent also regions (Figs. 6 and 7). Bottom waters averaged over the whole MPAs are undersaturated throughout the analysis period (on the continental shelf, only those in the Weddell Sea are initially supersaturated; second column in Fig. 6). In contrast, the saturation state in the top 200 m of the water column exceeds a value of 1 in all MPAs in the 1990s (ranging from 1.21 in the East Antarctic MPA to 1.39 in the Weddell Sea; solid lines in the first column of Fig. 6). By the 2090s, it decreases to 0.62–0.68 across regions for the highest-emission scenario and to 1.03–1.14 for the lowest-emission scenario. In all MPAs, the saturation state displays seasonal variability in the top ~50 m (dotted and dashed lines in Fig. 7a–e). As expected from the seasonal cycle of biological activity, sea surface temperature and the entrainment of carbon into the upper ocean, winter is generally projected to be undersaturated earlier than summer. For the highest-emission scenario SSP5-8.5, the onset of undersaturated conditions at the surface is fairly consistent across all MPAs (Fig. 7a–e), ranging from 2052 to 2060 for winter (June–August), from 2066 to 2069 for the annual mean and from 2076 to 2085 for summer (December–February; latest in the Weddell Sea). Differences in the onset of undersaturation are larger across scenarios than across regions. For the emission scenario SSP3-7.0, surface waters become undersaturated in the annual mean between 2074 and 2083 across MPAs, with the proposed Antarctic Peninsula MPA and the South Orkney Islands Southern Shelf MPA being the only regions for which surface waters become undersaturated in the summer months before 2100. For the emission scenario SSP2-4.5, surface waters reach undersaturation within the twenty-first century during winter for the Ross Sea region MPA and the Antarctic Peninsula and East Antarctic MPAs. Under the lowest-emission scenario (SSP1-2.6), the upper ocean remains supersaturated with respect to aragonite across all MPAs until at least the end of the century.

Marine organisms are highly sensitive to the rate at which OA progresses, as this determines the time span available for possible acclimation or adaptation78. In the upper 50 m of the water column, our model projections suggest several decades of adaptation time between when 50% and 90% of all waters become undersaturated (Fig. 7f–j). For a given isoline of undersaturated volume, the number of years passing between the first and last month to reach this threshold varies across MPA regions and especially across emission scenarios (more compressed or elongated shape of isolines in Fig. 7f–j). While 20-28 years pass in the highest emission scenario between when the first (typically in late fall or winter) and last month (typically in late spring or summer) reach 50% undersaturation, this is 28–39 years across MPAs for the second-highest emission scenario SSP3-7.0. Given that for the SSP2-4.5 scenario, the threshold of 50% undersaturated volume is reached as early as 2060 for March and April in the Ross Sea region MPA, but not yet in summer by 2100, the time span between when the first and last month reach a given threshold appears to be longer the lower the emission scenario, providing ecosystems with an opportunity to acclimate or adapt to a changing environment under higher mitigation scenarios.

Climate-change feedbacks accelerate ocean acidification on the continental shelves
In addition to the evolution of atmospheric CO2 levels, climate-change feedbacks, i.e., changes in the physical environment in response to atmospheric warming, will alter the projected rate of ocean acidification2. Computing the total climate effect from two simulations with varying and constant climate forcing, respectively (see Methods), the simulated net climate effect in the 2090s for the SSP5-8.5 emission scenario is to decrease pH on the continental shelf (red colors in Fig. 8a, b). In the open ocean, the net climate effect decreases the top 200 m-average pH in most regions (Fig. 8a), but mostly increases bottom pH (Fig. 8b). The latter is likely due to a combination of less Antarctic Bottom Water formation, which results in less anthropogenic carbon reaching the abyss, and a southwards shift of open-ocean water masses low in anthropogenic carbon following changes in atmospheric wind systems73,74. The only exceptions to this spatial pattern are downstream of the dense-water formation regions on the Weddell Sea and Ross Sea continental shelf (where climate change decreases bottom pH; Fig. 8b) and some open-ocean regions in the Weddell Sea and East Antarctica for the top 200-m-average pH (where climate change increases top 200 m pH; Fig. 8a). In the latter regions, this can be attributed to enhanced upwelling due to increased winds, bringing waters to the upper ocean whose pH is higher than the pH of surface waters under this high-emission scenario73,74. Relative to the total change in pH between the 1990s and the 2090s, the climate-change effect is largest in the Weddell Sea and Ross Sea region MPAs, where it explains 19% and 16% (top 200 m average) and 20% and 19% (bottom), respectively, of the total change in pH on the continental shelf.

Methods
Description of FESOM-REcoM and all model experiments
For this study, we use the same model setup as refs. 73,74. We will summarize its main features hereafter, but refer the reader to the other publications for further detail. All model experiments are conducted with the global Finite Element Sea ice Ocean Model (FESOM) version 1.497, which includes a sea-ice98 and an ice-shelf component99 with constant ice-shelf geometry derived from RTopo-2100. The biogeochemical cycles of carbon, nitrogen, silicon, iron and oxygen are resolved by coupling FESOM to the Regulated Ecosystem Model version 2 (REcoM2)101,102. REcoM2 includes two phytoplankton groups (silicifying diatoms and a mixed small phytoplankton group) and two zooplankton groups and allows for variable stoichiometry.

The model equations are solved on a model grid with eddy-permitting resolution on Antarctic continental shelves (<5 km in southernmost parts; Supplementary Fig. 8). The grid resolution is lower in the open ocean (<150 km). 79% and 62% of all surface model grid cells are south of 60°S and 70°S, respectively. The model grid has 99 z-levels in the vertical. At the surface, all simulations are forced with 3-h atmospheric output from the model experiments of the AWI Climate Model (AWI-CM) that contributed to the “Coupled Model Intercomparison Project Phase 6 (CMIP6)"76. The model experiments are started in 1950 and initialized with output from the AWI-CM (physical tracers of FESOM) and with output from a simulation for the “Regional Carbon Cycle Assessment and Processes 2 (RECCAP2)" project (biogeochemical tracers of REcoM2)103.

For this study, eight model simulations are analyzed (4× simA, simB, 2× simC, simD) as outlined in the following: Following a historical simulation from 1950 to 2014, we simulate four emission scenarios for 2015–2100: SSP1-2.6 (lowest-emission scenario), SSP2-4.5, SSP3-7.0 and SSP5-8.5 (highest emission scenario). In each case, the ocean model receives fluxes of momentum, heat and freshwater from the 3-h atmospheric output corresponding to the given scenario and the atmospheric CO2 boundary condition for the ocean model increases from 312 ppm in 1950104 to 446, 603, 867 and 1135 ppm, respectively, by 210075 (simA). As such, simA represents the net carbon fluxes (the sum of the natural and anthropogenic components).

To isolate the anthropogenic carbon component, we conduct an additional simulation from 1950 to 2100 with varying climate, but with a constant atmospheric CO2 concentration boundary condition from the year 1950 (simD). The anthropogenic component of the dissolved inorganic carbon (DIC) pool (C_anth) can then be computed as the difference between the DIC in simA and that in simD. Due to computational constraints, simD is only available for the high-emission scenario SSP5-8.5. For easier comparability with existing observation-based estimates, anthropogenic carbon concentrations are reported in μmol kg–1 in the manuscript and we use monthly mean surface-referenced potential density to convert all model fields from the model units (mmol m−3). We note that since simD was generated using the 1950 atmospheric CO2 concentration, the anthropogenic carbon quantified in this study is only that which has accumulated since 1950 and not since pre-industrial times. Thus, the resulting model-based values of C_anth are likely biased low compared to observation-based estimates which include all anthropogenic carbon. Yet, since most of the increase in atmospheric CO2 levels occurred after 1950104, our model-based C_anth estimate can be assumed to capture the vast majority of the signal. The lower simulated bottom C_anth concentrations in the East Antarctic open-ocean sector in the 1990s (<1 μmol kg–1) than suggested by observations (up to 25 μmol kg–114,15,22,23) maybe attributed to the absence of shelf water masses, which are dense enough to efficiently transfer anthropogenic carbon to the abyss in this sector. However, we acknowledge the difficulty (a) to compare different observation-based estimates to each other due to the uncertainty arising from the use of various back-calculation techniques18 and (b) to directly compare the observation-based estimates from various years to the decadal-average model tracer.

To assess the model drift, we run a control simulation simB, in which both climate variability and atmospheric CO2 concentrations are held constant. For this experiment, the ocean model receives atmospheric CO2 from the year 1950 and repeated year 1955 momentum, heat and freshwater fluxes. This year was identified to best represent “normal" atmospheric conditions, as determined from an assessment of the Southern Annular Mode and El Niño Southern Oscillation in the AWI-CM model output (see ref. 73 for details). Overall, the surface drift in carbonate chemistry variables is minimal, whereas some subsurface drift exists in simB (see Supplementary Fig. 9 for pH as an example). Any deep-ocean model drift can likely at least partially be attributed to a delayed adjustment of the deep ocean to upper ocean carbonate chemistry conditions. However, we note that since the model drift is generally much smaller than the acidification signal in the different emission scenarios, it only has a small impact on our results (with the notable exception of the lowest-emission scenario for the proposed Antarctic Peninsula MPA; Supplementary Fig. 9).

Furthermore, two complementary model experiments for 1950-2100 are performed in which climate variability is held constant, while atmospheric CO2 concentrations increase (simC). By computing simA minus simC of any model tracer or flux, we can isolate the effect of climate change on the projected changes in these tracers or fluxes. Due to computational limitations, simC is only available for the intermediate scenario SSP2-4.5 and the high-emission scenario SSP5-8.5. For this manuscript, we quantify the total climate effect, thus combining the impact of, e.g., warming and changes in circulation, sea-ice cover, freshwater input and biological productivity on the projected model fields (see Supplementary Figs. 3–5).

Marine Protected Areas
Ocean acidification is assessed in five Marine Protected Areas (MPAs), of which two exist already (Ross Sea region and South Orkney Islands Southern Shelf) and three are proposed (Weddell Sea, East Antarctic, Antarctic Peninsula)105. Masks on the model grid for the different MPAs are derived from previously published coordinates105,106. For this study, we only consider the MPA area outside of the ice-shelf cavities and “continental shelf" and “open ocean" are separated at the 2000 m isobath. Based on the model grid, the surface area in each MPA corresponds to 1.44⋅106 km2 for the Weddell Sea (53% on the continental shelf), 0.97⋅106 km2 for the East Antarctic (29% on the continental shelf), 1.59⋅106 km2 for the Ross Sea (45% on the continental shelf), 0.56⋅106 km2 for the Antarctic Peninsula (73% on the continental shelf), 0.11⋅106 km2 for the South Orkney Islands (0% on the continental shelf). As the South Orkney Islands Southern Shelf MPA is entirely defined as “open ocean" based on the model topography, we only report values for the whole MPA for this MPA in all figures. In total, 60% of the continental shelf area outside of the ice-shelf cavities is covered by the five MPAs assessed in this study. The area-weighted average grid resolution outside of the ice-shelf cavities corresponds to 35 km in the Weddell Sea MPA (spread 7–88 km; 7–55 km for the continental shelf; Supplementary Fig. 8), 46 km in the East Antarctic MPA (spread 6–93 km; 6–44 km for the continental shelf), 54 km in the Ross Sea region MPA (spread 4–138 km; 4–75 km for the continental shelf), 30 km in the Antarctic Peninsula MPA (spread 2–84 km; 2–45 km for the continental shelf) and 72 km in the South Orkney Islands Southern Shelf MPA (spread 57–85 km). We note that while there are between 1250 and 3632 model grid cells in the four largest MPAs, only 22 model grid cells lie within the South Orkney Islands Southern Shelf MPA.

Calculation of carbonate chemistry
We calculate monthly mean pH and the saturation states of aragonite (Ω_arag) and calcite (Ω_calc) offline using the Python routines to model the ocean carbonate system (mocsy v2.0)107 (code is available at https://github.com/jamesorr/mocsy, last access February 1, 2023). As input parameters to the functions, we use the monthly model output of dissolved inorganic carbon, alkalinity, potential temperature, salinity, silicic acid, phosphate (obtained from model nitrate field using the Redfield ratio16) and sea-level pressure from the atmospheric output of the AWI-CM. The change in acidity reported in the manuscript is calculated from a change in hydrogen ion concentration ([H+]) between the 2090s of a given emission scenario and the 1990s of the historical simulation.

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_1": "The study presents novel high-resolufion ocean simulafions invesfigafing the impact of future climate change projecfions on ocean acidificafion of Antarcfic Marine Protected Areas (MPAs). While the study has the potenfial to make a valuable contribufion to ocean acidificafion (OA) and biodiversity in a future world, I recommend the study needs substanfial revisions to realise its potenfial.\nFollowing is a list of general issues I have with the paper and suggesfions for improvement.\n1. The focus on MPAs seems to be contrived, and the fitle and key conclusions are not clearly demonstrated in the study. For example, in the last sentence of the abstract - why does the study show the need \"for confinuity and expansion of MPAs\" - the whole of Southern Ocean will experience similar OA. What makes expansion and confinuity important? What does your study provide on the confinuity quesfion? I'm not convinced the fitle and the last sentence of the abstract have been clearly demonstrated.\n2. The paper states the shelf regions experience faster OA than the open ocean. However, the simulafions show much more nuanced behaviour. In the low emissions simulafions, the open ocean has more OA than the shelf region. It is only the two high emissions where the shelves show more OA than the open ocean. I think this is an interesfing result that warrants more invesfigafion. Establishing MPAs may be important to preserving Antarcfic biodiversity, but as you show, under high CO2 emissions scenarios, the OA impacts will be severe. The more policy-relevant issue for Antarcfic biodiversity is to limit our emissions. If biodiversity is on the shelf crifical, then keeping to low emissions scenarios would substanfially reduce the OA impacts and have the most benefit for the shelf regions. To be more relevant, I recommend focusing on how the different scenarios alter the trajectory and impact of OA in the open ocean and shelf regions. If we really go along the RCP8.5 scenario, the impacts will be catastrophic for many ecosystems, and the expansion of MPAs will not prevent this. The needed message is the benefit we gain by limifing our emissions.\nSpecific Comments\nl3-4 there have been many studies of OA in the Southern Ocean. The unique bit here is the befter resolufion of the shelf regions. Use the improve resolufion to provide new insights in the future OA.\nl11-12 - need more analysis to show how this preserves ecosystem integrity\nl18-19 - cite the Revelle factor\nl33-34 - MPAs will comprise 60% of Antarcfic Shelf water. Why does going to more areas improve resilience to OA?\nl48-51 - What is the role of subducfion of AABW on future OA impacts on these benthic ecosystems?\nl68-69 - more severe OA on the shelf than the open ocean, not true for all emission scenarios\nl81 - why did you lump the upper 2000 m of the ocean? biological reason? please jusfify.\nl102-105 - to first order, OA is driven by atmospheric CO2 and verfical ocean mixing\nl114-115 - more severe OA on the shelf than the open ocean, not true for all emission scenarios\nl121-122 - under the two high emission scenarios, aragonite is chemically unstable at the surface - this is a dramafic change in the chemical state of the ocean\nl175-176 - dramafic OA in the high emission scenarios. Why is the OA in the Weddell much less than other regions in the low emissions scenarios? Preserving sea ice cover is important? is also important to preserving ice shelves and dramafic sea level rise.\nl167-185 - the role of ocean warming and sea ice changes on the rate of OA and its impact.\nl210 - I suggest either expanding the results to discuss and show dissolved oxygen simulafions to remove this. Where did the 61.3 hypoxic threshold come from? how does these threshold change with emissions scenarios? is it avoided in the low emissions scenarios?\nl217- Is there exisfing evidence of the impact of fishing on the Antarcfic Ecosystems? What is it?\nFigure 1. East Antarcfica, Ross Sea and Weddell Sea MPAs show shelf areas have less OA impact than the open ocean in low emissions scenarios. Why? I think this is an important feature of the results that do require a high-resolufion simulafion to show. It also important if the goal is to preserve biodiversity in the shelf regions under OA.\nFigure 2. Why upper 2000m?\nFigure 3. similar to figure 1.", "reviewer_2": "Review of Severe 21st-century ocean acidificafion demands confinuance and expansion of Antarcfic Marine Protected Areas by Nissen et al.\nThis paper uses a high-resolufion ocean-sea ice-biogeochemistry model to explore ocean acidificafion in five Antarcfic Marine Protected Areas (two adopted, three proposed) under four emission scenarios. Their major findings are that surface pH declines significantly in all MPAs by 2100, and to a greater extent from the lowest to the highest emissions scenario. They also show that by 2100 aragonite undersaturafion occurs ubiquitously across all MPAs examined under all but the lowest emission scenario. They also invesfigate the effects of verfical mixing on ocean acidificafion and the transport of anthropogenic carbon to the subsurface and deep ocean, and projected changes in calcite undersaturafion.\nThis work is of a very high quality and will make a substanfial contribufion to the field, due to its sound scienfific approach and findings as well as its strong relevance to policy making. The work is fimely in relafion to decision making at internafional levels, both with respect to global climate change and protecfion of Antarcfic marine systems. As well as being important in its own field, this paper will also be of interest and importance to a broader readership due to its broad relevance across the remit of global climate change and its impacts, and informing policy in this space. There are some minor issues and quesfions that I have outlined below, that I hope will help to improve the manuscript. As such, I believe that this work will be suitable for publicafion in Nature Communicafions, after minor/moderate revisions.\nThe methodology is robust in supporfing the results reported and conclusions drawn, and is based on previously published work and ongoing world-leading research efforts. The data analysis, interpretafion and conclusions reported in this paper are of a high standard in general, although I do have some points for clarificafion that I have outlined below. These require aftenfion, but if safisfactorily addressed, they will certainly not prohibit publicafion. The methods descripfion is sufficiently detailed for the purposes of this paper, and refers to other published work for more detail. One minor point here is that one of the references cited is Nissen et al., 2023, in review. If that paper is not published before this one, that reference will need to be removed.\nIn the following, I provide a small number of more major or overarching comments, followed by minor and editorial comments.\nMajor comments:\nThis work has the potenfial to be very valuable for scienfific and broader audiences. However, I felt that there were opportunifies missed to really emphasise this value and the key points of the work. In parficular, the final paragraph of the main text (parficularly lines 222-231) was not as compelling as it could have been. It feels a bit like a list of statements, rather than a well-crafted and coherent narrafive. There are also a number of places where I felt that stronger wording could be used to really emphasise the importance of the work, for example “is advisable”, “are not spared”, “best policy tools”. I recommend that the authors revisit this secfion to really get the most impact out of their high-quality scienfific work.\nRelated to this, I felt that the framing of OA as one of mulfiple stressors on the system could be improved to be clearer and more compelling, both in the introducfion (line 27-29; 59-62) and in the final paragraph (line 224-228). I suggest that more of a focus is placed on cumulafive impacts (rather than just menfioning them) and the importance of increasing resilience in the system to the changes underway.\nMy final suggesfion for a major improvement would be to explain more clearly what the different SSPs are and what they represent. I did not feel that this was adequately explained, in terms of the different emissions pathways and outcomes for CO2 concentrafions and warming, and what was explained was buried in the methods. Parficularly if this work is to be used by people outside of the immediate field (e.g. other scienfists, policy makers), I think it would really help in conveying the main messages of the paper if the SSPs were more clearly explained in the early stages of the main text.\nMinor comments:\nTitle: I am not convinced confinuance is right in this context. I suggest changing to confinuafion, which is more accurate.\nLine 3: ‘liftle is known’. Given what is known, I think this is probably an overstatement. I would suggest rewording to reflect that we do have some knowledge, but that significant gaps and uncertainfies remain.\nLine 7: here you make a compelling statement on changes in hydrogen ion concentrafion, but this is not addressed anywhere else in the main manuscript or supplementary informafion to substanfiate this claim. This should be incorporated and at least menfioned in the main manuscript, or removed here.\nLine 23-24: ‘Antarcfic shelf waters are a present-day sink for Canth’. I think it would be useful here to add a brief descripfion of seasonal changes in sink/source dynamics, so that the reader has the full picture of what makes up the net annual sink.\nLine 34: East Antarcfic should be East Antarcfica here (because of the preceding ‘in’).\nFigure 1: I think it should be noted that the y-axis scale for the Weddell Sea is different to the others, and ideally, the ficks should include minimum and maximum bounds (rather than having any data points outside of the bounded scale).\nLine 37: for the broad readership of Nature Communicafions, I think it is necessary to state what Phaeocysfis is. Hence, I would add ‘the haptophyte Phaeocysfis’ (or prymnesiophyte, although that may be too specific).\nLine 53: should black be capitalised?\nLine 57: there is considerable debate amongst the biological community as to whether there are any keystone species in the Southern Ocean (either Antarcfic krill or silverfish), so I suggest the authors consider whether it is appropriate to use this terminology here without any substanfiafion. Especially the way the sentence is constructed ‘keystone species, e.g. … upper trophic level organisms’ does not seem right to me without naming any organisms, so I suggest revising.\nLine 61: among with. Should be either among or with, or possibly along with\nLine 67-69: I suggest adding that confinental shelf ecosystems are also more sensifive to the impacts of OA, to strengthen your point further.\nLine 70-71: simulated top 2000 m average and boftom Canth concentrafions. It becomes clear what this means later on, but on the first menfion, it is ambiguous. I suggest spelling it out more clearly on first use and then using this terminology for the rest of the paper.\nFigure 2: some of the text is too small to read; I suggest enlarging.\nLine 91-92: severe shelf/MPA OA. I suggest spelling this out as ‘severe OA on shelves and in the MPAs studied’ or similar, to improve readability.\nLine 99-100: …up to five fimes stronger surface decline. This is awkward to read; I suggest rewording for clarity.\nLine 121-123: ‘it is projected to rise…’. Is this for all MPAs or a subset? It would help the reader’s understanding to state this explicitly here.\nFigure 5: text is too small for ice panels. Also, the label for 2100 appears to be misaligned in panel g\nLine 149-151: I think it would be useful to state at the end of this sentence ‘to at least end of century’ or ‘by 2100’ or similar to really make it clear.\nLine 153: adaptafion. You could add acclimafion here too.\nLine 173-174: you could also point out here that this is also true for volume in the 2090s, as shown in figure 4, to further strengthen your case.\nLine 182-185: would it also be worth stafing here that the projected increase in PP also contributes to this effect?\nLine 192: acclimafizafion. Is this correct or do you mean acclimafion?\nLine 191-196: after respecfively (line 196), I suggest adding a statement that this means that benthos are likely to have a smaller tolerance range to variability in condifions and also menfion that this is in addifion to their limited ability to move.\nLine 214: have should be has (referring to reducfion).\nLine 216: …is worrisome. Related to my major comment about strengthening wording to be more compelling, I think it would be beneficial here to use stronger wording and to elaborate on what you mean.\nLine 230: In addifion to my major comment about this paragraph, I suggest adding ‘and direct human impacts’ after ‘environmental change’.\nLine 231: I suggest specifying ‘global emissions of greenhouse gases’\nLine 478: <100 km. From looking at the figure, this does not appear to be true for the region between 50 and 60 S in the Pacific and Atlanfic sectors. Should it be >100 or <150?\nLine 512: due should be due to\nLine 531: state these what, so that this is not left hanging.\nLine 542 (and 543, 544, 545): I suggest using standard scienfific notafion (x106) rather than Mio.\nLines 544-548: It is rather confusing that the authors state that 73% of the Antarcfic Peninsula MPA area is on the shelf (i.e. 27% is not) and then to say that ‘the vast majority’ of grid points are defined as shelf. This also appears to go against what is stated in the text, which is that the whole of the Peninsula area is over the shelf. It strikes me that 27% is enough to run the analysis for the open ocean component. However, I do trust the authors’ judgement on this and their approach to the analysis, so I suspect it is just a case of this wording being confusing in the methods secfion. Please clarify.\nReferences:\nIn general, there is very good coverage of the important references in this field and the study is placed appropriately within the wider literature. There are a small number of references that I felt were missing and would be beneficial to add for comprehensive coverage. These are:\nDeppeler, S., Petrou, K., Schulz, K. G., Westwood, K., Pearce, I., Mckinlay, J., et al. (2018). Ocean acidificafion of a coastal Antarcfic marine microbial community reveals a crifical threshold for CO2 tolerance in phytoplankton producfivity. Biogeosciences 15, 209–231. doi: 10.5194/bg-15-209-2018\nGuft, J., Bertler, N., Bracegirdle, T. J., Buschmann, A., Comiso, J., Hosie, G., et al. (2015). The Southern ocean ecosystem under mulfiple climate change stresses – an integrated circumpolar assessment. Glob. Change Biol. 21, 1434–1453. doi: 10.1111/gcb.12794\nHancock, A. M., Davidson, A. T., Mckinlay, J., Mcminn, A., Schulz, K. G., and Van Den Enden, R. L. (2018). Ocean acidificafion changes the structure of an Antarcfic coastal profistan community. Biogeosciences 15, 2393–2410. doi: 10.5194/bg-15-2393-2018\nHenley, S. F., Cavan, E. L., Fawceft, S. E., Kerr, R., Monteiro, T., Sherrell, R. M., et al. (2020) Changing Biogeochemistry of the Southern Ocean and Its Ecosystem Implicafions. Front. Mar. Sci. 7:581. doi: 10.3389/fmars.2020.00581\nTortell, P. D., Payne, C. D., Li, Y. Y., Trimborn, S., Rost, B., Smith, W. O., et al. (2008). CO2 sensifivity of Southern Ocean phytoplankton. Geophys. Res. Left. 35:L04605.\nTrimborn, S., Brenneis, T., Sweet, E., and Rost, B. (2013). Sensifivity of Antarcfic phytoplankton species to ocean acidificafion: Growth, carbon acquisifion, and species interacfion. Limnol. Oceanogr. 58, 997–1007. doi: 10.4319/lo.2013.58.3. 0997\nWestwood, K. J., Thomson, P. G.,Van Den Enden, R. L.,Maher, L. E., Wright, S. W., and Davidson, A. T. (2018). Ocean acidificafion impacts primary and bacterial producfion in Antarcfic coastal waters during austral summer. J. Exp.Mar. Biol. Ecol. 498, 46–60. doi: 10.1016/j.jembe.2017.11.003\nThere are a number of places where the presentafion of number ranges is grammafically incorrect. These should either be presented as ‘between x and y’, ‘from x to y’ or ‘x-y’. Examples of incorrect construcfions are at lines 179 (between December-February), 487 (from 1950-2014), 556 (between 1250-3632). Please correct these.\nA minor grammafical point would be that there are lots of uses of an Oxford comma, which strictly speaking is incorrect and these should be removed. Examples are at lines 39 (after whales), 40 (after bivalves), 50 (after foraminifera), 490 (after heat), 534 (after input).\nSupplementary informafion\nSupp Figure 1: I suggest making the images larger to occupy some of the large amount of white space and to make them easier to read.\nSupp Figure 2: To improve readability, I suggest adding a y-axis scale to panel d to apply to panels d and e, in the same way that the scale on panel a applies to a, b and c. I would also suggest nudging the two lines of the y-axis label slightly further apart to avoid the 2s colliding. It would also help to make the labels ‘annual mean’ and ‘DJF mean’ more prominent for clarity.\nSupp Figure 3: In line 3 of the capfion, profile should be profiles.\nSupp Figure 4: In line 5 of the capfion, I think cb is a typo. I also think the y axis of panel b should say calc, not arag.\nSupp Figure 5: in line 3 of the capfion, the comma should be a semi-colon (;)\nThese comments and suggesfions should all be amenable to being addressed by the authors, and in this case I believe the work would be ready for publicafion in Nature Communicafions. I am happy to review it again, or if the editor is happy handling this themselves, that is fine for me too.\nSian Henley\nUniversity of Edinburgh, UK\n9/6/2023", "reviewer_3": "The study of Nissen and colleagues explores the implicafions provided by the high-resolufion modelling of a much more severe OA in the Southern Ocean than reported ever before. The study excels in the modelling outputs, the scenarios are superbly linked to the physical-chemical process and produce state-of-the-art science on the ocean acidificafion over this century. The study really shows the importance of the model improvements and the implicafions it could bring.\nOn the other hand, the authors used the model outputs to suggest that the current predicfions of the MPAs and its connecfivity are not sufficient given the projected increases in OA. While this is a solid implicafion of the model results, the MPA efficiency cannot be evaluated only based on the saturafion state (of 1) alone. As the MPAs are inherently linked to the protecfion of marine biology, the paper insufficiently covers the link between the chemistry and the biology, leaving a big gap in the interpretafion. So far, in the literature, there are numerous studies for variety of species and funcfional groups for which specific pH or omega saturafion state THERESHOLDS exists. Instead of just using a general omega =1 (which is even insufficient for the marine calcifiers impacted by dissolufion), the authors have unique opportunity to apply the thresholds for different climate scenarios and show species sensifivity (or resilience). That would be a much stronger link to the MPAs due to climate change/OA and associated loss of habitat.\nWith that, I would suggest that the authors separate the pelagic and benthic habitats and assess the impacts separately, i.e. not only produced the change in the average over the upper 2000m, but actually more applicable for the pelagic and benthic biota, for example pteropods occupy the upper 200m, so project the threshold changes for that habitats, and equally the boftom for the adult benthic calcifiers. As it is now, it is not accurate enough in terms of biological representafion. This should significantly strengthen the implicafions of why the MPA expansion/reconsiderafion is needed.\nThe weakest point so far is the discussion on the MPA, implicafions, the only solufion the enlargement along with the mifigafion. There are several other opfions, like fisheries management, both in catch per unit effort change and fiming of fisheries, etc. I think this secfion needs to be scienfifically beefed-up content wise, best to examine the MPAs strategies and alternafives in the best managed MPAs across the world."}, "author_response": "Response to comments by all reviewers\nWe thank all three reviewers for their time and thoughts spent on our paper. All comments\nhelped to improve the paper. In summary, in the revised manuscript, we have made the\nfollowing major changes:\n• We have changed the title of the manuscript and reworked the discussion surrounding\nMarine Protected Areas. We think that the new pieces reflect the conclusions from our\nown analysis more clearly. We now highlight more clearly that both emission mitigation\nefforts and fisheries management, e.g., with MPAs, are needed to safeguard Antarctic\necosystems.\n• In our writing, we put a larger emphasis on highlighting scenario differences, in particular\nthe fact that the Antarctic continental shelf only experiences more severe ocean\nacidification than open ocean waters for the two highest-emission scenarios.\n• We now include a more detailed description and discussion of climate-change feedbacks\nto illustrate their sizeable contribution to the severe ocean acidification on the Antarctic\ncontinental shelf under the highest-emission scenario.\n• By reporting numbers for the top 200 m of the water column and the bottom layer in the\nrevised manuscript (instead of for the top 2000m), we tie our findings more closely to\nhabitats of calcifying organisms (pteropods in the top 200m and benthic organisms at the\nseafloor).\n• We include new time-series figures of pH and the saturation states (Ω) with respect to\naragonite and calcite in the manuscript. Thereby, we hope to make our findings more\nuseful to scientists studying organisms who are sensitive to a threshold different from\ne.g., Ω=1.\nReviewer #1 (Remarks to the Author):\nThe study presents novel high-resolution ocean simulations investigating the impact of future\nclimate change projections on ocean acidification of Antarctic Marine Protected Areas (MPAs).\nWhile the study has the potential to make a valuable contribution to ocean acidification (OA) and\nbiodiversity in a future world, I recommend the study needs substantial revisions to realise its\npotential.\nWe thank reviewer #1 for this feedback. In the revised version of the manuscript, we have\nimplemented all suggestions, which improved the manuscript.\nFollowing is a list of general issues I have with the paper and suggestions for improvement.\n1. The focus on MPAs seems to be contrived, and the title and key conclusions are not clearly\ndemonstrated in the study. For example, in the last sentence of the abstract - why does the\nstudy show the need \"for continuity and expansion of MPAs\" - the whole of Southern Ocean will\nexperience similar OA. What makes expansion and continuity important? What does your study\nprovide on the continuity question? I'm not convinced the title and the last sentence of the\nabstract have been clearly demonstrated.\nOne of the main challenges in the design, implementation and evaluation of Antarctic Marine\nProtected Areas (MPAs) is the scarcity of observational and modeling data on marine\necosystem stressors at high Southern Ocean latitudes. Since our model onfiguration generates\na more realistic process representation on the Antarctic continental shelf than previous efforts,\n1\nwe aim to make our model results directly usable for those designing and implementing\nAntarctic MPAs.\nWe agree that the manuscript would benefit from additional text describing the link between\nMPAs and environmental stressors such as ocean acidification (OA). MPAs promote genetic,\nspecies, and ecosystem diversity and ultimately resilience to other stressors such as ocean\nacidification through the prohibition or reduction of human activities such as fishing (e.g.,\nRoberts et al., 2017). The projected severe OA by our model thus suggests continuation and\nexpansion of Antarctic MPAs in order to increase ecosystem resilience to these environmental\nchanges. If MPAs were stopped altogether and no other regulation of fishing activities was put\nin place, high-latitude ecosystems would thus be expected to be more vulnerable to climate\nchange. Nonetheless, we agree with the reviewer on their second major comment (see below)\nthat emissions reductions are equally important for minimizing impacts on marine ecosystems.\nUltimately, both MPAs and emissions reductions are necessary to safeguard Antarctic marine\necosystems.\nWe realize that the link between our findings and the need for continuation and expansion of\nMPAs is of more indirect nature. To more adequately reflect this in the paper, we have changed\nthe title of the manuscript to “Severe 21st-century ocean acidification in Antarctic Marine\nProtected Areas” and the second half of the abstract to now read:\n“[…] By 2100, we project pH declines of up to 0.36 (total scale) for the top 200 m of the water\ncolumn, corresponding to a 131% increase in hydrogen ion concentration relative to the 1990s.\nVigorous vertical mixing of anthropogenic carbon on the continental shelves produces severe\nOA within the proposed Weddell Sea, Antarctic Peninsula and East Antarctic MPAs and the\nexisting Ross Sea MPA, where pH decreases similarly throughout the water column. As a\nresult, end-of-century aragonite undersaturation is ubiquitous across MPAs under the three\nhighest emission scenarios. Given the cumulative threat to marine ecosystems by\nenvironmental change and direct human activities such as fishing, our findings call for strong\nemission-mitigation efforts and further management strategies to reduce pressures on\necosystem integrity, such as the continuation and expansion of Antarctic MPAs.”\nFurther, we have reworked the introduction to introduce the link more clearly between\nimplementing MPAs and resilience to environmental change:\n“By preserving genetic, species and ecosystem diversity through limitation or prohibition of\nhuman activities (e.g., fishing), the implementation of MPAs can increase resilience of marine\necosystems to environmental change, including those resulting from climate change45.”\nLastly, we kindly refer the reviewer to our answer to the second major comment, which details\nhow we put a more balanced emphasis on the need to reduce emissions of greenhouse gases\nand to continue and expand Antarctic MPAs.\n2. The paper states the shelf regions experience faster OA than the open ocean. However, the\nsimulations show much more nuanced behaviour. In the low emissions simulations, the open\nocean has more OA than the shelf region. It is only the two high emissions where the shelves\nshow more OA than the open ocean. I think this is an interesting result that warrants more\ninvestigation. Establishing MPAs may be important to preserving Antarctic biodiversity, but as\nyou show, under high CO2 emissions scenarios, the OA impacts will be severe. The more\npolicy-relevant issue for Antarctic biodiversity is to limit our emissions. If biodiversity is on the\nshelf critical, then keeping to low emissions scenarios would substantially reduce the OA\n2\nimpacts and have the most benefit for the shelf regions. To be more relevant, I recommend\nfocusing on how the different scenarios alter the trajectory and impact of OA in the open ocean\nand shelf regions. If we really go along the RCP8.5 scenario, the impacts will be catastrophic for\nmany ecosystems, and the expansion of MPAs will not prevent this. The needed message is the\nbenefit we gain by limiting our emissions.\nWe thank the reviewer for this comment. As the reviewer correctly states, the different scenarios\nshow vastly different OA trajectories for the 21st-century, which we did not emphasize enough in\nthe original manuscript. Indeed, much can be gained (or much less may be lost) by reducing\ngreenhouse gas emissions and committing to a low-emission trajectory for the remainder of the\ncentury.\nIn particular, the severity of the projected ocean acidification is much lower for the SSP1-2.6\nand SSP2-4.5 scenarios than for the SSP3-7.0 and SSP5-8.5 scenarios, and as a result, waters\non the Antarctic continental shelf are only more severely affected than open-ocean waters in the\nlatter two scenarios. In addition to the different trajectories in atmospheric CO concentration,\n2\nthe scenarios also differ in the strength of climate-change feedbacks, e.g., enhanced ocean\nacidification due to reduced sea-ice cover. In the highest-emission scenario, these feedbacks\naggravate the projected ocean acidification by ~20%. In the revised manuscript, we now\nemphasize these scenario differences, in particular the avoidability of severe acidification under\nthe lowest-emission scenario and the drivers of severe acidification under the highest-emission\nscenario.\nThe title in the first result section was changed to:\n“More severe ocean acidification on continental shelves than in the open ocean under high-\nemission scenarios.”\nFurther, we have added statements to emphasize the scenario differences in the result and\ndiscussion sections:\n“Over the 21st century, this shelf–open ocean gradient is sustained for the lower-emission\nscenarios, but it reverses for the two highest-emission scenarios in the regions encompassed by\nthe Weddell Sea, East Antarctic and Ross Sea MPA […].”\n“For other regions and the intermediate-emission scenario SSP2-4.5, the simulated climate-\nchange feedback is smaller or even opposite in sign (Fig. 8 and Supplementary Fig. 8). While a\nsmaller climate-change feedback can likely largely be attributed to a smaller decrease in sea-ice\ncover and a smaller increase in ice-shelf basal melt, respectively (Supplementary Figures 4),\nthe contribution of changes in CO solubility and of a redistribution of water masses is possibly\n2\nnon-negligible, especially where climate-change feedbacks act to increase pH (see e.g., open-\nocean regions near the Antarctic Peninsula in Supplementary Figures 5). Overall, this reflects\nthe complex spatio-temporal interplay of the many factors contributing to the total climate-\nchange feedback. Our model experiments, conducted with a more realistic process\nrepresentation on the Antarctic continental shelf than earlier modeling studies that investigated\nSouthern Ocean climate-change feedbacks2,76,77, demonstrate that climate-change feedbacks\non OA can be substantial under high-emission scenarios. While the projected upper ocean\nacidification under the high-emission scenario SSP5-8.5 in our model is very similar to the\nacidification previously reported for the high-latitude Southern Ocean in Earth system models78,\nthe bottom acidification rates on the Antarctic continental shelf are about two times larger in our\nmodel simulations (pH declines by more than 0.35 as opposed to by less than 0.2 in ref78). Our\n3\nfindings illustrate the benefits of following a low-emission trajectory over the 21st century, which\nwould minimize climate-change feedbacks on OA.”\nWe also kindly refer the reviewer to our answer on the comment on L. 175-176, where we\ndescribe climate-change feedbacks in more detail and outline the changes applied to the result\nsection.\nLastly, we fully agree with the reviewer that limiting our emissions is critical. Both emissions\nreductions and a reduction or prohibition of fishing activities will be key tools in the coming\ndecades when aiming to reduce pressures on unique high-latitude marine ecosystems. As a\nnumber of uncertainties remain regarding the quantitative ecosystem-wide impacts of both\nocean acidification and fishing (especially when these act in concert), our modeling results call\nfor a) emissions reductions to minimize ocean acidification, b) more process studies to enhance\nour understanding of cumulative impacts of multiple ecosystem stressors and c) a simultaneous\ncontinuation of efforts to limit or prohibit fishing activities in high-latitude waters.\nTo clarify these points, we have reworked the final paragraph of the discussion in the revised\nmanuscript, which now reads:\n“Our 21st-century projections call for strong emission-mitigation efforts, as high-latitude\nSouthern Ocean waters are only spared from severe OA in the lowest-emission scenario\n(SSP1-2.6) and as climate-change feedback substantially aggravate OA on the Antarctic\ncontinental shelf under the highest-emission scenarios (SSP5-8.5). OA across all emission\nscenarios within the proposed and adopted MPAs is comparable to OA in continental shelf\nareas not protected within an MPA (Supplementary Figure 7). This implies two things for the\ndesign and evaluation of MPAs: Firstly, as long as some portion of Antarctic waters remains\noutside of MPAs, these regions could serve as an important reference area for differentiating\nthe ecosystem impacts of fishing from climate change and thus assessing the effectiveness of\nMPAs27-29. Secondly, given that ecosystems in high-latitude waters outside of the MPAs will be\nsimilarly affected by severe OA, a reduction of fishing activities in a larger fraction of Antarctic\ncoastal waters could be considered to reduce cumulative stressors on the system. In that\ncontext, our findings support the notion of today’s Weddell Sea acting as a climate-change\nrefuge29, and the adoption of the Weddell Sea MPA should therefore have high priority. The\nactive fisheries for Antarctic toothfish and Antarctic krill have been suggested to already be\npotentially impacting ecosystems in the Ross Sea88,89 and near the Antarctic Peninsula90,91,\nrespectively. As climate change progresses, cumulative impacts from fishing and environmental\nchange will thus become increasingly likely and possibly more devastating than the impacts of\neach stressor alone92. Therefore, better understanding the complex interactions of OA with\nother ecosystem stressors including fishing is key for a sustainable management of Antarctic\nmarine ecosystems under changing environmental conditions, which will likely make a larger\nfraction of the previously ice-covered high-latitude Southern Ocean accessible to fishing\nactivities (Fig. 7). Altogether, the reduction of greenhouse gas emissions together with\nsimultaneous management of fishing and other human activities, e.g., within MPAs, are\nnecessary for safeguarding Antarctic marine ecosystems.”\nSpecific Comments\nl3-4 there have been many studies of OA in the Southern Ocean. The unique bit here is the\nbetter resolution of the shelf regions. Use the improve resolution to provide new insights in the\nfuture OA.\nWe have rephrased the sentence as follows:\n4\n“Despite a particular sensitivity to ocean acidification (OA), significant gaps remain surrounding\nthe future carbonate chemistry of waters on the Antarctic continental shelf.”\nl11-12 - need more analysis to show how this preserves ecosystem integrity\nPlease see our answer to the first major point above, where we explain how we have revised\nthe wording in the abstract and elsewhere.\nl18-19 - cite the Revelle factor\nDone as suggested. The sentence now reads:\n“The Southern Ocean is especially sensitive to OA due to the prevalence of high CO\n2\nconcentrations in cold waters, the upwelling of carbon-rich deep waters with low pH values and\na high Revelle factor8,9,12.”\nl33-34 - MPAs will comprise 60% of Antarctic Shelf water. Why does going to more areas\nimprove resilience to OA?\nThis study assesses current (two) and proposed (three) MPAs. It is only with the proposed\nMPAs, which have not yet been adopted, that MPAs will comprise 60% of the Antarctic shelf\nwater. As noted above, we made clearer in the text what role MPAs play in promoting\nresilience.\nl48-51 - What is the role of subduction of AABW on future OA impacts on these benthic\necosystems?\nIn Antarctic Bottom Water formation regions, OA signals are more quickly transferred to the\nbottom layer, both on the continental shelf and downstream in the open ocean. As a result,\nbenthic ecosystems along these flow pathways will readily be exposed to OA. While the\nassumption of a higher susceptibility of these organisms to OA (relative to those in the pelagic\nrealm) is conceivable due to their long lifespan and immobility, we have a limited understanding\nof adaptation and acclimation potential in these organisms.\nWe kindly refer the reviewer to the revised discussion section, in which we discuss the possibly\nhigh sensitivity of benthic organisms to ocean acidification, also in the context of AABW\nsubduction:\n“While we have a limited understanding of adaptation and physiological acclimation in these\norganisms on multi-decadal time scales74,77,78, it is conceivable that benthic organisms have a\nhigher sensitivity to changing conditions than of mobile pelagic organisms due to the smaller\nvariability in pH and Ω at depth than in the surface layer (simulated monthly Ω in the 1990s\narag\naveraged over the Antarctic continental shelf spans 0.91-0.93 and 1.32-1.67 below 500 m and\nabove 50 m, respectively). The exposure to smaller pH variability implies that benthic organisms\nlikely have a smaller tolerance range, making them more susceptible to OA given their limited\nability to move. We note that in the Weddell Sea, changes in the physical environment cause\nthe transfer of newly formed dense waters to the abyss to be less efficient by 2100 under the\nhighest-emission scenario69,70, reducing the decadal rate of decline in bottom pH in the whole\nMPA from 0.03 (2040-2085) to 0.012 (2086-2100; based on a linear regression of the solid dark\nblue line in Fig. 3b). However, in the two highest emission scenarios, the projected pH by 2100\nis <7.8 for all MPAs (Fig. 1), a level at which many detrimental effects have been reported for\nprimary producers, zooplankton, fish and benthic organisms3,4,63–67.”\n5\nl68-69 - more severe OA on the shelf than the open ocean, not true for all emission scenarios\nGood catch! In the revised version of the manuscript, we provide more detail on scenario\ndifferences and highlight these differences more clearly (including climate-change feedbacks for\nthe SSP2-4.5 and SSP5-8.5 scenarios). We refer the reviewer to our answer to the second\nmajor point above, which details all the modifications done in the manuscript in response to this\npoint.\nl81 - why did you lump the upper 2000 m of the ocean? biological reason? please justify.\nThis choice was made to more easily synthesize our findings.\nWe agree with the reviewer that the link between changes in water chemistry and biology at\ndifferent depths could be made clearer for the reader. In the revised manuscript, we report our\nfindings for the top 200m of the water column and for the bottom layer to better reflect benthic\nand pelagic habitats of calcifying organisms such as pteropods and benthic ecosystems.\nWe have further modified Figure 1 and Figure 2 of the manuscript (see Figs. 1 & 2 below). All\nnumbers reported in the text were adapted accordingly. Please note that in Figure 2, we have\nfurther decided to also show panels for the regions “all shelves” and “all open ocean” for a\ncircumpolar view on the invasion of anthropogenic carbon into the ocean.\nFig. 1: Revised Fig. 1 of the manuscript.\nl102-105 - to first order, OA is driven by atmospheric CO2 and vertical ocean mixing\nWe agree with the reviewer and have adapted the respective sentence as follows:\n“Notably, this change in vertical gradient is less pronounced on the continental shelves in the\nRoss Sea MPA and Weddell Sea MPA (dashed lines), reflecting the more efficient downward\ntransfer of the OA signal where dense waters are formed and highlighting the key role of vertical\nmixing.”\nl114-115 - more severe OA on the shelf than the open ocean, not true for all emission scenarios\nWe have thoroughly reworked this aspect of the manuscript, and we refer the reviewer to our\nanswer to the second major point above for all changes.\nl121-122 - under the two high emission scenarios, aragonite is chemically unstable at the\nsurface - this is a dramatic change in the chemical state of the ocean\nWe entirely agree with the reviewer on this point. To keep the focus of this part of the\nmanuscript on the results, we have not made any change to the indicated lines. However, we\nwould like to point the reviewer to the revised discussion section, in which we now state:\n“Aragonite undersaturation is ubiquitous from surface to depth across all proposed and adopted\nMPAs by 2100, implying that aragonite-forming organisms such as pteropods11,59,60,62 will be\nunable to find a refuge with supersaturated conditions and will hence be exposed to conditions\nthat are chemically unstable for their shells.”\n7\nl175-176 - dramatic OA in the high emission scenarios. Why is the OA in the Weddell much less\nthan other regions in the low emissions scenarios? Preserving sea ice cover is important? is\nalso important to preserving ice shelves and dramatic sea level rise.\nWe thank the reviewer for this comment. Indeed, our modeling results highlight that preserving\nsea-ice cover and keeping ice-shelf basal melt rates low are important factors to minimizing\nocean acidification. In general, a reduced sea-ice cover exposes a larger ocean surface area to\nthe atmosphere, facilitating additional oceanic uptake of anthropogenic CO and hence\n2\naggravating ocean acidification. Similarly, a higher input of freshwater from ice-shelf basal\nmelting reduces the buffer capacity of near-coastal waters and increases ocean acidification.\nIn the present-day, the Weddell Sea has the highest sea-ice cover of all five MPA regions (in\nagreement with observations, see e.g., Eayrs et al., 2019). When this sea-ice cover is\nsignificantly reduced towards the end of the 21st-century in the highest-emission scenarios, a\nmuch larger surface area in the Weddell Sea is exposed to much higher atmospheric CO\n2\nlevels, resulting in accelerated ocean acidification rates for this region. This explains why by the\nyear 2100, the Weddell Sea does not act as the climate-change refuge anymore that it is today\n(see e.g., Teschke et al., 2021 and our manuscript).\nTo put more emphasis on the dynamics at play and to illustrate ocean acidification feedbacks\ninvolving the physical climate system, we have dedicated a new sub-section in the result section\nto this topic. In particular, we have added new figures to the manuscript (see Figures 3 & 4\nbelow, corresponding to Figure 8 and Supplementary Figure 5 of the revised manuscript) and\nadded the following text:\n“Climate-change feedbacks accelerate ocean acidification on the continental shelves. In\naddition to the evolution of atmospheric CO levels, climate-change feedbacks, i.e., changes in\n2\nthe physical environment in response to the atmospheric warming, will alter the projected rate of\nocean acidification2. Computing the total climate effect from two simulations with varying and\nconstant climate forcing, respectively (see Methods), the simulated net climate effect in the\n2090s for the SSP5-8.5 emission scenario is to decrease pH on the continental shelf (red colors\nin Fig. 8a & b). In the open ocean, the net climate effect decreases the top 200 m-average pH in\nmost regions (Fig. 8a), but mostly increases bottom pH (Fig. 8b). The latter is likely due to a\ncombination of less Antarctic Bottom Water formation, which results in less anthropogenic\ncarbon reaching the abyss, and a southward shift of open-ocean water masses low in\nanthropogenic carbon following changes in atmospheric wind systems69,70. The only exceptions\nto this spatial pattern are downstream of the dense-water formation regions on the Weddell Sea\nand Ross Sea continental shelf (where climate change decreases bottom pH; Fig. 8b) and some\nopen-ocean regions in the Weddell Sea and East Antarctica for the top 200 m-average pH\n(where climate change increases top 200 m pH; Fig. 8a). In the latter regions, this can be\nattributed to enhanced upwelling due to increased winds, bringing waters to the upper ocean\nwhose pH is higher than the pH of surface waters under this high-emission scenario69,70.\nRelative to the total change in pH between the 1990s and the 2090s, the climate-change effect\nis largest in the Weddell Sea and Ross Sea MPAs, where it explains 19% and 16% (top 200 m\naverage) and 20% and 19% (bottom), respectively, of the total change in pH on the continental\nshelf.”\nIn the discussion section, we have further elaborated on this point, and the text reads:\n“Besides the reduced capping effect of sea ice for air-sea exchange following the sea-ice\nretreat, this can be attributed to the lower buffer capacity resulting in more oceanic CO uptake\n2\nper unit primary production in an acidified ocean75 and, to a lesser extent, an overall increased\n8\nprimary production69. For other regions and the intermediate-emission scenario SSP2-4.5, the\nsimulated climate-change feedback is smaller or even opposite in sign (Fig. 8 and\nSupplementary Fig. 8). While a smaller climate-change feedback can likely largely be attributed\nto a smaller decrease in sea-ice cover and a smaller increase in ice-shelf basal melt,\nrespectively (Supplementary Figures 4), the contribution of changes in CO solubility and of a\n2\nredistribution of water masses is possibly non-negligible, especially where climate-change\nfeedbacks act to increase pH (see e.g., open-ocean regions near the Antarctic Peninsula in\nSupplementary Figures 5). Overall, this reflects the complex spatio-temporal interplay of the\nmany factors contributing to the total climate-change feedback. Our model experiments,\nconducted with a more realistic process representation on the Antarctic continental shelf than\nearlier modeling studies that investigated Southern Ocean climate-change feedbacks2,76,77,\ndemonstrate that climate-change feedbacks on OA can be substantial under high-emission\nscenarios. While the projected upper ocean acidification under the high-emission scenario\nSSP5-8.5 in our model is very similar to the acidification previously reported for the high-\nlatitude Southern Ocean in Earth system models78, the bottom acidification rates on the\nAntarctic continental shelf are about two times larger in our model simulations (pH declines by\nmore than 0.35 as opposed to by less than 0.2 in ref78). Our findings illustrate the benefits of\nfollowing a low-emission trajectory over the 21st century, which would minimize climate-change\nfeedbacks on OA.”\nFig. 4: New Supplementary Figure 5 in the revised manuscript.\nl167-185 - the role of ocean warming and sea ice changes on the rate of OA and its impact.\nPlease see our comment above for a detailed answer on this point.\nl210 - I suggest either expanding the results to discuss and show dissolved oxygen simulations\nto remove this. Where did the 61.3 hypoxic threshold come from? how does these threshold\nchange with emissions scenarios? is it avoided in the low emissions scenarios?\nThe threshold 61.3 mmol kg-1 (or 63 mmol m-3) cited in the discussion section is the threshold\ncommonly used to delineate well-oxygenated waters from hypoxic waters in the literature (e.g.,\nBreitburg et al., 2018). If oxygen concentrations fall below this threshold, negative impacts on\nmarine organisms are often considered to become increasingly likely (Breitburg et al., 2018).\nWe acknowledge that critical oxygen thresholds are highly species-specific and any species’\nability to acclimatize and adapt to changing oxygen conditions will also be impacted by the rate\nof change and the variability in oxygen conditions it is exposed to. Even though the main topic of\nour paper is ocean acidification, this environmental stressor does not act in isolation in the\nfuture ocean, and it is important to discuss warming and deoxygenation together with\nacidification. To better highlight the importance of these cumulative impacts (also in response to\na comment by reviewer #2, see below), we have included the depth profiles of temperature\n10\nchange and oxygen change in the revised manuscript (Fig. 5 below, corresponding to Fig. 4 in\nthe revised manuscript).\nIn the discussion section, we have slightly revised the sentence in question:\n“While our model projections indicate oxygen concentrations above the typically used hypoxic\nthreshold of 63 mmol m-3 82 in the Antarctic MPAs for all scenarios (Supplementary Fig. 3), the\nprojected decline in oxygen concentrations of up to ∼50 mmol m-3 might nonetheless negatively\nimpact high-latitude ecosystems in conjunction with the projected warming of up to 1°C and\nOA83 (see last column in Fig 4).”\nFig. 5: New Figure 4 in the revised manuscript.\nl217- Is there existing evidence of the impact of fishing on the Antarctic Ecosystems? What is it?\nThere are primarily two active fisheries in the high-latitude Southern Ocean: Antarctic krill and\nAntarctic toothfish (e.g., Ainley & Pauly 2013; Ryan et al., 2023). While uncertainty surrounding\n11\nthe number, size, connectivity, and ecosystem dynamics of toothfish populations throughout the\nSouthern Ocean has to be acknowledged, previous studies for the Ross Sea have suggested\nthat fishing for toothfish has impacted Weddell Seals, Ross Sea killer whales, Adelie penguins,\nand potentially other species (e.g., Ainley et al., 2017; Salas et al., 2017). Similarly, fishing for\nAntarctic krill, which occurs primarily adjacent to the western Antarctic Peninsula and Scotia\nSea, has grown more concentrated in coastal areas, increasingly overlapping with predators like\npenguins and whales (Trivelpiece et al., 2011; Ainley & Pauly 2013; Hinke et al., 2017; Ryan et\nal., 2023). According to recent research, the cumulative catch of Antarctic krill may be greater\nthan the amount consumed by local predators, and greater than the local replenishable\npopulation of krill (Trathan et al., 2022). Given that krill is an important grazer for high-latitude\nphytoplankton (e.g., Steinberg & Landry, 2017), such fishing-induced changes in krill\nabundances can therefore be expected to also impact the base of the foodweb.\nUnder climate change, a larger fraction of the high-latitude Southern Ocean is projected to be\nice free (see our results), making these regions more accessible to fishing vessels. Therefore, to\nlimit future pressures on high-latitude ecosystems, both emission mitigation and fisheries\nmanagement (e.g., via a network of MPAs) are necessary.\nWe have added a sentence on the known impacts of fishing to the revised discussion section:\n“The active fisheries for Antarctic toothfish and Antarctic krill have been suggested to already be\npotentially impacting ecosystems in the Ross Sea87,88 and near the Antarctic Peninsula89,90,\nrespectively.”\nFigure 1. East Antarctica, Ross Sea and Weddell Sea MPAs show shelf areas have less OA\nimpact than the open ocean in low emissions scenarios. Why? I think this is an important\nfeature of the results that do require a high-resolution simulation to show. It also important if the\ngoal is to preserve biodiversity in the shelf regions under OA.\nIn the present-day and under lower-emission scenarios SSP1-2.6 and SSP2-4.5, the simulated\naverage pH is higher on the continental shelves than in the open ocean both when averaging\nover the top 2000 m of the water column (as done in the original submission) and when\naveraging over the top 200 m (as in the revised version, see Fig. 1 above, see also our answer\nto the reviewer’s comment on L. 81). We note that the difference in pH between the continental\nshelves and the open ocean is much smaller when only averaging over the top 200 m. This can\nbe understood with bottom topography and the vertical profile of pH (in general, higher at the\nsurface than at greater depths, see Fig. 4 of the revised paper). The continental shelves are\ntypically much shallower than 2000m, such that when averaging over the top 2000m, a much\nhigher volume of water (relatively speaking) is from the top 1000m for the continental shelves\nthan for open ocean, skewing the comparison between these two regions towards higher pH on\nthe continental shelf than in the open ocean. We attribute the differences that remain when\naveraging over the top 200m to differences in sea-ice cover, which shield the high-latitude\ncoastal regions from anthropogenic CO uptake relative to regions in the open ocean. We\n2\nrealize that the way of presenting our results in the submitted manuscript might have been\nmisleading. Therefore, and in response to a comment by reviewer #3 (on the difficulty to relate\nchanges in water chemistry to biological impacts when averaging over a large body of water\nsuch as the top 2000m, see below), we report averages separately for the top 200m and the\nbottom in the revised manuscript.\nPlease see our answer to the reviewer’s comment on L. 81 for changes in the text. Further, we\nrefer to the reader to our answer to the reviewer’s comment on L. 175-176, in which we detail\nhow we have included the impact of climate change on ocean acidification, such as via changes\nin sea-ice cover and ice-shelf basal melt rates.\nWe kindly refer the reviewer to our answer on the comment on L. 81 above.\nFigure 3. similar to figure 1.\nPlease see our answer to the reviewer’s comment on L. 175-176.\nReviewer #2 (Remarks to the Author):\nReview of Severe 21st-century ocean acidification demands continuance and expansion of\nAntarctic Marine Protected Areas by Nissen et al.\nThis paper uses a high-resolution ocean-sea ice-biogeochemistry model to explore ocean\nacidification in five Antarctic Marine Protected Areas (two adopted, three proposed) under four\nemission scenarios. Their major findings are that surface pH declines significantly in all MPAs\nby 2100, and to a greater extent from the lowest to the highest emissions scenario. They also\nshow that by 2100 aragonite undersaturation occurs ubiquitously across all MPAs examined\nunder all but the lowest emission scenario. They also investigate the effects of vertical mixing on\nocean acidification and the transport of anthropogenic carbon to the subsurface and deep\nocean, and projected changes in calcite undersaturation.\nThis work is of a very high quality and will make a substantial contribution to the field, due to its\nsound scientific approach and findings as well as its strong relevance to policy making. The\nwork is timely in relation to decision making at international levels, both with respect to global\nclimate change and protection of Antarctic marine systems. As well as being important in its\nown field, this paper will also be of interest and importance to a broader readership due to its\nbroad relevance across the remit of global climate change and its impacts, and informing policy\nin this space. There are some minor issues and questions that I have outlined below, that I hope\nwill help to improve the manuscript. As such, I believe that this work will be suitable for\npublication in Nature Communications, after minor/moderate revisions.\nThe methodology is robust in supporting the results reported and conclusions drawn, and is\nbased on previously published work and ongoing world-leading research efforts. The data\nanalysis, interpretation and conclusions reported in this paper are of a high standard in general,\nalthough I do have some points for clarification that I have outlined below. These require\nattention, but if satisfactorily addressed, they will certainly not prohibit publication. The methods\ndescription is sufficiently detailed for the purposes of this paper, and refers to other published\nwork for more detail. One minor point here is that one of the references cited is Nissen et al.,\n2023, in review. If that paper is not published before this one, that reference will need to be\nremoved.\nIn the following, I provide a small number of more major or overarching comments, followed by\nminor and editorial comments.\nWe thank Sian Henley for the positive feedback and for the detailed comments, which\ncontributed to improving the paper. Please see our answers to the comments below.\nWe note that in the meantime, the paper “Nissen et al., 2023, in review” has been published in\nJournal of Climate:\nSea Continental Shelves with Local and Remote Physical and Biogeochemical Implications is\nAvoidable in a 2°C Scenario. Journal of Climate, 36(19), 6613–6630.\nhttps://doi.org/10.1175/JCLI-D-22-0926.1\nThe reference in the revised manuscript was updated accordingly.\nMajor comments:\nThis work has the potential to be very valuable for scientific and broader audiences. However, I\nfelt that there were opportunities missed to really emphasise this value and the key points of the\nwork. In particular, the final paragraph of the main text (particularly lines 222-231) was not as\ncompelling as it could have been. It feels a bit like a list of statements, rather than a well-crafted\nand coherent narrative. There are also a number of places where I felt that stronger wording\ncould be used to really emphasise the importance of the work, for example “is advisable”,\n“are not spared”, “best policy tools”. I recommend that the authors revisit this section to really get the\nmost impact out of their high-quality scientific work.\nWe have revised the paragraph in question to strengthen the wording, and it now reads:\n“Our 21st-century projections call for strong emission-mitigation efforts, as high-latitude\nSouthern Ocean waters are only spared from severe OA in the lowest-emission scenario\n(SSP1-2.6) and as climate-change feedback substantially aggravate OA on the Antarctic\ncontinental shelf under the highest-emission scenarios (SSP5-8.5). OA across all emission\nscenarios within the proposed and adopted MPAs is comparable to OA in continental shelf\nareas not protected within an MPA (Supplementary Figure 7). This implies two things for the\ndesign and evaluation of MPAs: Firstly, as long as some portion of Antarctic waters remains\noutside of MPAs, these regions could serve as an important reference area for differentiating\nthe ecosystem impacts of fishing from climate change and thus assessing the effectiveness of\nMPAs27-29. Secondly, given that ecosystems in high-latitude waters outside of the MPAs will be\nsimilarly affected by severe OA, a reduction of fishing activities in a larger fraction of Antarctic\ncoastal waters could be considered to reduce cumulative stressors on the system. In that\ncontext, our findings support the notion of today’s Weddell Sea acting as a climate-change\nrefuge29, and the adoption of the Weddell Sea MPA should therefore have high priority. The\nactive fisheries for Antarctic toothfish and Antarctic krill have been suggested to already be\npotentially impacting ecosystems in the Ross Sea88,89 and near the Antarctic Peninsula90,91,\nrespectively. As climate change progresses, cumulative impacts from fishing and environmental\nchange will thus become increasingly likely and possibly more devastating than the impacts of\neach stressor alone92. Therefore, better understanding the complex interactions of OA with\nother ecosystem stressors including fishing is key for a sustainable management of Antarctic\nmarine ecosystems under changing environmental conditions, which will likely make a larger\nfraction of the previously ice-covered high-latitude Southern Ocean accessible to fishing\nactivities (Fig. 7). Altogether, the reduction of greenhouse gas emissions together with\nsimultaneous management of fishing and other human activities, e.g., within MPAs, are\nnecessary for safeguarding Antarctic marine ecosystems.”\nFurther, we have rephrased the sentence on L. 216 of the submitted manuscript (“is worrisome”)\nto now read:\n“The recent reduction in sea-ice cover due to the warming of waters around the Antarctic\nPeninsula has already negatively affected larval abundance of the Antarctic silverfish, which\nuses sea ice as spawning habitat86, suggesting that the 21st-century sea-ice retreat projected\nfor all MPAs will negatively impact circumpolar abundances of this species (Fig. 7k-o and\nSupplementary Fig. 8).”\nimproved to be clearer and more compelling, both in the introduction (line 27-29; 59-62) and in\nthe final paragraph (line 224-228). I suggest that more of a focus is placed on cumulative\nimpacts (rather than just mentioning them) and the importance of increasing resilience in the\nsystem to the changes underway.\nWe appreciate the reviewer’s feedback. In response to this comment, we have made several\nchanges to our manuscript. In particular, we have modified a part of the introduction, which now\nreads:\n“By preserving genetic, species and ecosystem diversity through limitation or prohibition of\nhuman activities (e.g., fishing), the implementation of MPAs can increase resilience of marine\necosystems to environmental change, including those resulting from climate change45.\nOA is one of many Southern Ocean ecosystem stressors arising from climate change, along\nwith warming, deoxygenation and changes in sea-ice cover and circulation. As such, a change\nin each of these factors individually or in a multitude of factors combined directly impacts the\nfitness of marine organisms and ecosystem functioning27,46–48. A large number of studies […]”\nFurther, in the discussion section, we have revised the final paragraph to now read:\n“As climate change progresses, cumulative impacts from fishing and environmental change will\nthus become increasingly likely and possibly more devastating than the impacts of each\nstressor alone91, complicating the assessment of the effectiveness of MPAs. Therefore, better\nunderstanding the complex interactions of OA with other ecosystem stressors including fishing\nis key for a sustainable management of Antarctic marine ecosystems under changing\nenvironmental conditions, which will likely make a larger fraction of the previously ice-covered\nhigh-latitude Southern Ocean accessible to fishing activities (Fig. 7).”\nLastly, we have included the vertical profiles of changes in temperature and oxygen in the main\ntext of the revised manuscript instead of only including them in the supplementary material (see\nFig. 5 above). We refer to these panels in the revised discussion section:\n“While our model projections indicate oxygen concentrations above the typically used hypoxic\nthreshold of 63 mmol m-3 82 in the Antarctic MPAs for all scenarios (Supplementary Fig. 3), the\nprojected decline in oxygen concentrations of up to ∼50 mmol m-3 might nonetheless negatively\nimpact high-latitude ecosystems in conjunction with the projected warming of up to 1°C and OA\n83 (Fig 4).”\nMy final suggestion for a major improvement would be to explain more clearly what the different\nSSPs are and what they represent. I did not feel that this was adequately explained, in terms of\nthe different emissions pathways and outcomes for CO2 concentrations and warming, and what\nwas explained was buried in the methods. Particularly if this work is to be used by people\noutside of the immediate field (e.g. other scientists, policy makers), I think it would really help in\nconveying the main messages of the paper if the SSPs were more clearly explained in the early\nstages of the main text.\n“[…] under four ”shared socioeconomic pathways” (SSP) emission scenarios69,70. The four SSP\nscenarios represent different pathways of societal development, ranging from SSP1 assuming\nan increasing importance of sustainable practices to the fossil-fuel intensive SSP571. By the\nyear 2100, the atmospheric forcing applied in this study corresponds to an increase in global 2\nm air temperatures relative to the 1990s of 1.2°C (SSP1-2.6), 2.3°C (SSP2-4.5), 3.4°C (SSP3-\n7.0) and 4.2°C (SSP5-8.5)72. Atmospheric CO levels in these scenarios have increased to 446\n2\nppm, 603 ppm, 867 ppm, and 1135 ppm71 by the year 2100, respectively.“\nMinor comments:\nTitle: I am not convinced continuance is right in this context. I suggest changing to continuation,\nwhich is more accurate.\nChanged as suggested.\nLine 3: ‘little is known’. Given what is known, I think this is probably an overstatement. I would\nsuggest rewording to reflect that we do have some knowledge, but that significant gaps and\nuncertainties remain.\nWe have rephrased the sentence as follows:\n“Despite a particular sensitivity to ocean acidification (OA), significant gaps remain surrounding\nthe future carbonate chemistry of waters on the Antarctic continental shelf.”\nLine 7: here you make a compelling statement on changes in hydrogen ion concentration, but\nthis is not addressed anywhere else in the main manuscript or supplementary information to\nsubstantiate this claim. This should be incorporated and at least mentioned in the main\nmanuscript, or removed here.\nWe agree with the reviewer. For this information to be placed in the abstract, it should also\noccur in the main text of the manuscript. In the revised manuscript, we have therefore added\ninformation on the increase in hydrogen concentration in the 2090s relative to the 1990s to\nFigure 3 of the revised manuscript (see Figure 9 below; this Figure was added in response to a\ncomment by reviewer #3) and its description in the result section.\nThe respective part reads:\n“Expressed as an increase in hydrogen ion concentration by the 2090s relative to the 1990s,\nthe acidity on the continental shelves increases by up to 144% (top 200 m; Weddell Sea) and\n130% (bottom; Weddell Sea), which is substantially more than for the whole-MPA averages\n(up to 131% and 80%; see numbers printed into panels in Fig. 3).”\nWe have also added a statement on the calculation of the increase in acidity to the revised\nmethod section:\n“The change in acidity reported in the manuscript is calculated from a change in hydrogen ion\nconcentration ([H+]) between the 2090s of a given emission scenario and the 1990s of the\nhistorical simulation”\nFurther, for consistency with changes in the analysis (top 2000 m in the submitted paper vs. top\n200 m in the revised version), we have modified the abstract:\n“By 2100, we project pH declines of up to 0.36 (total scale) for the top 200 m of the water\ncolumn, corresponding to a 131% increase in hydrogen ion concentration relative to the 1990s.”\nhere to add a brief description of seasonal changes in sink/source dynamics, so that the reader\nhas the full picture of what makes up the net annual sink.\nWe have added a sentence along these lines to the respective part of the introduction. It reads\nas follows:\n“This net sink is the result of strong biologically-driven uptake in summer, while sea-ice cover\ntypically prevents outgassing to the atmosphere in winter26. Shelf waters […]”\nLine 34: East Antarctic should be East Antarctica here (because of the preceding ‘in’).\nWe thank the reviewer for spotting this. Changed as suggested.\nFigure 1: I think it should be noted that the y-axis scale for the Weddell Sea is different to the\nothers, and ideally, the ticks should include minimum and maximum bounds (rather than having\nany data points outside of the bounded scale).\nWe have revised Figure 1 in response to comments by both reviewer #1 and #3 (see Figure 1\nabove). In the process, we have made sure that the y-axis scale is the same for all five MPAs\nand that the ticks include minimum and maximum bounds.\nLine 37: for the broad readership of Nature Communications, I think it is necessary to state what\nPhaeocystis is. Hence, I would add ‘the haptophyte Phaeocystis’ (or prymnesiophyte, although\nthat may be too specific).\nWe have modified the sentence to read “the haptophyte Phaeocystis”.\nLine 53: should black be capitalised?\nFor consistency with “emerald rockcod” we have rewritten to “black rockcod” in the revised\nmanuscript.\nLine 57: there is considerable debate amongst the biological community as to whether there are\nany keystone species in the Southern Ocean (either Antarctic krill or silverfish), so I suggest the\nauthors consider whether it is appropriate to use this terminology here without any\nsubstantiation. Especially the way the sentence is constructed ‘keystone species, e.g. … upper\ntrophic level organisms’ does not seem right to me without naming any organisms, so I suggest\nrevising.\nWe thank the reviewer for pointing this out. In the revised manuscript, we have rephrased the\nrespective part of the sentence to now read:\n“Altogether, acknowledging knowledge gaps on direct OA impacts for important species in the\nSouthern Ocean foodweb (e.g., Antarctic silverfish and upper-trophic level organisms), […]”\nLine 61: among with. Should be either among or with, or possibly along with\nWe have changed it to “along with”.\nLine 67-69: I suggest adding that continental shelf ecosystems are also more sensitive to the\nimpacts of OA, to strengthen your point further.\nWe have modified the last sentence of the introduction, and it now reads:\n“[…] resulting in more severe OA on the continental shelves, where OA-sensitive ecosystems\nreside4,42.”\nwhat this means later on, but on the first mention, it is ambiguous. I suggest spelling it out more\nclearly on first use and then using this terminology for the rest of the paper.\nWe have revised the start of the result section to now read:\n“Simulated C concentrations averaged over the top 200 m of the water column are similar in\nanth\nmagnitude on the continental shelves and in the open ocean under present-day conditions\nthroughout the Antarctic (Fig. 2a). In contrast, future top 200 m C concentrations and C\nanth anth\nconcentrations at the seafloor are at least two times higher on the continental shelves than in\nthe open ocean (Fig. 2b-d; high-emission scenario SSP5-8.5).”\nPlease note that the start of the section has been modified further, as the analysis in Fig. 2 of\nthe revised manuscript shows average anthropogenic carbon concentrations over the top 200m\ninstead of over the top 2000m (see submitted manuscript).\nPlease note that we have adapted Figure 2 in response to a comment by both reviewer #1 and\n#3, and we now show the average over the top 200m to make it easier to link the changes in\ncarbonate chemistry to biological impacts.\nFigure 2: some of the text is too small to read; I suggest enlarging.\nWe have increased the font sizes (see Fig. 2 above).\nLine 91-92: severe shelf/MPA OA. I suggest spelling this out as ‘severe OA on shelves and in\nthe MPAs studied’ or similar, to improve readability.\nChanged as suggested, and the sentence now reads:\n“The strong vertical mixing on the shelves (where most of the MPA area is located, Fig. 1) is the\nultimate cause of severe OA on continental shelves and in the MPAs studied.”\nLine 99-100: …up to five times stronger surface decline. This is awkward to read; I suggest\nrewording for clarity.\nThe sentence now reads:\n“This is caused by a pH decline that is up to five times stronger at the surface than at 1500 m\nacross all MPAs for all except the lowest emission scenario […]”\nLine 121-123: ‘it is projected to rise…’. Is this for all MPAs or a subset? It would help the\nreader’s understanding to state this explicitly here.\nAgreed, we have rephrased to:\n“[…] it is projected to rise to the surface in all MPAs by 2100 for the two highest-emission\nscenarios […]”\nFigure 5: text is too small for ice panels. Also, the label for 2100 appears to be misaligned in\npanel g\nWe have increased the font size of the legend in the sea-ice panels and aligned the label in\npanel g (see Figure 6 below).\nthe revised manuscript.\nLine 149-151: I think it would be useful to state at the end of this sentence ‘to at least end of\ncentury’ or ‘by 2100’ or similar to really make it clear.\nAgreed, rephrased as follows:\n“[…] the upper ocean remains supersaturated with respect to aragonite across all MPAs until at\nleast end of century.”\nAgreed, changed to:\n“Marine organisms are highly sensitive to the rate at which OA progresses, as this determines\nthe time span available for possible acclimation or adaptation71.”\nLine 173-174: you could also point out here that this is also true for volume in the 2090s, as\nshown in figure 4, to further strengthen your case.\nAdded as suggested:\n“Based on our model experiments, the volume of supersaturated water is indeed highest in this\nregion in both the 1990s and the 2090 […]”\nLine 182-185: would it also be worth stating here that the projected increase in PP also\ncontributes to this effect?\nWe have added this information to the sentence:\n“[…] this can be attributed to the lower buffer capacity resulting in more oceanic CO uptake per\n2\nunit primary production in an acidified ocean75 and, to a lesser extent, an overall increased\nprimary production69.”\nLine 192: acclimatization. Is this correct or do you mean acclimation?\nWe thank the reviewer for spotting this, we of course meant acclimation. Corrected in the\nrevised text.\nLine 191-196: after respectively (line 196), I suggest adding a statement that this means that\nbenthos are likely to have a smaller tolerance range to variability in conditions and also mention\nthat this is in addition to their limited ability to move.\nWe have added the following statement to the text:\n“The exposure to smaller pH variability implies that benthic organisms likely have a smaller\ntolerance range, making them more susceptible to OA given their limited ability to move.”\nLine 214: have should be has (referring to reduction).\nWe thank the reviewer for spotting this. It was corrected in the revised text.\nLine 216: …is worrisome. Related to my major comment about strengthening wording to be\nmore compelling, I think it would be beneficial here to use stronger wording and to elaborate on\nwhat you mean.\nWe have rephrased this sentence to:\n“The recent reduction in sea-ice cover due to the warming of waters around the Antarctic\nPeninsula has already negatively affected larval abundance of the Antarctic silverfish, which\nuses sea ice as spawning habitat84, suggesting that the 21st-century sea-ice retreat projected\nfor all MPAs will negatively impact circumpolar abundances of this species (Fig. 7k-o).”\nLine 230: In addition to my major comment about this paragraph, I suggest adding ‘and direct\nhuman impacts’ after ‘environmental change’.\nA revised version of this sentence was added to the revised introduction:\n20\n“By preserving genetic, species and ecosystem diversity through limitation or prohibition of\nhuman activities (e.g., fishing), the implementation of MPAs can increase resilience of marine\necosystems to environmental change, including those resulting from climate change45.”\nLine 231: I suggest specifying ‘global emissions of greenhouse gases’\nWe have changed the text as suggested by the reviewer.\nLine 478: <100 km. From looking at the figure, this does not appear to be true for the region\nbetween 50 and 60 S in the Pacific and Atlantic sectors. Should it be >100 or <150?\nWe thank the reviewer for pointing this out. The text was changed to say “<150” in the revised\nmanuscript.\nLine 512: due should be due to\nWe have corrected the sentence.\nLine 531: state these what, so that this is not left hanging.\nChanged as suggested:\n“By computing simA minus simC of any model tracer or flux, we can isolate the effect of climate\nchange on the projected changes in these tracers or fluxes.”\nLine 542 (and 543, 544, 545): I suggest using standard scientific notation (x106) rather than\nMio.\nWe have changed the text as suggested by the reviewer.\nLines 544-548: It is rather confusing that the authors state that 73% of the Antarctic Peninsula\nMPA area is on the shelf (i.e. 27% is not) and then to say that ‘the vast majority’ of grid points\nare defined as shelf. This also appears to go against what is stated in the text, which is that the\nwhole of the Peninsula area is over the shelf. It strikes me that 27% is enough to run the\nanalysis for the open ocean component. However, I do trust the authors’ judgement on this and\ntheir approach to the analysis, so I suspect it is just a case of this wording being confusing in the\nmethods section. Please clarify.\nWe thank the reviewer for this comment, as it made us realize that there was a bug in the\nanalysis, upon which we based the decision to only show whole-MPA averages for the Antarctic\nPeninsula MPA. In the revised version of the manuscript, we separately show all main results\nfor the continental shelf in this region. We have adapted all Figures accordingly (see Fig. 1, 5, 7,\n9-11 in this document).\nAdditionally, we have modified the respective part of the method section to now read:\n“As the South Orkney Islands Southern Shelf MPA is entirely defined as ”open ocean” based on\nthe model topography, we only report values for the whole MPA for this MPA in all Figures.”\nReferences:\nIn general, there is very good coverage of the important references in this field and the study is\nplaced appropriately within the wider literature. There are a small number of references that I\nfelt were missing and would be beneficial to add for comprehensive coverage. These are:\nDeppeler, S., Petrou, K., Schulz, K. G., Westwood, K., Pearce, I., Mckinlay, J., et al. (2018).\nOcean acidification of a coastal Antarctic marine microbial community reveals a critical\n21\nthreshold for CO2 tolerance in phytoplankton productivity. Biogeosciences 15, 209–231. doi:\n10.5194/bg-15-209-2018\nGutt, J., Bertler, N., Bracegirdle, T. J., Buschmann, A., Comiso, J., Hosie, G., et al. (2015). The\nSouthern ocean ecosystem under multiple climate change stresses – an integrated circumpolar\nassessment. Glob. Change Biol. 21, 1434–1453. doi: 10.1111/gcb.12794\nHancock, A. M., Davidson, A. T., Mckinlay, J., Mcminn, A., Schulz, K. G., and Van Den Enden,\nR. L. (2018). Ocean acidification changes the structure of an Antarctic coastal protistan\ncommunity. Biogeosciences 15, 2393–2410. doi: 10.5194/bg-15-2393-2018\nHenley, S. F., Cavan, E. L., Fawcett, S. E., Kerr, R., Monteiro, T., Sherrell, R. M., et al. (2020)\nChanging Biogeochemistry of the Southern Ocean and Its Ecosystem Implications. Front. Mar.\nSci. 7:581. doi: 10.3389/fmars.2020.00581\nTortell, P. D., Payne, C. D., Li, Y. Y., Trimborn, S., Rost, B., Smith, W. O., et al. (2008). CO2\nsensitivity of Southern Ocean phytoplankton. Geophys. Res. Lett. 35:L04605.\nTrimborn, S., Brenneis, T., Sweet, E., and Rost, B. (2013). Sensitivity of Antarctic phytoplankton\nspecies to ocean acidification: Growth, carbon acquisition, and species interaction. Limnol.\nOceanogr. 58, 997–1007. doi: 10.4319/lo.2013.58.3. 0997\nWestwood, K. J., Thomson, P. G.,Van Den Enden, R. L.,Maher, L. E., Wright, S. W., and\nDavidson, A. T. (2018). Ocean acidification impacts primary and bacterial production in Antarctic\ncoastal waters during austral summer. J. Exp.Mar. Biol. Ecol. 498, 46–60. doi:\n10.1016/j.jembe.2017.11.003\nWe thank the reviewer for these additional references. We have included these in the revised\nintroduction.\nThere are a number of places where the presentation of number ranges is grammatically\nincorrect. These should either be presented as ‘between x and y’, ‘from x to y’ or ‘x-y’. Examples\nof incorrect constructions are at lines 179 (between December-February), 487 (from 1950-\n2014), 556 (between 1250-3632). Please correct these.\nWe thank the reviewer for pointing this out. We have corrected this as suggested.\nA minor grammatical point would be that there are lots of uses of an Oxford comma, which\nstrictly speaking is incorrect and these should be removed. Examples are at lines 39 (after\nwhales), 40 (after bivalves), 50 (after foraminifera), 490 (after heat), 534 (after input).\nWe have screened the text and have removed Oxford commas.\nSupplementary information\nSupp Figure 1: I suggest making the images larger to occupy some of the large amount of white\nspace and to make them easier to read.\nWe have changed the layout of the panels to make better use of the white space (see Fig. 7\nbelow).\nSupp Figure 2: To improve readability, I suggest adding a y-axis scale to panel d to apply to\npanels d and e, in the same way that the scale on panel a applies to a, b and c. I would also\nsuggest nudging the two lines of the y-axis label slightly further apart to avoid the 2s colliding. It\nwould also help to make the labels ‘annual mean’ and ‘DJF mean’ more prominent for clarity.\nWe thank the reviewer for these suggestions. We have implemented them all (see Fig. 8\nbelow).\nSupp Figure 3: In line 3 of the caption, profile should be profiles.\nChanged as suggested.\nSupp Figure 4: In line 5 of the caption, I think cb is a typo. I also think the y axis of panel b\nshould say calc, not arag.\nWe thank the reviewer for spotting these errors. We have corrected both.\nSupp Figure 5: in line 3 of the caption, the comma should be a semi-colon (;)\nChanged as suggested.\nThese comments and suggestions should all be amenable to being addressed by the authors,\nand in this case I believe the work would be ready for publication in Nature Communications. I\nam happy to review it again, or if the editor is happy handling this themselves, that is fine for me\ntoo.\nSian Henley\nUniversity of Edinburgh, UK\n9/6/2023\nReviewer #3 (Remarks to the Author):\nThe study of Nissen and colleagues explores the implications provided by the high-resolution\nmodelling of a much more severe OA in the Southern Ocean than reported ever before. The\nstudy excels in the modelling outputs, the scenarios are superbly linked to the physical-chemical\nprocess and produce state-of-the-art science on the ocean acidification over this century. The\nstudy really shows the importance of the model improvements and the implications it could\nbring.\nOn the other hand, the authors used the model outputs to suggest that the current predictions of\nthe MPAs and its connectivity are not sufficient given the projected increases in OA. While this\n24\nis a solid implication of the model results, the MPA efficiency cannot be evaluated only\nbased on the saturation state (of 1) alone. As the MPAs are inherently linked to the protection\nof marine biology, the paper insufficiently covers the link between the chemistry and the\nbiology, leaving a big gap in the interpretation. So far, in the literature, there are numerous\nstudies for variety of species and functional groups for which specific pH or omega saturation\nstate THERESHOLDS exists. Instead of just using a general omega =1 (which is even\ninsufficient for the marine calcifiers impacted by dissolution), the authors have unique\nopportunity to apply the thresholds for different climate scenarios and show species\nsensitivity (or resilience). That would be a much stronger link to the MPAs due to climate\nchange/OA and associated loss of habitat.\nWith that, I would suggest that the authors separate the pelagic and benthic habitats and\nassess the impacts separately, i.e. not only produced the change in the average over the upper\n2000m, but actually more applicable for the pelagic and benthic biota, for example\npteropods occupy the upper 200m, so project the threshold changes for that habitats, and\nequally the bottom for the adult benthic calcifiers. As it is now, it is not accurate enough in\nterms of biological representation. This should significantly strengthen the implications of\nwhy the MPA expansion/reconsideration is needed.\nThe weakest point so far is the discussion on the MPA, implications, the only solution the\nenlargement along with the mitigation. There are several other options, like fisheries\nmanagement, both in catch per unit effort change and timing of fisheries, etc. I think this section\nneeds to be scientifically beefed-up content wise, best to examine the MPAs strategies and\nalternatives in the best managed MPAs across the world.\nWe thank the reviewer for this constructive feedback. We agree that by focusing our results on\naverages over the top 2000m of the water column, we have made it too difficult in the submitted\nmanuscript to link the reported changes in carbonate chemistry to biological impacts. In\nresponse to the reviewer’s comment, we have changed the way in which we report our findings\nin the revised manuscript.\nIn particular, we now report changes in pH and in the saturation states (Ω) with respect to\naragonite and calcite as averages over the top 200m of the water column (pelagic habitat) and\nin the bottom layer (benthic habitat). This change applies to Figure 1 in the submitted\nmanuscript (see Figure 1 above, which shows the revised version). In addition, to complement\nthe figures in the submitted manuscript, we have added time series plots of pH and Ω to the\narag\nmain part of the revised paper and of Ω to the revised supplementary material (see Figures 9-\ncalc\n11 below). With these additions, we hope that our findings are more relevant for those studying\nbiological impacts of ocean acidification, as we realize that different species will be impacted\nafter different critical thresholds in pH, Ω or Ω have been crossed. We refer the reviewer to\narag calc\nthe third paragraph of our introduction, in which we provide examples for the sensitivities of\nspecific species.\nIn the Results section, the revised or new parts read as follows:\n“In the 1990s, waters on the continental shelves have a higher pH compared to the average\nover the regions encompassed by the whole MPA (dashed black lines on top and to the right of\nthe solid black lines in Fig. 3 and Fig. 4, respectively). Averaged over the top 200 m, the pH in\nAntarctic coastal waters is up to 0.05 higher in the 1990s than in the regions encompassed by\nthe whole MPAs (with a maximum for the East Antarctic MPA), while this difference amounts to\nup to 0.1 for bottom pH (Weddell Sea and East Antarctic MPA; Fig. 1). Over the 21st century,\nthis shelf–open ocean gradient is sustained for the lower-emission scenarios, but it reverses for\nthe two highest-emission scenarios in the regions encompassed by the Weddell Sea, East\nlines in Fig. 3 and Fig. 4, respectively). By 2100, the average pH on the continental shelves is\nup to 0.01 (top 200 m) and 0.04 (bottom) lower than in the area of the whole MPA, again\ndemonstrating the overall stronger acidification in the shallow continental shelf seas than in the\nopen ocean (Fig. 1).”\n“More critically, virtually all (>95%) waters in the MPAs are undersaturated with respect to\naragonite for the three highest-emission scenarios, with this ubiquitous undersaturation only\nbeing avoidable for the lowest-emission scenario SSP1-2.6 (see also Fig. 6).”\n“The onset of undersaturated conditions with respect to aragonite varies with depth and across\nseasons, scenarios and to some extent also regions (Fig. 6 & Fig. 7). Bottom waters averaged\nover the whole MPAs are undersaturated throughout the analysis period (on the continental\nshelf, only those in the Weddell Sea are initially supersaturated; second column in Fig. 6). In\ncontrast, the saturation state in the top 200 m of the water column exceeds a value of 1 in all\nMPAs in the 1990s (ranging from 1.21 in the east Antarctic MPA to 1.39 in the Weddell Sea;\nsolid lines in the first column of Fig. 6). By the 2090s, it decreases to 0.62-0.68 across regions\nfor the highest-emission scenario and to 1.03-1.14 for the lowest-emission scenario.”\nRelating to the reviewer’s summary of our main findings, we want to point out that the levels of\nacidification projected with our model for the upper ocean are in close agreement with those\npreviously published using Earth System Models (Kwiatkowski et al., 2020). For the same high-\nemission scenario, differences in the projections arise for the coastal areas and especially at the\nsubsurface, where our model simulations project acidification rates which are two times larger\nthan those in Earth system models. We attribute these differences to the more realistic\nrepresentation of dynamics on the Antarctic continental shelf in our model setup compared to\nmost existing Earth System Models. In the revised manuscript, we have added a statement\nalong these lines to the discussion section:\n“Our model experiments, conducted with a more realistic process representation on the\nAntarctic continental shelf than earlier modeling studies that investigated Southern Ocean\nclimate-change feedbacks2,76,77, demonstrate that climate-change feedbacks on OA can be\nsubstantial under high-emission scenarios. While the projected upper ocean acidification under\nthe high-emission scenario SSP5-8.5 in our model is very similar to the acidification previously\nreported for the high-latitude Southern Ocean in Earth system models78, the bottom acidification\nrates on the Antarctic continental shelf are about two times larger in our model simulations (pH\ndeclines by more than 0.35 as opposed to by less than 0.2 in ref78).”\nWe also appreciate the feedback by the reviewer on the discussion of our findings in the context\nof MPAs. We have revised the final paragraph of the manuscript, which now reads:\n“Our 21st-century projections call for strong emission-mitigation efforts, as high-latitude\nSouthern Ocean waters are only spared from severe OA in the lowest-emission scenario\n(SSP1-2.6) and as climate-change feedback substantially aggravate OA on the Antarctic\ncontinental shelf under the highest-emission scenarios (SSP5-8.5). OA across all emission\nscenarios within the proposed and adopted MPAs is comparable to OA in continental shelf\nareas not protected within an MPA (Supplementary Figure 7). This implies two things for the\ndesign and evaluation of MPAs: Firstly, as long as some portion of Antarctic waters remains\noutside of MPAs, these regions could serve as an important reference area for differentiating\nthe ecosystem impacts of fishing from climate change and thus assessing the effectiveness of\nMPAs27-29. Secondly, given that ecosystems in high-latitude waters outside of the MPAs will be\nsimilarly affected by severe OA, a reduction of fishing activities in a larger fraction of Antarctic\ncoastal waters could be considered to reduce cumulative stressors on the system. In that\ncontext, our findings support the notion of today’s Weddell Sea acting as a climate-change\nrefuge29, and the adoption of the Weddell Sea MPA should therefore have high priority. The\nactive fisheries for Antarctic toothfish and Antarctic krill have been suggested to already be\npotentially impacting ecosystems in the Ross Sea88,89 and near the Antarctic Peninsula90,91,\nrespectively. As climate change progresses, cumulative impacts from fishing and environmental\nchange will thus become increasingly likely and possibly more devastating than the impacts of\neach stressor alone92. Therefore, better understanding the complex interactions of OA with\nother ecosystem stressors including fishing is key for a sustainable management of Antarctic\nmarine ecosystems under changing environmental conditions, which will likely make a larger\nfraction of the previously ice-covered high-latitude Southern Ocean accessible to fishing\nactivities (Fig. 7). Altogether, the reduction of greenhouse gas emissions together with\nsimultaneous management of fishing and other human activities, e.g., within MPAs, are\nnecessary for safeguarding Antarctic marine ecosystems.”\npercent increase in acidity, which was computed from the H+ concentration in the 2090s and the\n1990s.\nCited literature\nAinley, D. G., & Pauly, D. (2013). Fishing down the food web of the Antarctic continental shelf and slope.\nPolar Record, 50(01), 92-107. doi:10.1017/s0032247412000757\nAinley, D. G., Crockett, E. L., Eastman, J. T., Fraser, W. R., Nur, N., O’Brien, K., . . . Siniff, D. B. (2017).\nHow overfishing a large piscine mesopredator explains growth in Ross Sea penguin populations: A\n30\nframework to better understand impacts of a controversial fishery. Ecological Modelling, 349, 69-75.\ndoi:10.1016/j.ecolmodel.2016.12.021\nBreitburg, D., Levin, L. A., Oschlies, A., Grégoire, M., Chavez, F. P., Conley, D. J., Garçon, V., Gilbert, D.,\nGutiérrez, D., Isensee, K., Jacinto, G. S., Limburg, K. E., Montes, I., Naqvi, S. W. A., Pitcher, G. C.,\nRabalais, N. N., Roman, M. R., Rose, K. A., Seibel, B. A., … Zhang, J. (2018). Declining oxygen in the\nglobal ocean and coastal waters. Science, 359(6371). https://doi.org/10.1126/science.aam7240\nEayrs, C., Holland, D., Francis, D., Wagner, T., Kumar, R., & Li, X. (2019). Understanding the Seasonal\nCycle of Antarctic Sea Ice Extent in the Context of Longer‐Term Variability. Reviews of Geophysics,\n57(3), 1037–1064. https://doi.org/10.1029/2018RG000631\nHinke, J. T., Cossio, A. M., Goebel, M. E., Reiss, C. S., Trivelpiece, W. Z., & Watters, G. M. (2017).\nIdentifying Risk: Concurrent Overlap of the Antarctic Krill Fishery with Krill-Dependent Predators in the\nScotia Sea. PLoS One, 12(1), e0170132. doi:10.1371/journal.pone.0170132\nKwiatkowski, L., Torres, O., Bopp, L., Aumont, O., Chamberlain, M., Christian, J. R., Dunne, J. P.,\nGehlen, M., Ilyina, T., John, J. G., Lenton, A., Li, H., Lovenduski, N. S., Orr, J. C., Palmieri, J., Santana-\nFalcón, Y., Schwinger, J., Séférian, R., Stock, C. A., … Ziehn, T. (2020). Twenty-first century ocean\nwarming, acidification, deoxygenation, and upper-ocean nutrient and primary production decline from\nCMIP6 model projections. Biogeosciences, 17(13), 3439–3470. https://doi.org/10.5194/bg-17-3439-2020\nRoberts, C. M., O’Leary, B. C., McCauley, D. J., Cury, P. M., Duarte, C. M., Lubchenco, J., Pauly, D.,\nSáenz-Arroyo, A., Sumaila, U. R., Wilson, R. W., Worm, B., & Castilla, J. C. (2017). Marine reserves can\nmitigate and promote adaptation to climate change. Proceedings of the National Academy of Sciences,\n114(24), 6167–6175. https://doi.org/10.1073/pnas.1701262114\nRyan, C., Santangelo, M., Stephenson, B., Wilson, E., & Savoca, M. (2023). Commercial krill fishing\nwithin a foraging supergroup of fin whales in the Southern Ocean. Ecology, 104(4), e4002.\nSalas, L., Nur, N., Ainley, D. G., Burns, J., Rotella, J., & Ballard, G. (2017). Coping with the loss of large,\nenergy-dense prey: a potential bottleneck for Weddell Seals in the Ross Sea. Ecological Applications,\n27(1), 10-25.\nSteinberg, D. K., & Landry, M. R. (2017). Zooplankton and the Ocean Carbon Cycle. Annual Review of\nMarine Science, 9(1), 413–444. https://doi.org/10.1146/annurev-marine-010814-015924\nTeschke, K., Brtnik, P., Hain, S., Herata, H., Liebschner, A., Pehlke, H., & Brey, T. (2021). Planning\nmarine protected areas under the CCAMLR regime – The case of the Weddell Sea (Antarctica). Marine\nPolicy, 124(December 2020), 104370. https://doi.org/10.1016/j.marpol.2020.104370\nTrathan, P. N., Warwick-Evans, V., Young, E. F., Friedlaender, A., Kim, J. H., & Kokubun, N. (2022). The\necosystem approach to management of the Antarctic krill fishery - the ‘devils are in the detail’ at small\nspatial and temporal scales. Journal of Marine Systems, 225. doi:10.1016/j.jmarsys.2021.103598\nTrivelpiece, W. Z., Hinke, J. T., Miller, A. K., Reiss, C. S., Trivelpiece, S. G., & Watters, G. M. (2011).\nVariability in krill biomass links harvesting and climate warming to penguin population changes in\nAntarctica. Proceedings of the National Academy of Science, 108(18), 7625-7628.\ndoi:10.1073/pnas.1016560108\nReviewer #1 (Remarks to the Author):\nThe authors have provided an excellent and detailed response to the first reviews. As clearly arficulated\nin the response reviews and in the revised manuscript, the authors have addressed my original\ncomments and I recommend publishing the paper. I have no further comments.\nReviewer #2 (Remarks to the Author):\nNissen et al. have addressed all of my comments from the first round of review in a safisfactory manner.\nThe manuscript text has changed quite substanfially, as have some of the figures. This further work has\ncertainly led to improvements in the quality of the manuscript. In my opinion, this manuscript will be\nacceptable for publicafion in Nature Communicafions once some mafters arising from this resubmifted\nversion have been addressed.\nThe only moderate-to-major comment would be that some of the new secfions do not seem as well\npolished and streamlined as they might be. This is parficularly the case for the discussion and\nconclusions, where I thought the wording could be fighter overall and this would help in maximising the\nimpacfful delivery of the work done. I would recommend that the authors go back through this secfion\nand the other new secfions and make sure the wrifing is as clear, concise and compelling as it can be.\nThere is nothing wrong, as such, with it at present; I just feel like some of the text could be befter\npolished and streamlined to really make the most of these important findings and considerafions.\nIn addifion, I have the following minor points to be addressed.\nLine 82: I suggest \"... will have increased...\"\nLine 92: I suggest bringing \"[in the] high-emission scenario SSP5-8.5\" out of the brackets as this is an\nimportant part of the sentence\nLine 108: there is inconsistency as to whether you name this MPA as South Orkney Southern Shelf or\nSouth Orkney Islands Southern Shelf. Ensure that this is correct and consistent throughout. Note: I think\nthe shortening to South Orkney MPA later in the text is acceptable, once it has been defined properly\nearlier on.\nLine 131: 'is altered' should be 'are altered' (for magnitude and sign).\nLine 149: should this be upper 200 m, given the changes to the analysis since the original submission? If\nso, this should be changed on the figure and in its capfion as well. I'm not sure which is right in this\ninstance, but check. Check this for figure S7 as well.\nLines 219-224: it would be useful to idenfify which scenarios you are talking about somewhere here. I\nassume SSP5-8.5 and SSP3-7.0, but it would be worth being explicit.\nLine 245-246: should be Supplementary Figure 4\nLine 247: \"is possibly non-negligible\" seems very vague and rather clunky. I would suggest \"could also be\na factor\" or \"cannot be ruled out\" for improved clarity.\nLine 248: should be Supplementary Figure 5\nLine 259: I would suggest finishing this sentence with \"in the Southern Ocean\" for completeness.\nLine 268: \"of\" not required - I suggest delefing.\nLine 276-279: it would be useful here to state \"at all depths\" or similar (if this is true), or to define the\ndepth range(s) you are referring to.\nLine 279-282: I suggest rewording to \"Even though it remains unclear in laboratory experiments to what\nextent...\". Also, for completeness, I would add explicit menfion of impacts to their prey\nand/or predators (and hence how organisms not directly impacted are affected by indirect effects).\nLine 301: climate-change feedbacks?\nLine 302: should be \"highest-emission scenario\"\nLine 318: \"for sustainable management\" or \"for the sustainable management\"\nFigure S2: following my comments in the first round of reviews, I think line 2 of this capfion should read\n\"...to calcite\", consistent with the omega-calc in brackets\nI believe that all of these comments and suggesfions are amenable to being addressed, and once this has\nbeen done, the manuscript will be ready for publicafion. I am happy to review the second round of\nrevisions if required, or for the editor to sign off if they feel my comments in this round have been\naddressed safisfactorily.\nSian Henley\nUniversity of Edinburgh\n20/10/2023\nReviewer #3 (Remarks to the Author):\nThe revised manuscript by Nissen et al. improved the quality of the interpretafion with respect to the\nprojected changes over the shelf and MPAs areas. Overall, the modelling results are excellent and could\nand should serve to make future decisions on the MPAs in the Southern Ocean.\nHowever, the study with the latest improvements, is severely unbalanced in text wrt to MPA\nframing. Most of the text deals with the modelling outputs and only the last page starts\ndiscussing the implicafions for the MPA, while the fitle and the abstract point out this to be major\nforce behind this MS. While the MS describes the modelling efforts in detail, it falls short of what\nto do with them, the implicafions are too weak, too vague and inadequate. I strongly suggest\nrestructuring, the MPAs text needs to be extended, more precise- like where are suitable areas,\nwhere should that confinuous expansion be and over what extent. Otherwise, such MS cannot\nreally be used for policy informed discussions, with high relevance for the Nature.\nIn general, seeing more nuanced results of this study now, I have serious reservafions about the current\nthinking about expanding MPAs. As this study finds out, MPAs would see the greatest OA severity\nprecisely in the MPAs. The decision to expand the areas would contradict the common sense of\nextending the areas that would be most compromised. In contrast, MPAs should be posifioned in the\nareas with the greatest protecfion that can act as a refugee. Simply allowing for only a refence area (line\n305) that authors cite is merely not enough. The informafion from the modelling should point out where\nthe areas of potenfial refugee are the greatest (including the projecfions and feedback) and then build\nthe case on this. As it currently is, I simply see such jusfificafion to be too weak.\nUpon building the case of the greatest refugee, this also means that the areas need to be looked at more\ncomprehensively, not evaluafing only OA, but also warming and hypoxia, because intense warming could\nmomentarily restructure the ecosystem. I find it inadequate to propose the expansion of MPAs without\ntaking and evaluafing the extent of other stressors. I suggest the authors to delineate the projected\nchanges in warming, hypoxia and OA for the three invesfigated areas (Weddel, East Ant, West Ant\nPeninsula), aligned them together and find most suitable refugee areas for the same funcfional groups\nalready considered. I think the hypoxia threshold currently used is OK, it might be the most early-\nwarning but is sufficient. As for thermal reference, a lot of these thresholds exist in the literature. Once\nall three stressors are considered, a more precise advice on where the expansion of the MPAs should be-\nthat would be the most comprehensive advice that the CAMLR needs to make the next steps.\nMinor comments:\nLine 47-49: Need to be some quanfitafive citafion of MPA protecfion, increased in the diversity\nprotecfion etc.\nDemonstrate high biodiversity in the MPAs with mor references -line 260\nRef 62, 63, 60, 61, 67\nLine 186 several years of adaptafion fime?\nImmobility – line 263- that is only true for the benthic organisms, expand the text for this to be relevant\nLine 309 – at least some evaluafion what the reducfion of fishing could do\nReviewer #1 (Remarks to the Author):\nThe authors have provided an excellent and detailed response to the first reviews. As clearly\narticulated in the response reviews and in the revised manuscript, the authors have addressed\nmy original comments and I recommend publishing the paper. I have no further comments.\nWe thank reviewer #1 for the positive feedback.\nReviewer #2 (Remarks to the Author):\nNissen et al. have addressed all of my comments from the first round of review in a satisfactory\nmanner. The manuscript text has changed quite substantially, as have some of the figures. This\nfurther work has certainly led to improvements in the quality of the manuscript. In my opinion,\nthis manuscript will be acceptable for publication in Nature Communications once some matters\narising from this resubmitted version have been addressed.\nThe only moderate-to-major comment would be that some of the new sections do not seem as\nwell polished and streamlined as they might be. This is particularly the case for the discussion\nand conclusions, where I thought the wording could be tighter overall and this would help\nmaximising the impactful delivery of the work done. I would recommend that the authors go\nback through this section and the other new sections and make sure the writing is as clear,\nconcise and compelling as it can be. There is nothing wrong, as such, with it at present; I just\nfeel like some of the text could be better polished and streamlined to really make the most of\nthese important findings and considerations.\nWe thank Sian Henley for carefully reading our revised manuscript. We have revised the text\nfollowing the suggestions below. Further, we made some additional minor modifications in the\ndiscussion section in an attempt to streamline the text (please see track-change document).\nIn addition, I have the following minor points to be addressed.\nLine 82: I suggest \"... will have increased...\"\nChanged as suggested.\nLine 92: I suggest bringing \"[in the] high-emission scenario SSP5-8.5\" out of the brackets as this\nis an important part of the sentence\nChanged as suggested.\nLine 108: there is inconsistency as to whether you name this MPA as South Orkney Southern\nShelf or South Orkney Islands Southern Shelf. Ensure that this is correct and consistent\nthroughout. Note: I think the shortening to South Orkney MPA later in the text is acceptable,\nonce it has been defined properly earlier on.\nWe thank the reviewer for pointing out this inconsistency. In the revised manuscript, we now\nconsistently refer to this MPA as the “South Orkney Islands Southern Shelf MPA”. Similarly, we\nhave also ensured consistent naming of the second adopted MPA, i.e., the “Ross Sea region\nMPA”.\nChanged as suggested.\nLine 149: should this be upper 200 m, given the changes to the analysis since the original\nsubmission? If so, this should be changed on the figure and in its caption as well. I'm not sure\nwhich is right in this instance, but check. Check this for figure S7 as well.\nWe thank the reviewer for paying such close attention. We confirm that what is currently stated\nin the text, figure, and figure caption is correct: This analysis still covers the upper 2000m of the\nwater column, as we think that the division into volumes with a specific omega range is more\nmeaningful when applied to a larger part of the water column/habitat than when only applying\nthis division to the top 200m.\nLines 219-224: it would be useful to identify which scenarios you are talking about somewhere\nhere. I assume SSP5-8.5 and SSP3-7.0, but it would be worth being explicit.\nWe are here referring to the emission scenarios SSP2-4.5, SSP3-7.0 and SSP5-8.5. We have\nclarified this as follows in the revised text:\n“Under the intermediate to high emission scenarios SSP2-4.5, SSP3-7.0 and SSP5-8.5,\necosystems in the shallow continental shelf seas of the proposed and adopted Antarctic MPAs\nwill be exposed to severe OA by 2100. For the SSP3-7.0 and SSP5-8.5 scenarios, aragonite\nundersaturation is ubiquitous […]”\nLine 245-246: should be Supplementary Figure 4\nChanged as suggested.\nLine 247: \"is possibly non-negligible\" seems very vague and rather clunky. I would suggest\n\"could also be a factor\" or \"cannot be ruled out\" for improved clarity.\nWe have rephrased as suggested to:\n“[…] the contribution of changes in CO solubility and of a redistribution of water masses could\n2\nalso be a factor […]”\nLine 248: should be Supplementary Figure 5\nChanged as suggested.\nLine 259: I would suggest finishing this sentence with \"in the Southern Ocean\" for\ncompleteness.\nChanged as suggested.\nLine 268: \"of\" not required - I suggest deleting.\nChanged as suggested.\nthe depth range(s) you are referring to.\nWe have revised this sentence as follows:\n“However, in the two highest-emission scenarios, the projected pH by 2100 is <7.8 throughout\nthe water column for all MPAs (Fig. 1) […]”\nLine 279-282: I suggest rewording to \"Even though it remains unclear in laboratory experiments\nto what extent...\". Also, for completeness, I would add explicit mention of impacts to their prey\nand/or predators (and hence how organisms not directly impacted are affected by indirect\neffects).\nWe have rephrased the sentence to now read:\n“Even though it remains unclear in laboratory experiments to what extent a longer acclimation of\nadult organisms can reduce the severe impacts reported for egg development and juveniles ,\n82\nstrong OA would almost certainly disrupt food webs, as OA might affect even those organisms\nwhich are not directly negatively impacted by OA themselves through direct OA effects on their\nprey or predators.”\nLine 301: climate-change feedbacks?\nChanged as suggested.\nLine 302: should be \"highest-emission scenario\"\nChanged as suggested.\nLine 318: \"for sustainable management\" or \"for the sustainable management\"\nChanged to “for sustainable management”.\nFigure S2: following my comments in the first round of reviews, I think line 2 of this caption\nshould read \"...to calcite\", consistent with the omega-calc in brackets\nThis has been corrected in the Figure caption.\nI believe that all of these comments and suggestions are amenable to being addressed, and\nonce this has been done, the manuscript will be ready for publication. I am happy to review the\nsecond round of revisions if required, or for the editor to sign off if they feel my comments in this\nround have been addressed satisfactorily.\nSian Henley\nUniversity of Edinburgh\n20/10/2023\nReviewer #3 (Remarks to the Author):\nThe revised manuscript by Nissen et al. improved the quality of the interpretation with respect to\nthe projected changes over the shelf and MPAs areas. Overall, the modelling results are\nexcellent and could and should serve to make future decisions on the MPAs in the Southern\nOcean.\nHowever, the study with the latest improvements, is severely unbalanced in text wrt to MPA\nframing. Most of the text deals with the modelling outputs and only the last page starts\ndiscussing the implications for the MPA, while the title and the abstract point out this to be major\nforce behind this MS. While the MS describes the modelling efforts in detail, it falls short of what\nto do with them, the implications are too weak, too vague and inadequate. I strongly suggest\nrestructuring, the MPAs text needs to be extended, more precise- like where are suitable areas,\nwhere should that continuous expansion be and over what extent. Otherwise, such MS cannot\nreally be used for policy informed discussions, with high relevance for the Nature.\nIn general, seeing more nuanced results of this study now, I have serious reservations about the\ncurrent thinking about expanding MPAs. As this study finds out, MPAs would see the greatest\nOA severity precisely in the MPAs. The decision to expand the areas would contradict the\ncommon sense of extending the areas that would be most compromised. In contrast, MPAs\nshould be positioned in the areas with the greatest protection that can act as a refugee. Simply\nallowing for only a refence area (line 305) that authors cite is merely not enough. The\ninformation from the modelling should point out where the areas of potential refugee are the\ngreatest (including the projections and feedback) and then build the case on this. As it currently\nis, I simply see such justification to be too weak.\nUpon building the case of the greatest refugee, this also means that the areas need to be\nlooked at more comprehensively, not evaluating only OA, but also warming and hypoxia,\nbecause intense warming could momentarily restructure the ecosystem. I find it inadequate to\npropose the expansion of MPAs without taking and evaluating the extent of other stressors. I\nsuggest the authors to delineate the projected changes in warming, hypoxia and OA for the\nthree investigated areas (Weddel, East Ant, West Ant Peninsula), aligned them together and\nfind most suitable refugee areas for the same functional groups already considered. I think the\nhypoxia threshold currently used is OK, it might be the most early-warning but is sufficient. As\nfor thermal reference, a lot of these thresholds exist in the literature. Once all three stressors are\nconsidered, a more precise advice on where the expansion of the MPAs should be- that would\nbe the most comprehensive advice that the CAMLR needs to make the next steps.\nWe appreciate the reviewer’s feedback, however, much of what is suggested is very much\nbeyond the scope of this paper. Below, we seek to clarify the goal and scope of our study and\nits implications.\nThe goal of our study is to present novel future projections of ocean acidification within the\nbounds of existing (adopted and proposed) Antarctic MPAs. As such, most of the manuscript\ntext focuses on presenting the modeling results in these predefined regions. Serving as a\nmotivation for our study and providing the analysis framework, MPAs are prominently mentioned\nin the abstract and introduction of the manuscript, and our findings on ocean acidification are\nplaced into the context of MPA policymaking in the discussion section. We thus believe the title\nof our manuscript adequately summarizes its content. After the first round of reviews, we have\nmade major modifications to the manuscript. In particular, in response to comments by reviewer\n#1, who is happy with the revised manuscript, we decided to put less emphasis on making\nrecommendations for MPAs in the revised manuscript and instead highlight our modeling results\nmore. With our manuscript, we do not endeavor to propose modifications to existing MPA\nboundaries -- these have already been established by means of bioregionalization and political\ncompromises (Brooks et al., 2020, 2021). We emphasize that priorities for protection, and\nresultant boundaries of the MPAs, are a policy decision, and ultimately a political process, which\n4\ncan be supported by science. Here we seek to build on and provide that science which could be\nutilized in the policy process.\nWe agree with the reviewer that a comprehensive assessment of Antarctic MPA boundaries is\nneeded for the CCAMLR community, especially one which considers the present-day\ndistributions and future projections of all ecosystem stressors including acidification. However,\nsuch an assessment is well beyond the scope of this manuscript, which focuses on projections\nof acidification within the existing (adopted and proposed) MPA boundaries. To address this\nreviewer point, we have added a sentence in the discussion section to clarify future research\npriorities:\n“Future work should include a joint assessment of the evolution of all ecosystem stressors in\nAntarctic coastal waters over the 21 century to identify regions of greatest and least risk for\nst\nmarine organisms.”\nFinally, we believe that MPA design and implementation should indeed consider regions\ncharacterized by rapid change, as a reduction in other stressors (e.g., fishing) in these regions\nwill contribute to reducing the cumulative threat to ecosystems.\nMinor comments:\nLine 47-49: Need to be some quantitative citation of MPA protection, increased in the diversity\nprotection etc.\nIn the revised manuscript, we have added two more citations (Lester et al., 2009; Edgar et al.,\n2014), which quantify the positive impact of MPAs on marine ecosystems, e.g., in\npreserving biodiversity:\n“[…] the implementation of MPAs can increase resilience of marine ecosystems to\nenvironmental change, including those resulting from climate change .”\n47–49\nDemonstrate high biodiversity in the MPAs with mor references -line 260\nRef 62, 63, 60, 61, 67\nWe have added two references to the revised manuscript (De Broyer et al., 2014; Douglass et\nal., 2014) illustrating the high biodiversity in the Southern Ocean MPAs. We cite these new\nreferences both in the revised introduction and the revised discussion section:\n“Designed to protect the unique high-latitude Southern Ocean biodiversity ,[…]”\n27,28\n“Given the high biodiversity in MPAs , [..]”\n27,28\nLine 186 several years of adaptation time?\nYes. Compared to organisms with a short generation time of days or weeks, e.g.,\nphytoplankton, all organisms with a substantially longer generation time of years to decades will\nrequire a much longer time to successfully adapt to OA. For these organisms, a lower rate of\nOA will thus be especially beneficial. Further, substantial adaptation to OA in these organisms\ncould only occur over a single generation if enough genetic variability is already present in the\npopulation, i.e., if no new mutations are necessary (Kelly et al., 2013). But, depending on the\ngeneration time, this would still take several years at least.\nrelevant\nWith other organisms being listed in the previous sentence, the purpose of this sentence is to\nexplain why the impacts on benthic organisms can be expected to be substantial. We therefore\ndecided to leave this sentence unchanged, but instead restate the expected negative impacts\non the other listed organism groups in the preceding sentence, which now reads:\n“Given the high biodiversity in MPAs, the projected severe OA under higher-emission scenarios\nwill likely impact organisms on many trophic levels, ranging from primary producers (growth) to\n51\nfish (metabolic capacity and mortality) and calcium carbonate-forming benthic\n3,66\norganisms (shell dissolution; Fig. 1) .“\n4,68\nLine 309 – at least some evaluation what the reduction of fishing could do\nTo link this statement in the discussion back to what was already stated in the introduction, we\nhave changed this part of the sentence to now read:\n“[…] a reduction of fishing activities in a larger fraction of Antarctic coastal waters could be\nconsidered to reduce cumulative stressors on the system and to preserve genetic, species and\necosystem diversity […]”\n47–49\nFurther, we have included citations to references demonstrating the positive impacts of reduced\nfishing pressure (see our answer above to the minor comment on L. 47-49).\nCited literature:\nBrooks, C. M., Bloom, E., Kavanagh, A., Nocito, E. S., Watters, G. M., & Weller, J. (2021). The Ross Sea,\nAntarctica: A highly protected MPA in international waters. Marine Policy, 134, 104795.\nhttps://doi.org/10.1016/j.marpol.2021.104795\nBrooks, C. M., Chown, S. L., Douglass, L. L., Raymond, B. P., Shaw, J. D., Sylvester, Z. T., & Torrens, C.\nL. (2020). Progress towards a representative network of Southern Ocean protected areas. PLOS ONE,\n15(4), e0231361. https://doi.org/10.1371/journal.pone.0231361\nDouglass, L. L., Turner, J., Grantham, H. S., Kaiser, S., Constable, A., Nicoll, R., Raymond, B., Post, A.,\nBrandt, A., & Beaver, D. (2014). A Hierarchical Classification of Benthic Biodiversity and Assessment of\nProtected Areas in the Southern Ocean. PLoS ONE, 9(7), e100551.\nhttps://doi.org/10.1371/journal.pone.0100551\nDe Broyer, C., Koubbi, P., Griffiths, H.J., Raymond, B., Udekem d’Acoz, C. d’, Van de Putte, A.P., Danis,\nB., David, B., Grant, S., Gutt, J., Held, C., Hosie, G., Huettmann, F., Post, A., Ropert-Coudert, Y. (eds.):\nBiogeographic Atlas of the Southern Ocean. 510 pp., 2014. Cambridge, SCAR. ISBN 978-0-948277-28-3\nEdgar, G. J., Stuart-Smith, R. D., Willis, T. J., Kininmonth, S., Baker, S. C., Banks, S., Barrett, N. S.,\nBecerro, M. A., Bernard, A. T. F., Berkhout, J., Buxton, C. D., Campbell, S. J., Cooper, A. T., Davey, M.,\nEdgar, S. C., Försterra, G., Galván, D. E., Irigoyen, A. J., Kushner, D. J., … Thomson, R. J. (2014).\nGlobal conservation outcomes depend on marine protected areas with five key features. Nature,\n506(7487), 216–220. https://doi.org/10.1038/nature13022\nEcology, 27(4), 980–990. https://doi.org/10.1111/j.1365-2435.2012.02061.x\nLester, S. E., Halpern, B. S., Grorud-Colvert, K., Lubchenco, J., Ruttenberg, B. I., Gaines, S. D., Airamé,\nS., & Warner, R. R. (2009). Biological effects within no-take marine reserves: A global synthesis. Marine\nEcology Progress Series, 384, 33–46. https://doi.org/10.3354/meps08029\n7"}]

Decision letter