Earth system simulations suggest that the Proterozoic ocean was greener but less productive

Domain: chemistry
Published: 2026-02-17
Editorial outcome: major_revision

Abstract
Geological records suggest that marine phytoplankton might have arisen in the Proterozoic while zooplankton remained absent, and marine productivity was not excessively low. However, quantitative estimates of phytoplankton biomass and net primary productivity remain elusive. Here, we use the Community Earth System Model version 1.2.2, modifying biological module and boundary conditions, to simulate marine biogeochemical cycles in the Proterozoic. The simulations demonstrate that, within the expected range of nutrient levels, phytoplankton at sea surface was more than 2 times denser than present, sustaining a greener ocean due to the absence of predators. Heavier surface chlorophyll in the Proterozoic would block sunlight from reaching subsurface layers. This so-called self-shielding effect would decrease subsurface net primary productivity significantly. Simulations show that, through the combined influence of low nitrate level under a low-oxygen environment, the absence of diatoms, and self-shielding, the Proterozoic net primary productivity was only approximately 60% and 30% of the present level in warm (almost ice-free) and cold (sea-ice reaches around 30°N/S) periods, respectively. These findings are subject to uncertainties in model framework and Proterozoic nutrients levels; a slightly less green ocean or more productive ocean was possible if the phosphorus level was much lower or higher than the present level.

Introduction
The Proterozoic Eon covers over 40% of Earth’s history from 2500 to 538.8 Ma (million years ago), with its climate being warm in the middle (Boring Billion) but extremely cold near both ends (Snowball Earth events)1,2. Based on geochemical and palaeontological records, the primary productivity during the Proterozoic might have been substantial (between ~5 and ~40% of the present-day level)3–6. During the Precambrian, nearly all global productivity was generated by the marine biosphere, while roughly half of productivity came from the land biosphere after the mid-Palaeozoic when vegetation colonized the continents3. The Proterozoic marine community would primarily be composed of small phytoplankton (e.g., cyanobacteria and green algae), with zooplankton likely absent until the Ediacaran1,5,7. The oxygen isotope records indicate that the gross primary productivity during the mid-Proterozoic might have been ~40% of the preindustrial level if the atmospheric oxygen level (pO2) was 1–10% of the present atmospheric level (PAL)4, consistent with geochemical simulation results6. An active marine biosphere in the Proterozoic could have been important for the evolution of different Earth components. The biological processes may have affected the climate by consuming atmospheric CO2, and (or) injecting organic cloud nuclei into the atmosphere8–10. The marine photosynthesis is critical for the evolution of the atmospheric as well as marine oxygenation state11. The increase in marine productivity and oxygen levels was probably important for the evolution of animals3. However, our understanding of the Proterozoic marine biogeochemical cycles is still rudimentary.

The primary productivity in the ocean is largely determined by the variations in temperature, nutrients, and light availability. Other than the large temperature variations, the Proterozoic was also characterized by very different nutrient levels from today due mainly to the low pO2 at that time. For example, the environment was likely iron-rich, supplying abundant iron to the marine ecosystem12,13; denitrification would be enhanced in an anoxic ocean14,15, leading to nitrogen limitation of the primary productivity; the phosphorus (P) level could have also been lower due to limited oxic respiration and (or) removal by minerals16,17, but some geochemical evidence suggested otherwise18. The dimmer Sun during the Proterozoic could have also affected the productivity. Because zooplankton had not appeared during the Proterozoic1,7, the bloom of surface phytoplankton could have blocked sunlight and suppressed the subsurface primary productivity, just as sometimes observed on the present-day Earth, where predators are absent19,20.

Previous studies involving Proterozoic biogeochemical simulations were based mostly on simplified models such as conceptual models16,21 and box models8,22,23. Recently, an ocean general circulation model has been used to explain the banded iron formations during a Neoproterozoic Snowball Earth event24. Although the Proterozoic biogeochemical cycle has been simulated with an atmosphere-ocean general circulation model (AOGCM), that study mainly focused on the role of the ocean in modulating the atmospheric CO2 concentration (pCO2) and super-greenhouse climate in the aftermath of the Marinoan Snowball Earth event25. Therefore, although serving their purposes well, many of the important processes affecting the Proterozoic ecosystem were omitted in the approaches employed by these previous studies. The simplified models could not reveal the spatial structure of the ecosystem, while the complex model25 neglected some of the differences in ecological structure between the Proterozoic and the present, for example, the absence of zooplankton. It is essential to employ an AOGCM that is adapted to the Proterozoic to systematically study its ecosystem.

Here, we use an AOGCM, Community Earth System Model version 1.2.2 (CESM1.2.2), to simulate the marine biogeochemical cycle during both warm (pCO2 = 2240 ppmv) and cold (pCO2 = 280 ppmv) climate states of the Proterozoic, and compare it to that from a preindustrial (PI) simulation (see “Methods”). In the cold state, the annual mean sea-ice edges reach ~30° latitude (Fig. 1C), while in the warm state, sea ice is almost absent. Although the continental configuration used here was reconstructed for the late Neoproterozoic (see “Methods”), the fundamental characteristics of the ecosystem across the entire Proterozoic may have been analogous since the continents remained at relatively low latitudes for the whole eon26,27. Moreover, the sensitivity simulations (see “Methods”) could have covered the uncertainties due to the evolution of continental configuration. Since the diatom and zooplankton were likely absent during the Proterozoic1,7, we modify the composition of the ecosystem (only consider the small phytoplankton (<20 µm) and diazotroph, following the strategy employed by Gianchandani et al.24; see “Methods”) and boundary conditions accordingly (see “Methods” and Supplementary Table 1). Similar simulations were carried out and the climatology analyzed previously by Liu et al.28 with the only difference being that the biogeochemical cycle was not turned on. These previous simulations can be compared to the ones performed herein to see the influence of the biogeochemical cycle on the surface albedo. Our model results indicate that, within the expected nutrient regimes, the biomass of phytoplankton in the Proterozoic model setup was higher than that in present-day Earth when predatory zooplankton were absent. Consequently, the denser chlorophyll, causing a greener ocean surface than the present level, would have blocked the subsurface layers from receiving sunlight and reduced the primary productivity there. The total productivity of the Proterozoic ocean simulated by the CESM1.2.2 was likely lower than that of the present-day ocean.

Results
Greener Proterozoic ocean
Simulation results show that, without grazing by zooplankton, more phytoplankton would have survived in the upper ocean during the Proterozoic. The global mean chlorophyll averaged within the upper 150 m is 0.10 mg/m3 in PI (Fig. 1A), similar to the observations29. By contrast, the global mean chlorophyll is 0.24 and 0.15 mg/m3 during the warm and cold periods of the Proterozoic, respectively (Fig. 1B, C). Moreover, chlorophyll in PI would have varied smoothly over the globe, with the majority of oceans having values of less than 0.15 mg/m3 (Fig. 1A), while the chlorophyll may have reached >0.3 mg/m3 over most of the low-latitude oceans in the Proterozoic (Fig. 1B, C). If the permanently ice-covered regions in the cold case are excluded, the mean chlorophyll becomes 0.30 mg/m3. That is, the simulated concentration of chlorophyll in the upper ocean of the Proterozoic was much higher than that of PI in both the warm and the cold periods. Correspondingly, the plankton carbon within the upper 150 m of ocean was also much higher in the Proterozoic model simulations than in PI (Fig. 1D–F and Supplementary Fig. 1).

The model simulations further indicate that the difference in the concentration of chlorophyll within the upper 10 m of ocean between the Proterozoic and PI could have been even more dramatic (Supplementary Fig. 2); over regions where primary production is active, the concentration of chlorophyll in the former is generally over 10 times that in the latter (compare Fig. 2A–C and Supplementary Fig. 2A–C). During the warm period of the Proterozoic, the primary production may have been active from the equator to approximately 50° latitude (Fig. 2B), covering ~70% of the ocean area; during the cold period, all open ocean (i.e., not covered by sea ice) would have remained production active (Fig. 2C). Therefore, most parts of the simulated Proterozoic ocean would look much greener than the modern ocean (Supplementary Fig. 2). The high-latitude oceans of the Proterozoic were barren in life even during the warm period, because the temperature there would still be too low for phytoplankton to flourish while the cold-tolerant diatoms have not evolved yet30.

The much higher concentration of chlorophyll in the near-surface ocean in the Proterozoic model simulation is primarily due to the absence of zooplankton. In the modern ocean, over 85% of the phytoplanktonic net primary productivity (NPP) is grazed by zooplankton (Supplementary Fig. 3A31), and the small phytoplankton contributes only ~50% of the chlorophyll. In contrast, the small phytoplankton contribute ~90% of the chlorophyll in the Proterozoic setup of our model. The rest of the chlorophyll is mainly from diatoms (~45%) and diazotrophs (~10%) in the present-day and Proterozoic, respectively. Due to the absence of grazers, the planktonic carbon can easily reach 3 mmol/m3 in the upper 50 m and can even be >7 mmol/m3 (Fig. 1E, F), which is nearly impossible in the modern ocean (Fig. 1D32,33). The small phytoplankton constitutes ~85% of the upper-ocean biomass in the Proterozoic, according to the model simulation results, while only taking up 40% in the modern ocean. When the zooplankton is added back to the Proterozoic ocean (see “Methods” for Sensitivity Simulation Group 1 and Supplementary Table 2), surface chlorophyll decreases substantially (Supplementary Fig. 4), confirming that the absence of zooplankton was the key trigger of the greener Proterozoic ocean.

Less productive Proterozoic ocean
Although the simulated Proterozoic ocean is characterized by more massive phytoplankton, the model results show that its total NPP is less than the PI ocean’s. The simulated global total NPP is about 2907 teramoles per year (Tmol/yr) and 1500 Tmol/yr in the warm and cold periods, respectively, ~60 and ~30% of the present level (4754 Tmol/yr) (Fig. 2A–C). The present global mean euphotic depth is about 80 m, defined as the maximum depth at which NPP can occur34 (Supplementary Fig. 5A). But the productive euphotic layer would thin to ~40 and ~30 m in the warm and cold Proterozoic ocean, respectively (Supplementary Fig. 5B, C). This smaller total NPP in the simulated Proterozoic is partially due to the absence of diatoms because it contributes only 20% of the total NPP in the present ocean; excluding the influence of diatoms, the global simulated NPP of the warm and cold Proterozoic oceans is still about 25% and 60% less than that of the present ocean, respectively.

Unlike in the modern ocean, where NPP is maintained almost everywhere except the polar oceans (Fig. 2A), NPP is limited to a few zonal stripes in the Proterozoic setup of our model. When the Proterozoic climate is warm, the model results show that NPP concentrates in the equatorial region where upwelling is strong and between roughly 30° and 50° latitudes of both hemispheres where the temperature is still relatively high and vertical mixing is strong28 with significant iron deposition from dust (Fig. 2B and Supplementary Fig. 6A). The NPP in these three latitudinal bands in the upper 20 m of the warm Proterozoic ocean may have been much higher than those in PI (Fig. 2D, E). When the Proterozoic climate is cold, the NPP concentrates in the equatorial region only since the mid-latitude region becomes cold or sea-ice covered (Fig. 2C, F), giving a much lower global NPP.

The simulated NPP decreases with depth because of colder and darker ambient conditions, but the rate of decrease could have been much higher in the Proterozoic than in the present ocean (Fig. 2D–F, G–I). For example, the NPP decreases from ~90 to 60 (×10−7) mmol/m3/s in the upper 50 m near the equator in the present ocean (Fig. 2D) while it decreases abruptly from ~150 to 10 (×10−7) mmol/m3/s in the warm Proterozoic ocean as shown by the simulation results (Fig. 2E). This rapid decrease of NPP with depth should be an important reason why the global total NPP (contributed by small phytoplankton and diazotroph) is lower in the simulated warm Proterozoic than in the present (Supplementary Fig. 7), even though the near-surface NPP is much higher (Fig. 2D–F). The massive phytoplankton (chlorophyll, Fig. 1B, C) floating at the surface would have blocked the sunlight from reaching the subsurface and thus decreased the NPP beneath. This phenomenon is termed the self-shielding effect35,36 as will be discussed in more detail in the next section. However, note that the different nutrient levels between the Proterozoic and PI, especially the marine nitrate (N), are also important for the Proterozoic oceans being less productive than PI oceans (see “Discussion”).

Self-Shielding Effect
The subsurface ocean of the Proterozoic indeed receives much less sunlight than that of the present, simulated by the CESM1.2.2 (Figs. 3A–C and 4). In the warm Proterozoic scenario, the global mean solar radiation received in the second layer (10–20 m depth) of the ocean is 22.6 W/m2, about 15 W/m2 less than the present-day level (Fig. 3A, B). Compared to the warm case, the solar radiation received in the subsurface ocean of the cold case is also low, but is relatively high along ~30° latitude and part of the equator. This relatively high value is due to the low NPP and chlorophyll near the sea-ice edges, where the temperature is low, but the surface radiation is high; the high values along the equator are coincident with the low NPP (Fig. 2C) and chlorophyll (Fig. 1C) there. In fact, the pattern of the subsurface solar radiation in all three cases (Fig. 3A–C) corresponds well with that of the NPP (Fig. 2A–C) and chlorophyll (Fig. 1A–C), indicating that the high surface NPP and chlorophyll are the primary reasons why the Proterozoic subsurface ocean is deprived of sunlight. As described above, the high surface NPP and chlorophyll in the simulated Proterozoic ocean are due to the absence of zooplankton (Supplementary Fig. 4).

Whether the self-shielding effect is the reason why the simulated Proterozoic biological productivity is lower than the present can be checked by looking at the major limiting factor of productivity that is output by CESM1.2.237. In the present, N is the most important limiting factor for the growth of small phytoplankton in much of the low to mid-latitudes, except in the South Pacific and Southern Ocean, where Fe is the main limiting factor (Fig. 3D), consistent with both observations38 and other simulation results29. During the warm Proterozoic, the simulation results indicate that N is still the dominant limiting factor in the mid-high latitudes due to its much lower deposition rate to the ocean compared to the present (Supplementary Table 1) and the enhanced denitrification effect under the anoxic Proterozoic ocean14,15 (Supplementary Fig. 8). However, in lower latitudes where simulated small phytoplankton flourish (Fig. 1B, E) and the surface NPP is high (Fig. 2E), sunlight becomes the most limiting factor (Fig. 3E). For the cold case, the low temperature and sunlight are the most limiting factors in the extratropics and tropics, respectively (Fig. 3F). The fact that sunlight is the most limiting factor for primary productivity in the warm regions of the Proterozoic indicates that self-shielding could have been the major reason for its lower total NPP. The Proterozoic ocean has been thought to be less productive, probably due to nutrient shortage (especially N)16, but here we show that the self-shielding effect, induced by phytoplankton aggregation, could have played an even more important role under the feasible Proterozoic nutrient background (Methods). The simulated greener but less productive Proterozoic ocean compared to the PI regime is summarized in the schematic Fig. 4.

Methods
Model description
To simulate the marine biogeochemical cycle during the Proterozoic, the Community Earth System Model version 1.2.2 (CESM1.2.2) has been employed in this work, which has been broadly used in the deep time simulations64,65. CESM1.2.2 includes six components, namely atmosphere, ocean, land, sea ice, land ice, and rivers, which interact with each other through a coupler66. The land ice component is not activated in this study. The atmosphere and land components are both operated on the T31 grid with a horizontal resolution of 3.75° × 3.75°. The ocean component (Parallel Ocean Program version 2, POP2)67 and sea ice component are operated on the g37 grid with a uniform 3.6° spacing in the zonal direction and variable spacing (0.6°–3.4°) in the meridional direction. The atmosphere and ocean have 26 and 60 layers in the vertical direction, respectively.

For the horizontal diffusion, the anisotropic mixing of momentum68 and Gent and Mcwilliams69 parameterization, which drives the mixing of tracers along isopycnal surfaces with activated submesoscale mixing, has been employed in the model. In the 720 Ma continental configuration used here, the vast ocean without continents in the mid-high latitudes of the Northern Hemisphere would give rise to excessively strong westerly ocean currents (~70 cm/s with ~20° meridional width), warranting higher tracer diffusivities than the default70. Thus, we have increased the horizontal diffusivity (variable ah in the model) by a factor of 5 (from 800 to 4000 m2/s), as employed in previous work using the same continental configuration and resolution28,70. For vertical mixing, the K-profile parameterization has been used in POP2, in which the interior mixing coefficients are computed at every grid point according to relevant physical processes71. These physical processes include surface wave breaking, shear instability, convection, background internal wave breaking, and tidal dissipation. For the present-day, the background internal wave breaking is prescribed to a universal constant (also represented by vdc1 with a value of 0.16 cm2/s), and the tidal dissipation is horizontally variable and decreases exponentially from the bottom to the top. In the deep-time simulations, because the tidal dissipation is unknown, the background and tidal dissipation together (κ) are represented by a function that depends on depth (z) only,

k = vdc1 + vdc2 * tan^-1 (z - 1000 m) * 4.5 × 10^-3 m^-1 (1)

where vdc1 = 0.524 cm2/s and vdc2 = 0.313 cm2/s as recommended by NCAR-suggested deep-time standards and previous work28,72.

For the purpose of this study, the biogeochemical elemental cycling (BEC) model embedded in POP2 has been activated, which consists of the upper ocean (0–150 m) ecological and full-depth biogeochemical dynamics37,73. The internal sources and sinks of carbon (C), oxygen (O), phosphorus (P), nitrogen (N), silicate (Si), and iron (Fe) in BEC are driven by three functional groups of phytoplankton and one zooplankton. Higher-trophic-level predators and heterotrophic bacteria have been implicitly resolved by the parameterized loss terms associated with zooplankton and scavenging of organic matter, respectively37,73. The trophic complexity (phytoplankton–zooplankton–detritus) of type-based BEC is relatively competitive among marine biogeochemical models employed in Phases 5 and 6 of the Coupled Model Intercomparison Project (CMIP5 and CMIP6)74. The phytoplankton groups, grazed by the zooplankton, include (pico/nanocalcareous) small phytoplankton (<20 µm), N-fixing diazotrophs, and diatoms. Here, only the former two phytoplankton groups have been involved in the simulations, because the diatom and zooplankton are not believed to have evolved until the end of the Permian30 and Ediacaran7, respectively. Moreover, the biomass of large phytoplankton (e.g., dinophyta) is less than that of small phytoplankton and contributes limited NPP in the modern Earth, thus, typical marine biogeochemical models always omit various types of large phytoplankton29,74. Although the primary marine phytoplankton community might be cyanobacteria during the Proterozoic, the metabolite and biomass (e.g., H:C and O:C ratios) contents are similar to those of modern phytoplankton75–77. Thus, the model strategy of ecosystem simplification based on the modern Earth has been widely employed in the simulations of Neoproterozoic24 and Permian78 biogeochemistry.

The organic carbon in the ocean, mainly in the form of DOC and particulate organic carbon (POC), is consumed by a few remineralization processes in the model, and the rest is permanently buried into the seafloor. These remineralization processes include the direct oxidation by oxygen in the seawater, the denitrification in both seawater and the sediments79,80, and the remineralization by ferric iron, manganese oxides, and sulfate. The anoxic remineralization utilizing these latter oxidants is lumped into one process in CESM1.2.2, and its flux is formulated to be equal to the organic carbon flux at the seafloor minus the POC settled into sediments and organic carbon consumed by denitrification80. The settling fluxes of particles are parameterized based on the marine production, particle aggregation, and physical processes of seawater (e.g., advection)37,73. A maximum burial efficiency of 80%81 is imposed on this POC flux at the seafloor, and the buried organic matter is lost instantaneously from the ocean domain. To avoid drift of the ocean nutrient inventories, an additional input of nutrients is needed to balance the loss of nutrients by this POC burial73,82. That is, the nutrients lost due to the permanent burial of these POC are put back into the ocean also instantaneously. The BEC model has been shown to perform well based on a wide range of metrics for the studies of the present83,84 and paleo Earth78.

The silicate weathering model, employed for the boundary condition settings in BEC, is essentially the same as that in Park et al.85 but with an improvement to reduce the bias in global total weathering flux65,86. This model considers the processes of regolith generation and physical erosion in the vertical depth and is thus capable of reflecting the influence of supply-limited and kinetically limited conditions simultaneously87. The silicate weathering rate depends on the surface temperature, runoff, surface slope, and lithology, with the former two simulated in CESM1.2.2, while the latter two have been set as described in the next section.

Boundary conditions for the standard simulations
The continental configuration employed here is appropriate for 720 Ma in the Proterozoic27 with slight modification to increase model stability28,70. Due to the lack of surface topography reconstruction and the understanding that the surface of deep-time Earth was generally smooth88, the surface is assumed to be basically flat. The land surface is set to desert since plants had not colonized the continents during the Precambrian89. The solar constant is set to 1285 W/m2, 6% weaker than the present value90. Atmospheric oxygen concentration (pO2) is prescribed at 1% PAL (PAL: present atmospheric level) with globally uniform distribution, and then BEC calculates the dissolved oxygen in the ocean based on Henry’s law and relevant piston velocity for the marine biogeochemical simulations11. The climate effects of atmospheric aerosols might be significant13,91 but are beyond the scope of the current study, and thus are omitted in the atmosphere model. The orbital parameters are assumed to be those of the year 1990; the concentrations of CH4 and N2O are prescribed to be 805.6 and 276.7 ppbv, respectively, as those in the preindustrial. All the settings above are similar to those in previous modeling studies of the Snowball Earth events28,70. To be consistent with Liu et al.28 so that many of the BEC-induced changes (e.g., mixed-layer depth) can be calculated, atmospheric dust in the atmosphere model is assumed to be zero. To simulate the marine biogeochemical cycle during the Proterozoic in both warm and cold periods, two experiments are carried out in which pCO2 is set to 2240 and 280 ppmv, respectively.

The boundary conditions of BEC include the nutrients deposited from the atmosphere and injected by runoff into the ocean. Because dust is an important source of Fe for marine life92, the spatial distribution of dust deposition from a previous simulation is prescribed. Specifically, we use the results of Liu et al.91 from the experiment in which pCO2 = 280 ppmv and surface erodibility = 0.01875 (Supplementary Fig. 6A). In this simulation, the amount of dust deposition over the ocean was about 6 times the present level. The Fe is assumed to be 3.5% of the dust mass, 0.8% of which is bioavailable based on models and observations93,94. The nitrogen deposition input in BEC contains NOy (e.g., NO, NO2, and HNO3) and NHx (e.g., NH3 and NH4+). During the Precambrian, the natural NOy came from the volcanoes and photochemical reactions under a low oxygen level95,96. Here we borrow the NOy deposition rate (3.52 × 108 kg/yr) from the photochemical simulations in which the N2O outgassing rate is set to 1 PAL while pO2 = 1% PAL97. The pO2 has varied from about 0.001% to 10% PAL during the Proterozoic11, but the 1% PAL pO2 state may cover most Meso-NeoProterozoic11 and thus has been selected here. Meanwhile, the primary source of NHx should be NH3 from volcanoes and NH2 generated by the subsequent photochemistry, both of which are highly soluble. The present NH3 volcanic outgassing rate (3.72 × 107 kg/yr) is used as the deposition rate of NHx for the Proterozoic following the strategy in Kasting and Walker95. Both NOy and NHx deposition rates are about one order of magnitude lower than the present level due to the lack of biota sources (e.g., agriculture and biomass burning) with a globally uniform distribution in the Precambrian98.

The riverine inputs of nutrients to the ocean include dissolved inorganic carbon (DIC), DOC, dissolved inorganic phosphorus (DIP), dissolved organic phosphorus (DOP), dissolved inorganic nitrogen (DIN), dissolved organic nitrogen (DON), dissolved silicate (DSi), dissolved iron (DFe), and alkalinity (ALK), which should all be specified according to Proterozoic conditions. Due to the barren continents during the Proterozoic, the organic components (i.e., DOC, DOP, and DON) in runoff are neglected herein. Similarly, the majority of DIN in modern runoff originates from nitrogen fixation by terrestrial life99 as there is little nitrogen in basic rocks100, and thus DIN can also be omitted here. The DSi is set to zero because diatoms have not yet emerged. The DFe in runoff is fixed to 1.5 Tmol/yr based on the biogeochemical model for the low pO2 Precambrian101. The weathering rates (WR) are calculated by the weathering model described above, assuming a uniform felsic (acid volcanic rock) lithology and using the climate fields from the simulation (with pCO2 = 2240 and 280 ppmv) of a previous study28. The global total DIC and ALK are calculated to be equal to twice the calculated weathering rate85. DIP is assumed to be 0.0382% of the weathering flux based on fieldwork for the acidic volcanic rocks102. The spatial distribution of DIC, DIP, DFe, and ALK fluxes is scaled by the pattern of simulated runoff flowing into the ocean in CESM1.2.2 (Supplementary Fig. 6B, C)28. All the boundary conditions are summarized in Supplementary Table 1. Due to the lack of globally gridded reconstructions for biogeochemical variables during the Proterozoic, their initial values are set to the present level and will evolve to a new equilibrium state under the boundary conditions above. All simulations were continued for 3500 years so that both the climate and the biogeochemical cycle (e.g., the total NPP, DIC, and DOC) reach an equilibrium state, and the final 100 years are averaged for analyses.

Sensitivity simulation groups
Six groups of sensitivity simulations have been carried out to estimate the influence of uncertainties in boundary conditions or model components on the main conclusions drawn from the standard simulations described above. (1) Inclusion of zooplankton in the Proterozoic. The zooplankton has been involved in the ocean simulation with the other boundary conditions the same as those in the pCO2 = 280 ppmv simulation. (2) Increase of Proterozoic solar constant. Based on the warm Proterozoic simulation, the solar constant is set to the present level with 280 ppmv pCO2 so that the climate state is similar to that of the warm standard simulation, while all other boundary conditions (e.g., nutrients) are identical to those in the warm simulation. (3) Variation in the vertical diffusivity. The vertical diffusivity (variable vdc1 in the model) has been increased to 0.8 and decreased to 0.4 cm2/s for the high and low vertical mixing scenarios103, respectively, based on the pCO2 = 2240 ppmv simulation. (4) Different atmospheric oxygen levels (pO2). The pO2 is set to 0.1% and 10% of the present level in the pCO2 = 2240 ppmv simulation. (5) Varying the phosphate reservoir. The marine phosphate level has been set to 500%, 200%, 50%, 25%, 10%, and 2.5% of the POL, with other conditions identical to those in the original pCO2 = 2240 ppmv simulation. (6) Lower iron input. This group includes five simulations. In the first one, the sources from the atmospheric dust deposition and riverine input are removed, so that only Fe input through the ocean bottom is considered. In the other four simulations, the Fe from the ocean bottom is further reduced to 50%, 25%, 10%, and 0% of the present level. The above boundary conditions for the sensitivity tests are summarized in Supplementary Table 2.

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_1": "This study investigates the productivity of the oceans during the Proterozoic with the CESM1.2.2 Earth system model (ESM), which couples an atmosphere-ocean general circulation model with an ocean biogeochemistry model. The main hypothesis is that the absence of zooplankton and complex forms of phytoplankton in the ocean leads to a biogeochemical regime different from todays'. This is an interesting hypothesis, which, to my knowledge, has not been investigated before. The authors find that the absence of grazing by zooplankton leads to a higher concentration of chlorophyll, i.e. phytoplankton, in the uppermost layers of the ocean. However, this means there is less sunlight available in the subsurface ocean, leading to overall less primary production in the ocean compared to today. This was tested for two (Neo-)Proterozoic setups, using high and low concentrations of atmospheric CO2. The author's findings are significant, because they offer new insight into an interesting period of Earth's past that will be a helpful piece in the puzzle of reconstructing the evolution of life on Earth, climate and Earth's atmospheric composition.\n\nThe method of simulating an equilibrium Proterozoic climate twice with different atmospheric CO2 concentrations is straightforward, but appropriate and sufficient. More test simulations (suggestion given below) could have been interesting, but the study is still helpful and sufficient in itself. The chosen model is appropriate, and so are the chosen boundary conditions and the model spin up. The results are displayed nicely with a clear line of thought, and the text is well written and easy to follow.\n\nThe study provides a description of how marine ecology could have possibly looked like in the Proterozoic, which is valid if it is also understood as this. Of course not everything can be tested for a period that spans around two billion years, and hence there are certain limitations. For example, there is quite some uncertainty around the availability of nutrients in the Proterozoic ocean (which, of course, have varied over time), meaning that nutrient limitation could have also played a more important role than presented here, reducing the described effect. Furthermore, in the current state of the manuscript, it is not clear to me, if not also the reduced strength of the sun during the Proterozoic could have been responsible for the reduced primary production in their model and during the Proterozoic in general. Lastly, the type of model that is used relies heavily on parametrized vertical and horizontal mixing (because of the coarse grid resolution), adding another major source of uncertainty, since mixing contributes to the availability of nutrients and the re-distribution of phytoplankton to depths.\n\nTherefore, my main suggestion is to add some more discussion on potential sources of uncertainty and possible other drivers of the observed behaviour. Specifically, I would like to see the authors expand on the following aspects:\n1. Could not the relatively weaker sun also play an important role in light availability as limiting factor? The sun was 4-15% weaker during the Proterozoic, gaining strength over time. This is not discussed in the manuscript at all.\n2. How is mixing in the surface ocean affecting the simulations? Is there potentially more mixing in the Proterozoic ocean, so that surface phytoplankton is less limited by nutrients?\nIdeally, the authors would conduct an additional, counter-factual test simulation, where in the Proterozoic setup they would add the zooplankton back into the model, to test their hypothesis that it is the absence of zooplankton that drives the higher chlorophyll, lower NPP pattern in their standard Proterozoic setup. At the very least, the two points above should be discussed in the final section of the manuscript.\n\nLine-by-line comments:\n- l. 29: warm and cold periods have not been introduced in abstract, so there must be more explanation what this is referring to\n- l. 41-42 & l 43-44: This summary is not quite correct. Ramme, Ilyina and Marotzke (2024, https://doi.org/10.1038/s41467-024-47873-6) did use a similar type of model (AOGCM+biogeochemistry) to \"seriously\" study biogeochemical cycles in the aftermath of a snowball Earth in the Proterozoic. Of course their focus is different from this study, so there is no overlap, but it needs to be clarified that such a model type has been used before.\n- l. 85-89: The authors refer to Fig. 2, when saying that the Proterozoic ocean should be much greener than the modern ocean, but Fig. 2 rather indicates that primary productions is a lot higher in the modern ocean. If they want to say that the Proterozoic ocean's are greener, they should refer to their Fig. S2 in the supplementary material, I believe.\n- l. 120: At this stage, vertical profiles (i.e. global horizontal averages) of global ocean NPP and light availability for all three setups (i.e. including the modern) would be helpful to better justify the conclusion that it is the self-shielding effect that makes the subsurface ocean darker.\n- Methods: Please add some description or reference for how ocean mixing is handled in the model simulations. What parametrizations were used? What is the strength of prescribed mixing parameters?\n\nTechnical comments:\n- l. 34: \"THE Proterozoic EON\"\n-l. 58-61: There is a missing closing bracket in this sentence.\n- l.73: I wouldn't say that the pre-industrial setup has small horizontal variation. Just the maximum values are much smaller and hence there is less amplitude in the variations in the pre-industrial setup.\n- l. 125: please specify the sentence in the brackets\n- Fig. 3: Figure caption is confusingly written. Please rewrite and specify: Is the limiting factor in panels (D-F) also displayed for the second ocean layer, or is this a vertical average?\n- Fig. S7 caption (5th line): Two occurrences of \"biogeochemical cycle\". Also, add a \"the\" in front of \"biogeochemical cycle\".", "reviewer_2": "Review of “A Greener but Less Productive Proterozoic Ocean” by Liu et al. for Nature Communications.\n\nThe manuscript by Liu et al. explores the consequences of zooplankton absence in the Proterozoic ocean and investigates whether light availability or nutrient supply was the primary limiting factor for net primary production (NPP). The central hypothesis is that, in a phytoplankton-dominated ocean without grazers, self-shading by surface-dwelling phytoplankton could have significantly reduced the penetration of sunlight to deeper waters, thereby limiting productivity. This is a compelling idea, and the exploration of self-shading as a regulatory mechanism is particularly interesting.\n\nHowever, while the scientific motivation is strong and the self-shading mechanism is conceptually elegant, the model setup ultimately leads to a flawed comparison between the Proterozoic and modern oceans. The authors combine low atmospheric O₂ concentrations with modern-day nutrient levels, a configuration that is inconsistent with the Proterozoic ocean scenario. As a result, the comparison between Proterozoic and modern NPP is misleading and undermines the credibility of the main conclusions. In my view, the manuscript requires substantial revision and additional sensitivity analyses before it can be considered for publication. My detailed comments are provided below.\n\nMajor comments:\nWhile the modeling approach is grounded in established methods, several aspects of the configuration are inconsistent with current understanding of the Proterozoic environment. Most importantly, the use of modern nutrient concentrations alongside low atmospheric O₂ does not represent a physically plausible state.\n\n1. Anoxic recycling of nutrients\nA large fraction of the Proterozoic ocean is believed to have been anoxic. Under such conditions, anaerobic remineralization processes become central to nutrient cycling. The CESM BEC model handles this partially by suppressing aerobic remineralization when O₂ falls below a threshold and enabling denitrification using nitrate as an alternative electron acceptor. However, ferric iron (Fe³⁺) was also likely an important electron acceptor in ferruginous conditions that dominated the Proterozoic. The manuscript should clarify whether microbial iron reduction is included in the model, and if not, this limitation should be explicitly acknowledged.\n\n2. Organic matter burial\nThe treatment of organic matter burial in the model is unclear. It is important to specify whether burial fluxes are turned off or offset by external nutrient sources. If organic matter is permanently buried, the manuscript should explain how this nutrient loss is compensated and how the ocean nutrient budget is closed in the simulations.\n\n3. Marine [NO₃⁻] and [PO₄³⁻]\nIt appears that the simulations are initialized with modern nitrate and phosphate concentrations. If this is the case, it is incompatible with current understanding of the Proterozoic nutrient inventory. Widespread ocean anoxia would likely have suppressed the marine nitrate reservoir (Kang et al., 2023; Motomura et al., 2023). Phosphate levels are less certain, with estimates ranging from below modern values (Laakso and Schrag, 2014) to up to five times higher (Planavsky et al., 2010). The authors should discuss this uncertainty in the main text and run sensitivity simulations using a plausible range of nutrient concentrations.\n\nAdditionally, the manuscript frames its findings as a direct comparison between Proterozoic and modern ocean productivity. This one-to-one comparison is problematic. It assumes that both systems operated under similar nutrient baselines, which is not supported by current evidence. Statements such as “less productive than the modern ocean” imply a universal benchmark that does not account for fundamental differences in redox state, nutrient supply, and biological structure. If light availability, rather than nutrients, is the primary limiting factor in the Proterozoic scenario modeled here, that distinction should be made clear throughout the manuscript. The authors should revise their framing to reflect that they are comparing the effect of self-shading on NPP, not comparing total productivity across two fundamentally different Earth system states.\n\n4. Atmospheric O₂:\nThe prescribed atmospheric O₂ concentration of 1% PAL is broadly consistent with estimates for the Proterozoic. However, when combined with modern nutrient inventories, it creates an unrealistic, perpetual disequilibrium. In the scenario discussed in the manuscript, I suspect that the surface ocean is oversaturated with O₂ and continuously outgasses to the atmosphere, while the deep ocean defaults to anoxia. This drives anaerobic remineralization throughout much of the water column, a process that may not be well parameterized in the model to begin with.\n\nIn a low-O₂ Earth system, atmospheric pO₂ should ideally evolve dynamically based on biogeochemical fluxes, since NPP can influence atmospheric oxygen even on seasonal timescales. Furthermore, oxygen sinks such as the oxidation of reduced gases (e.g., SO₂, H₂) may have played a significant role in the Proterozoic, unlike in today’s oxygen-rich atmosphere. These considerations should be factored into the model setup.\n\nThe most physically consistent approach would be to couple the ocean biogeochemistry model to a dynamic atmosphere in which O₂ and CO₂ evolve over time. While this would require significant model development, it would improve the physical realism of the simulations. As an alternative to a fully dynamic atmosphere, the authors could adjust prescribed O₂ and nutrient levels until the net ocean-atmosphere O₂ flux is close to zero. This would help avoid the artificial disequilibrium produced in the current model configuration. Sensitivity simulations using different prescribed O₂ levels would also help test the robustness of the study’s conclusions.\n\nMost importantly, all modeling assumptions and limitations should be clearly acknowledged in the revised manuscript.\n\n5. Figure colorbars:\nThe orientation of the colorbars in Figures 1, 2, and 3 is unconventional, they display higher values on the left and lower values on the right. Typically, colorbars are oriented from low (left) to high (right). This should be revised for clarity and consistency.\n\nMinor Comments:\n1. The introduction would benefit from greater detail on the current state of knowledge and prior work in this area. A more thorough overview would help contextualize the study and make the manuscript more comprehensive.\n2. The manuscript's language requires substantial revision. Here are some specific suggestions (non-exhaustive):\nLine 20–21: The first sentence is poorly structured and should be rephrased for clarity.\nLine 25: Use “phytoplankton at the sea surface” instead of “phytoplankton on the sea surface.”\nLine 26: Similarly, use “chlorophyll at the sea surface.”\nLines 29–30: The phrase “... sunlight was the key limiting factor ...” is misleading. A better formulation would be: “... poor sunlight penetration was the key limiting factor ...”\nLine 37: The word “Such” is unnecessary. Instead of “an active marine biogeochemical cycle,” consider using “an active marine biosphere.”\nLine 42: The phrase “has never been investigated seriously” may appear dismissive of previous work. Consider rephrasing to: “... has not yet been extensively investigated using a fully coupled model ...”\nLine 67: Replace “submerged layers” with “subsurface layers” or “abyssal layers,” depending on context.\nLine 110: The adjective “decent” in “... where a decent NPP ...” is informal and unnecessary. Simply use: “... where NPP is ...”\n\nReferences:\n- Planavsky, Noah J., et al. \"The evolution of the marine phosphate reservoir.\" Nature 467.7319 (2010): 1088-1090.\n- Laakso, Thomas A., and Daniel P. Schrag. \"Regulation of atmospheric oxygen during the Proterozoic.\" Earth and Planetary Science Letters 388 (2014): 81-91.\n- Kang, Junyao, et al. \"Nitrate limitation in early Neoproterozoic oceans delayed the ecological rise of eukaryotes.\" Science advances 9.12 (2023): eade9647.\n- Motomura, Kento, et al. \"The nitrate-limited freshwater environment of the late Paleoproterozoic Embury Lake Formation, Flin Flon belt, Canada.\" Chemical Geology 616 (2023): 121234.", "reviewer_3": "Review of Liu et al., NatComm\n\nIn their contribution Liu et al., explore two interesting mechanisms to throttle global primary productivity in the Proterozoic ocean. The first is to examine the effect of removing all predation from the Proterozoic environment, which the authors simulate to increase production in surface waters. A consequence of this increased production is the blocking of sunlight to deeper depths which the authors simulations suggest an overall decrease in NPP.\n\nOverall I found the ideas in the manuscript to be very interesting at a conceptual level, but to lack strong grounding to be considered meaningful in forwarding our understanding of the Proterozoic environment.\n\nDoes removing zooplankton increase surface production and thus particle density in surface waters? The authors reference observations from the Gulf of Mexico, but is this a general truth? For this argument to be convincing I would expect a broader global assessment of how the ratio of zooplankton to phytoplankton impacts NPP across many areas in the modern environment. My hunch is that there is much more complexity in such interactions than is presented in the current manuscript.\n\nDoes increasing surface water production create sunlight limitation at depth and have the net effect of decreasing overall global NPP? Maybe, but this appears to again be a distinct question which should be much more thoroughly explored through doing a deep dive into modern marine environments and even terrestrial environments. Again, perhaps this is true, but it is not clear from the current manuscript.\n\nWith the above comments in mind, I also think it is worth noting on whether such results are truly relevant to the Proterozoic, a 2 billion year interval of Earth’s past. The authors use a single continental configuration, however, this would have varied considerably across this eon. Moreover, the authors appear to have ignored virtually all geochemical data across this interval in their analysis and instead have opted to take modern values and explore how they might change with a different continental configuration and the imposed effects of no zooplankton. For example, if productivity was lower globally due to P limitation or metal limitation which may have decreased the rate of nitrogenase synthesis, would the self shielding effect still matter?\n\nAgain, I don’t want to be too negative here. The ideas are interesting I just don’t think that jumping from concept to a complex GCM without a lot of work in assessing these ideas in modern environments helps to forward these ideas. Moreover, jumping to the Proterozoic without exploring these effects more rigorously using data and insights that have presented for this eon I think is a missed opportunity.\n\nI’m sorry I can’t be more supportive at this time."}, "author_response": "Responses to reviewers’ comments\nThe detailed review and constructive comments of all reviewers are greatly appreciated.\nIn light of these comments, 17 additional experiments were carried out. With these new\nresults, we believe that the uncertainties in the original investigation have been\nsubstantially reduced and the conclusions are now more robust. Our point-to-point\nresponses to the reviewers’ comments are shown in red below and the related revisions\nare also highlighted in red in the revised manuscript.\nReviewer #1 (Remarks to the Author):\nThis study investigates the productivity of the oceans during the Proterozoic with the\nCESM1.2.2 Earth system model (ESM), which couples an atmosphere-ocean general\ncirculation model with an ocean biogeochemistry model. The main hypothesis is that\nthe absence of zooplankton and complex forms of phytoplankton in the ocean leads to\na biogeochemical regime different from todays’. This is an interesting hypothesis,\nwhich, to my knowledge, has not been investigated before. The authors find that the\nabsence of grazing by zooplankton leads to a higher concentration of chlorophyll, i.e.\nphytoplankton, in the uppermost layers of the ocean. However, this means there is less\nsunlight available in the subsurface ocean, leading to overall less primary production in\nthe ocean compared to today. This was tested for two (Neo-)Proterozoic setups, using\nhigh and low concentrations of atmospheric CO2. The author's findings are significant,\nbecause they offer new insight into an interesting period of Earth's past that will be a\nhelpful piece in the puzzle of reconstructing the evolution of life on Earth, climate and\nEarth's atmospheric composition.\nThe method of simulating an equilibrium Proterozoic climate twice with different\natmospheric CO2 concentrations is straightforward, but appropriate and sufficient.\nMore test simulations (suggestion given below) could have been interesting, but the\nstudy is still helpful and sufficient in itself. The chosen model is appropriate, and so are\nthe chosen boundary conditions and the model spin up. The results are displayed nicely\nwith a clear line of thought, and the text is well written and easy to follow.\nWe thank Reviewer #1 for the supportive and insightful comments, and are happy to\nmake the requested revisions and add sensitivity simulations as suggested below.\nThe study provides a description of how marine ecology could have possibly looked\nlike in the Proterozoic, which is valid if it is also understood as this. Of course not\neverything can be tested for a period that spans around two billion years, and hence\nthere are certain limitations. For example, there is quite some uncertainty around the\navailability of nutrients in the Proterozoic ocean (which, of course, have varied over\ntime), meaning that nutrient limitation could have also played a more important role\nthan presented here, reducing the described effect. Furthermore, in the current state of\nthe manuscript, it is not clear to me, if not also the reduced strength of the sun during\nthe Proterozoic could have been responsible for the reduced primary production in their\nmodel and during the Proterozoic in general. Lastly, the type of model that is used relies\nheavily on parametrized vertical and horizontal mixing (because of the coarse grid\nresolution), adding another major source of uncertainty, since mixing contributes to the\navailability of nutrients and the re-distribution of phytoplankton to depths.\nWe thank Reviewer #1 for pointing out these three potential uncertainties in the current\nsimulation approach. Addressing them, especially the first one, does help improve our\nunderstanding of the Proterozoic oceanic biogeochemical cycle.\nWe agree that nutrients would have significantly changed during the Proterozoic and\nmay affect our results. Thus, we have added two sets of sensitivity simulations related\nto phosphate (P) and iron (Fe), which were also suggested by Reviewers #2 and #3. In\nthe first set of six experiments, the effect of different concentrations of P was tested.\nSpecifically, the concentrations of 500%, 200%, 50%, 25%, 10%, and 2.5% of the\npresent oceanic level (POL) were tested, in which 500% POL and 2.5% POL are the\nupper- and lower-bound estimates, respectively, based on geochemical records\n(Guilbaud et al., 2020; Planavsky et al., 2010). These simulations were carried out only\nfor the warm case, that is, pCO =2240 ppmv (see Fig. R1-1 and Methods for Sensitivity\nP is 50% POL, and the mid- to low-latitude ocean remains greener than the present-day\nocean when P is only 25% POL (Fig. R1-1C-D; Table S3 in Supplementary Materials).\nWhen P is increased, the euphotic layer is even shallower (Fig. R1-1G-H) with a\nstronger self-shielding effect compared to our standard simulation (1 POL). In all cases\nexcept 500% POL, a smaller NPP compared to PI was obtained (Table S3). A recent\nstudy showed that continental silicate weathering was weak until late Paleozoic\n(Ouyang et al., 2025), so that output of P through river runoff to the oceans should have\nbeen lower. Thus, as long as the level of P is not much higher (>200% POL) or lower\n(<25% POL) than 1 POL, the Proterozoic ocean would be greener than the present-day\nocean but less productive. The main reason was the absence of zooplankton and the\nentailing self-shielding effect, under a background of very low nitrate (N) nutrient.\nIn the second set of five experiments (see Methods for Sensitivity Simulation Group 6),\nthe sensitivity of the biosphere to Fe was tested with P fixed to 1 POL. In the first\nexperiment, only the Fe input from the ocean bottom (with its value the same as today)\nis considered, with the atmospheric and riverine Fe inputs in the original experiments\nremoved (Fig. R1-2B). In this case, the Fe input flux was reduced to ~1% of our original\nwarm Proterozoic simulation but was still ~50% of the present-day total Fe flux. In the\nother four experiments, this flux (referred to as SedFe) is further reduced to 50%,\n25%, 10%, and 0% of its value (Fig. R1-2C-F). Model results show that the ocean is much\ngreener than the present even if the Fe flux is only 10% SedFe (Fig. R1-2E), indicating\nthat Fe is not a limiting factor for the flourishing of phytoplankton when zooplankton\nis absent.\nThe results above show that under extremely low nutrient levels (e.g., P reduced to ≤10%\nPOL), the biosphere could diminish so that talking about the self-shielding effect\nbecomes meaningless. However, as long as the nutrient level was not drastically\ndeficient compared to the present, as we reasoned in the original manuscript, the\nProterozoic ocean would be greener with strong self-shielding effect and less\nproductive than the present-day ocean.\nTo confirm the effect of a dimmer Sun on the biosphere, we have also carried out a\nsensitivity test with the present solar constant (see Methods for Sensitivity Simulation\nGroup 2). The model results demonstrate that the dimness of the Proterozoic Sun would\nplay a limited role in reducing primary production. Moreover, two additional\nsimulations with different diffusivities (see Methods for Sensitivity Simulation Group\n3) have been performed, and the results do not affect our main conclusions. Please see\nthe next section for detailed responses, where Reviewer #1 reinforced the uncertainties\nabout solar strength and mixing parameters.\nFig. R1-1. Simulated annual mean concentration of surface chlorophyll (A-F) and net\nprimary production within the upper 150 m (G-L) under the warm (pCO =2240 ppmv)\nPOL, 50% POL, 25% POL, 10% POL, and 2.5% POL as labeled in the top-left corner\nof each panel, where POL stands for present oceanic level. Both the grey contour lines\nin the A-F panels and light green bars at the top of the G-L panels indicate the edges of\nsea ice defined as the location where the gridbox sea-ice fraction is 15%. This figure is\nadded in the revised Supplementary Materials as Fig. S15.\nFig. R1-2. Simulated annual mean concentration of surface chlorophyll under warm\n(pCO =2240 ppmv) Proterozoic scenario. The Fe input from the ocean bottom was set\n2\nto 100%, 50%, 25%, 10%, and 0% of the present level (SedFe) without the Fe input\nfrom the atmosphere and runoff. The grey contour lines in the panels indicate the edges\nof sea ice defined as the location where the gridbox sea-ice fraction is 15%. This figure is\nadded in the revised Supplementary Materials as Fig. S16.\nLine 266-277: For P, it turns out its initial reservoir is too large to be affected by the\nspecified Proterozoic boundary conditions (Table S1) during the simulations (Fig. S14),\nthus additional sensitivity simulations with different initial P concentration have to be\ncarried out (see Methods for Sensitivity Simulation Group 5). Geochemical records\nindicate that the Proterozoic P could be 500% to 2.5% of the present oceanic level (POL)\n(Guilbaud et al., 2020; Laakso and Schrag, 2014; Planavsky et al., 2010). Simulation\nresults show that a much greener Proterozoic ocean will be obtained if P is increased to\n200% and 500% POL (Fig. S15A-B) with even stronger self-shielding effect and\nshallower productive layer (Fig. S15G-H). The global total NPP at P=200% POL is still\nlower than that in PI; only when P is increased to 500% POL, the total NPP is larger\nthan PI (Fig. S15G and Table S3). On the other hand, even though NPP is reduced to\none sixth of the PI value when P is reduced to 25% POL, the mid- to low-latitude ocean\nsurface remains slightly greener than the PI ocean surface (Fig. S15D and Table S3).\nThus, the Proterozoic ocean would be greener but less productive unless P was more\nthan twice or less than one fourth of the PI level (i.e., 1 POL).\nLine 278-283: For Fe, sensitivity simulations (see Methods for Sensitivity Simulation\nGroup 6) show that even when atmospheric and riverine dust inputs are completely\nremoved, and the Fe from ocean bottom is reduced to 10% of the present strength, a\nmuch greener ocean can still be maintained (Fig. S16E). This means that the uncertainty\nin Fe has almost no influence on our main findings. Therefore, these sensitivity tests\nindicate that the Proterozoic ocean would be greener but less productive for the most\nlikely ranges (25% POL < P < 200% POL, and loose ranges for N and Fe) of nutrients\nlevels.\nLine 455-461 (Sensitivity Simulation Groups in Methods): (5) Varying the phosphate\nreservoir. The marine phosphate level has been set to 500%, 200%, 50%, 25%, 10%,\nand 2.5% of the present oceanic level, with other conditions identical to those in the\noriginal pCO =2240 ppmv simulation. (6) Lower iron input. This group includes five\n2\nsimulations. In the first one, the sources from the atmospheric dust deposition and\nriverine input are removed, so that only Fe input through the ocean bottom is considered.\nIn the other four simulations, the Fe from ocean bottom is further reduced to 50%, 25%,\n10%, and 0% of the present level.\nTherefore, my main suggestion is to add some more discussion on potential sources of\nuncertainty and possible other drivers of the observed behaviour. Specifically, I would\nlike to see the authors expand on the following aspects:\n1. Could not the relatively weaker sun also play an important role in light availability\nas limiting factor? The sun was 4-15% weaker during the Proterozoic, gaining strength\nover time. This is not discussed in the manuscript at all.\nThanks for this valuable suggestion. Based on the warm Proterozoic simulation with\n94% of present solar constant (S0), we have performed a sensitivity test with the present\nsolar constant (100% S0) and decreased pCO to 280 ppmv to maintain a similar global\n2\nmean surface temperature. In order to control variables, other boundary conditions (e.g.,\nnutrients) are identical to those in the original pCO =2240 ppmv simulation (see\nalmost identical to that in the 94% S0 simulations (Fig. R1-3A-B), indicating that\nreducing the top-of-atmosphere insolation by 6% has a negligible effect on the\ngreenness and NPP of ocean. With the 100% of present solar constant, the global mean\nsolar radiation received in the second layer (10 m - 20 m depth) of the ocean is also\ncomparable with that in 94% S0 case (Fig. R1-3C-D), both are about 15 W/m2 less than\nthat in the PI condition. Thus, the dense surface phytoplankton and self-shielding effect\nplay a vital role in the subface light availability. Such discussion has been included in\nthe revised manuscript as shown below.\nFig. R1-3. Simulated net primary production within the upper 150 m ocean (A-B) and\nlight availability in the 10 - 20 m (second) ocean layer (C-D) in the warm Proterozoic\nscenario with 100% S0 (pCO =280 ppmv, top) and 94% S0 (pCO =2240 ppmv,\n2 2\nbottom). S0 stands for the present solar constant. This figure is added in the revised\nSupplementary Materials as Fig. S10.\nLine 237-240: Firstly, we show that the dimmer Sun during the Proterozoic is not the\nreason for the limited subsurface light availability; increasing the solar luminosity to\nthe present strength (see Methods for Sensitivity Simulation Group 2) has little\ninfluence on the surface greenness and NPP of the ocean (Fig. S10).\nLine 448-451 (Sensitivity Simulation Groups in Methods): (2) Increase of Proterozoic\nsolar constant. Based on the warm Proterozoic simulation, the solar constant is set to\nthe present level with 280 ppmv pCO so that the climate state is similar to that of the\n2\n'warm' standard simulation, while all other boundary conditions (e.g., nutrients) are\nidentical to those in the 'warm' simulation.\n2. How is mixing in the surface ocean affecting the simulations? Is there potentially\nmore mixing in the Proterozoic ocean, so that surface phytoplankton is less limited by\nnutrients?\nWe thank the reviewer for this comment, which highlights the importance and\nuncertainty of mixing processes parameterizations. We assume that the reviewer was\nconcerned with the vertical mixing, whose value (variable “vdc1” in the model) is by\ndefault 0.16 cm2/s for modern conditions. However, based on the NCAR-suggested\ndeep-time standards, we have set vdc1 = 0.524 cm2/s, which has been widely used in\nthe paleoclimate simulations due to the lack of reconstructed tidal effects (Baatsen et\nal., 2020). To test the sensitivity of our results to vdc1, we have carried out two\nsensitivity simulations with vdc1 equaling to 0.8 (high value) and 0.4 (low value) cm2/s\n(Lucas et al., 2013) for the warm Proterozoic scenario (pCO =2240 ppmv) (see\n(low) vdc1 value could increase (decrease) the NPP by about 22% (17%) compared to\nthe default vdc1 (0.524 cm2/s) simulation (Fig. R1-4A-B), and the phenomenon of the\ngreener Proterozoic ocean (and self-shielding effect) remains intact even in the low\nvdc1 scenario (Fig. R1-4E-F). The stronger vertical mixing parameter could indeed\nincrease the simulated NPP (still lower than the present-day value) by alleviating\nnutrient limitation as the reviewer anticipated (Fig. R1-4C-D), but the reconstructions\nof both day length (Mitchell and Kirscher, 2023) and orbital cycles (Zhou et al., 2024)\nsuggest that the tidal dissipation during the Proterozoic was likely much weaker than\nduring the Phanerozoic. Such discussion has been included in the revised manuscript\nas shown below.\nFig. R1-4. Simulated vertical NPP within the upper 150 m ocean (A-B), limiting factors\nfor small phytoplankton in the second layer (10 - 20 m) (C-D), and concentration of\nsurface chlorophyll (E-F) under pCO =2240 ppmv (warm) Proterozoic scenarios, when\n2\nvertical diffusivity parameters are high (0.8 cm2/s, top) and low (0.4 cm2/s, bottom).\nBoth the light green bars at the top of A-B and the contour lines in the C-F indicate the\nedges of sea ice defined as the location where the gridbox sea-ice fraction is 15%. This figure is added in the revised Supplementary Materials as Fig. S11.\nLine 241-249: Secondly, the uncertainty in the vertical diffusivity, which affects\nnutrient availability, does not affect the main conclusions. Increasing (decreasing)\nvertical diffusivity parameters by ~53% (24%) in warm Proterozoic simulation (see\nMethods for Sensitivity Simulation Group 3) would increase (decrease) the NPP by\n~22% (17%) (Fig. S11A-B) compared to the default simulation (Fig. 2E). Stronger\nvertical mixing would alleviate nutrient limitation and increase NPP (still lower than\nthe present-day value; Fig. S11C-D) but the reconstructions of both day length\n(Mitchell and Kirscher, 2023) and orbital cycles (Zhou et al., 2024) suggest that the\ntidal dissipation during the Proterozoic was likely much weaker than during the\nPhanerozoic. In the meantime, the greener Proterozoic surface ocean and related self-\nshielding effect are unaffected (Fig. S11E-F).\nLine 452-454 (Sensitivity Simulation Groups in Methods): (3) Variation of the vertical\ndiffusivity. The vertical diffusivity (variable “vdc1” in the model) has been increased\nto 0.8 and decreased to 0.4 cm2/s for the high and low vertical mixing scenarios (Lucas\net al., 2013), respectively, based on the pCO =2240 ppmv simulation.\nin the Proterozoic setup they would add the zooplankton back into the model, to test\ntheir hypothesis that it is the absence of zooplankton that drives the higher chlorophyll,\nlower NPP pattern in their standard Proterozoic setup. At the very least, the two points\nabove should be discussed in the final section of the manuscript.\nWe appreciate this constructive suggestion for attribution analysis, and we have\noperated a sensitivity test that involves zooplankton in the pCO =280 ppmv Proterozoic\n2\nscenario (see Methods for Sensitivity Simulation Group 1). The simulation results show\nthat surface chlorophyll would decrease by >10 times when including zooplankton (Fig.\nR1-5A-B). Thus, the absence of zooplankton should be the driving factor for the greener\nProterozoic ocean. Meanwhile, the euphotic layer is deeper in the zooplankton-involved\nsimulation; total NPP would decrease by ~15% compared to the zooplankton-excluded\nregime (Fig. R1-5C-D). That is because the zooplankton would consume a large amount\nof nutrients, leading to a nutrient-limited (especially N) ocean which suppresses NPP\n(Fig. R1-5E-F). Therefore, even if the self-shielding effect is removed by the\nzooplankton, the global NPP during the Proterozoic should still be much lower than in\nthe present because of N limitation. This lack of N in the Proterozoic ocean was mainly\ndue to the strong denitrification under low atmospheric O (please see Fig. R2-2 in the\n2\nresponse to Reviewer #2's comment).\nThe generally lower global NPP in the Proterozoic ocean is thus the consequence of\nthree reasons: 1) the absence of diatom reduces the global NPP by ~20% according to\nthe present-day budget. 2) the much lower N nutrient level due to the low O level\n2\nwould drive a low total NPP even if the biospheric composition was similar to today.\n3) without zooplankton consuming N, the productivity would not be limited by N but\nthe self-shielding effect would then prevent the NPP from increasing significantly. We\nhave mentioned these sensitivity simulations and related discussion in the revised\nmanuscript as follows.\nFig. R1-5. Simulated concentration of surface chlorophyll (A-B), vertical NPP within\nthe upper 150 m ocean (C-D), and limiting factors for small phytoplankton in the second\nlayer (10 - 20 m) under warm (pCO =2240 ppmv) Proterozoic scenario, when including\n2\nzooplankton (top) and excluding zooplankton (bottom). Both the contour lines in the\nA-B/E-F and light green bars at the top of C-D indicate the edges of sea ice defined as\nthe location where the gridbox sea-ice fraction is 15%. This figure is added in the\nrevised Supplementary Materials as Fig. S4.\nLine 57-58: denitrification would be enhanced in an anoxic ocean (Kang et al., 2023;\nMotomura et al., 2023), leading to nitrogen limitation to the primary productivity;\nLine 125-128: When the zooplankton is added back to the Proterozoic ocean (see\nMethods for Sensitivity Simulation Group 1 and Table S2), surface chlorophyll\ndecreases substantially (Fig. S4), confirming that the absence of zooplankton was the\nkey trigger of the greener Proterozoic ocean.\nLine 159-161: However, note that the different nutrient levels between the Proterozoic\nand PI, especially the marine nitrate (N), are also important for the Proterozoic oceans\nbeing less productive than PI oceans (see Discussion).\nLine 252-265: For N, although the initial marine nitrate concentration is set to the\npresent level, it achieves a new equilibrium level quickly with the specified boundary\nconditions. The boundary condition that affects N the most is pO because\n2\ndenitrification using nitrate will be triggered once the O2 concentration in the ocean is\nlower than some threshold (0.1 μmol/L in CESM1.2.2). For pO =1% PAL, used in all\n2\nsimulations presented above (Table S1), the oceanic and sedimentary denitrification is\nindeed much stronger than in PI (Fig. S8D-F and Fig. S12) and the final nitrate\nreservoirs are suppressed by over three orders of magnitude through enhanced\ndenitrification (Fig. S8A-C). Such phenomenon has also been demonstrated by\nprevious field observations and simulations (Kang et al., 2023; Motomura et al., 2023).\nThus, N is expected to be an important limiting factor for the Proterozoic ecosystem\n(Fig. 3E-F). If pO is increased to 10% PAL (see Methods for Sensitivity Simulation\n~7% compared to pO =1% PAL scenario (Fig. S13). When pO is reduced to 0.1%\n2 2\nPAL, the surface greening and self-shielding effect are still strong (Table S3). Thus, the\nuncertainty in N does not affect the main findings here.\nLine 446-448 (Sensitivity Simulation Groups in Methods): (1) Inclusion of zooplankton\nin the Proterozoic. The zooplankton has been involved in the ocean simulation with the\nother boundary conditions the same as those in the pCO =280 ppmv simulation.\noxygen levels (pO ). The pO is set to 0.1% and 10% of the present level in the\n2 2\npCO =2240 ppmv simulation.\n- l. 29: warm and cold periods have not been introduced in abstract, so there must be\nmore explanation what this is referring to\nThanks for the suggestion, the warm and cold Proterozoic climate states are now\nmentioned in the Abstract.\nLine 30-31: …in warm (almost ice-free) and cold (sea-ice reaches ~30°N/S) periods...\n- l. 41-42 & l 43-44: This summary is not quite correct. Ramme, Ilyina and Marotzke\n(2024, https://doi.org/10.1038/s41467-024-47873-6) did use a similar type of model\n(AOGCM+biogeochemistry) to \"seriously\" study biogeochemical cycles in the\naftermath of a snowball Earth in the Proterozoic. Of course their focus is different from\nthis study, so there is no overlap, but it needs to be clarified that such a model type has\nbeen used before.\nWe apologize for missing this important reference. We have modified these sentences\nand highlighted the Ramme et al. (2024) as the reviewer mentioned.\nLine 67-70: Although the Proterozoic biogeochemical cycle has been simulated with\nan atmosphere-ocean general circulation model (AOGCM), that study mainly focused\non the role of ocean in modulating the atmospheric CO concentration (pCO ) and\n2 2\nsuper-greenhouse climate in the aftermath of the Marinoan snowball Earth event\n(Ramme et al., 2024).\n- l. 85-89: The authors refer to Fig. 2, when saying that the Proterozoic ocean should be\nmuch greener than the modern ocean, but Fig. 2 rather indicates that primary\nproductions is a lot higher in the modern ocean. If they want to say that the Proterozoic\nocean's are greener, they should refer to their Fig. S2 in the supplementary material, I\nbelieve.\nThanks, we agree that Fig. S2 should be referred to in the last sentences about the\ngreener Proterozoic.\nLine 113-114: Therefore, most parts of the Proterozoic ocean would look much greener\nthan the modern ocean (Fig. S2).\n- l. 120: At this stage, vertical profiles (i.e. global horizontal averages) of global ocean\nNPP and light availability for all three setups (i.e. including the modern) would be\nhelpful to better justify the conclusion that it is the self-shielding effect that makes the\nsubsurface ocean darker.\nWe have added vertical profiles of light availability (Fig. 2G-I) along with NPP (Fig.\n2D-F) and mentioned the new panel in line 150 of the revised manuscript.\nFig. 2. Simulated net primary productivity and light availability in PI and Proterozoic\nconditions.\n- Methods: Please add some description or reference for how ocean mixing is handled\nin the model simulations. What parametrizations were used? What is the strength of\nprescribed mixing parameters?\nWe apologize for the insufficient information on the ocean mixing treatments in the\nmodel. More details are now added in the Methods and pasted below.\nLine 325-343 (in Methods): For the horizontal diffusion, the anisotropic mixing of\nmomentum (Smith and McWilliams, 2003) and Gent and Mcwilliams (1990)\nparameterization, which drives the mixing of tracers along isopycnal surfaces with\nactivated submesoscale mixing, has been employed in the model. In the 720 Ma\ncontinental configuration used here, the vast ocean without continents in the mid-high\nlatitudes of the Northern Hemisphere would give rise to excessively strong westerly\nocean currents (~70 cm/s with ~20° meridional width), warranting higher tracer\ndiffusivities than the default (Liu et al., 2013). Thus, we have increased the horizontal\ndiffusivity (variable “ah” in the model) by a factor of 5 (from 800 m2/s to 4000 m2/s),\nas employed in previous work using the same continental configuration and resolution\n(Liu et al., 2023; Liu et al., 2013). For vertical mixing, the K-profile parameterization\n(KPP) has been used in POP2, in which the interior mixing coefficients are computed\nat every grid point according to relevant physical processes (Large et al., 1994). These\nphysical processes include surface wave breaking, shear instability, convection,\nbackground internal wave breaking, and tidal dissipation. For the present-day, the\nbackground internal wave breaking is prescribed to a universal constant (also\nrepresented by vdc1 with a value of 0.16 cm2/s), and the tidal dissipation is horizontally\nvariable and decreases exponentially from the bottom to the top. In the deep-time\nsimulations, because the tidal dissipation is unknown, the background and tidal\ndissipation together (κ) are represented by a function that depends on depth (z) only,\nκ = vdc1 + vdc2 * tan-1[(z-1000 m) * 4.5×10-3 m-1]\nwhere vdc1 = 0.524 cm2/s and vdc2 = 0.313 cm2/s as recommended by NCAR-\nsuggested deep-time standards and previous work (Baatsen et al., 2020; Liu et al., 2023).\nTechnical comments:\n- l. 34: \"THE Proterozoic EON\"\nChanged.\n-l. 58-61: There is a missing closing bracket in this sentence.\nChanged.\n- l.73: I wouldn't say that the pre-industrial setup has small horizontal variation. Just the\nmaximum values are much smaller and hence there is less amplitude in the variations\nin the pre-industrial setup.\nWe have modified the sentence as Reviewer #1 suggested.\nLine 99-101: Moreover, chlorophyll in PI vary smoothly over the globe with the\nmajority oceans having values of smaller than 0.15 mg/m3 (Fig. 1A), while the\nchlorophyll reaches >0.3 mg/m3 over most of the low-latitude oceans in the Proterozoic\n(Fig. 1B-C).\n- l. 125: please specify the sentence in the brackets\nWe apologize for the vagueness of the description there. The sentence in the brackets\nhas now been changed to ‘contributed by small phytoplankton and diazotroph’ (line\n154-155). Here we want to remind the readers that the simulated Proterozoic ocean only\nincludes two simple phytoplanktons.\n- Fig. 3: Figure caption is confusingly written. Please rewrite and specify: Is the limiting\nfactor in panels (D-F) also displayed for the second ocean layer, or is this a vertical\naverage?\nSorry for the missing information. The limiting factors in panels (D-F) represent the\nvertical average within the upper 150 m and we have fixed the caption of Fig. 3.\n- Fig. S7 caption (5th line): Two occurrences of \"biogeochemical cycle\". Also, add a\n\"the\" in front of \"biogeochemical cycle\".\nChanged (now Fig. S9). We appreciate Reviewer #1 for the very careful checking!\nReviewer #2 (Remarks to the Author):\nReview of “A Greener but Less Productive Proterozoic Ocean” by Liu et al. for Nature\nCommunications.\nThe manuscript by Liu et al. explores the consequences of zooplankton absence in the\nProterozoic ocean and investigates whether light availability or nutrient supply was the\nprimary limiting factor for net primary production (NPP). The central hypothesis is that,\nin a phytoplankton-dominated ocean without grazers, self-shading by surface-dwelling\nphytoplankton could have significantly reduced the penetration of sunlight to deeper\nwaters, thereby limiting productivity. This is a compelling idea, and the exploration of\nself-shading as a regulatory mechanism is particularly interesting.\nWe appreciate the recognition of our idea from Reviewer #2 and are happy to make the\nrequested revisions and add sensitivity simulations as suggested below.\nHowever, while the scientific motivation is strong and the self-shading mechanism is\nconceptually elegant, the model setup ultimately leads to a flawed comparison between\nthe Proterozoic and modern oceans. The authors combine low atmospheric O₂\nconcentrations with modern-day nutrient levels, a configuration that is inconsistent with\nthe Proterozoic ocean scenario. As a result, the comparison between Proterozoic and\nmodern NPP is misleading and undermines the credibility of the main conclusions. In\nmy view, the manuscript requires substantial revision and additional sensitivity\nanalyses before it can be considered for publication. My detailed comments are\nprovided below.\nWe sincerely thank Reviewer #2 for the insightful comments, which guide us to carry\nout additional simulations and improve the robustness of our conclusions. We first wish\nto clarify that although the initial nutrient concentrations are set to modern levels,\nthe boundary conditions (especially for nutrient inputs) are set to be hopefully appropriate\nfor the Proterozoic and the model would dynamically iterate the nutrient concentrations\nto the new equilibrium state accordingly. For example, we have neglected the runoff\ninput of nitrogen (N) due to barren continents and prescribed atmospheric N deposition\nbased on photochemical model results (Liu et al., 2021); the simulated nitrate reservoir\nwas much lower than present-day level due to enhanced denitrification (please see the\nresponse to major comment 3 below for details), which should be consistent with the\nProterozoic situation as demonstrated by previous field observations and simulation\nstudies (Kang et al., 2023; Motomura et al., 2023).\nHowever, we completely agree with Reviewer #2 that additional sensitivity simulations\nare necessary for certain nutrients. First, although riverine input of phosphorus (P) has\nbeen set based on the calculated weathering rate (Methods), the initial P reservoir is too\nlarge to be changed within the duration of simulations. Due to the large uncertainty of\nmarine P level during the long Proterozoic, we have added sensitivity simulations with\na series of different P concentrations to address its importance to our results. (Please\nsee the response to major comment 3 below for details). Second, two additional\nsimulations with atmospheric O levels set to 0.1% and 10% PAL (present atmospheric\n2\nlevel) have been carried out for the major comment 4 below. Third, we have also\nconducted low-iron (Fe)-input simulations since the atmospheric and riverine Fe in our\nstandard runs are both set based on modeling studies, which also involve uncertainties\n(Liu et al., 2020; Watanabe et al., 2023). Moreover, the influence of adding zooplankton\nback to the Proterozoic ocean was also tested according to the suggestion of Reviewer\n#1 (Fig. R1-5 and related response above). Those additional sensitivity simulations\nmake our investigation more comprehensive and conclusions more robust.\nSpecifically, the results of these new experiments show that less green Proterozoic\nocean is possible if the nutrient level was extremely low; a more productive Proterozoic\nocean is also possible if the nutrient level was very high. However, we think a greener\nbut less productive ocean is still the most likely situation for the Proterozoic. The reason\nfor the smaller productivity was more complex than explained in the original\nmanuscript. Although we have shown that the self-shielding effect was important for\nlimiting the subsurface and total NPP, adding zooplankton back to the Proterozoic\nocean demonstrates that the total NPP would be even lower due to the severe limitation\nby N nutrient (Fig. R1-5 and related response above). The lack of N nutrient itself was\na result of low O level during the Proterozoic. Therefore, even if the biospheric\n2\ncomposition of the Proterozoic was the same as today, the total NPP would still be\nlower due to low O level, provided that P and Fe levels were also similar to today. We\n2\nhave modified our manuscript to reflect this new knowledge. Please see the texts below\nfor the detailed responses and the relevant revisions in the manuscript.\nMajor comments:\nWhile the modeling approach is grounded in established methods, several aspects of\nthe configuration are inconsistent with current understanding of the Proterozoic\nenvironment. Most importantly, the use of modern nutrient inventories alongside\nlow atmospheric O₂ does not represent a physically plausible state.\nWe are grateful to Reviewer #2 for demonstrating several important elements related\nto the model configuration and simulation settings. In the following responses, we will\nelaborate on the model treatments of elemental recycling and organic carbon burial, and\nnew sensitivity simulations to address the major comments raised by the reviewer. First\nand foremost, although the ‘initial’ nutrient levels are set to the modern level, the\n‘equilibrium’ nutrient concentrations, except P, would be adjusted to different levels\nbased on the Proterozoic boundary conditions. Thus, the simulations presented in the\noriginal manuscript partially represented the potential scenarios during the Proterozoic.\n1. Anoxic recycling of nutrients\nA large fraction of the Proterozoic ocean is believed to have been anoxic. Under such\nconditions, anaerobic remineralization processes become central to nutrient cycling.\nThe CESM BEC model handles this partially by suppressing aerobic remineralization\nwhen O₂ falls below a threshold and enabling denitrification using nitrate as an\nalternative electron acceptor. However, ferric iron (Fe³⁺) was also likely an important\nelectron acceptor in ferruginous conditions that dominated the Proterozoic. The\nmanuscript should clarify whether microbial iron reduction is included in the model,\nand if not, this limitation should be explicitly acknowledged.\nWe thank Reviewer #2 for pointing out this potential limitation in the model. The\nreviewer is correct that most of the Proterozoic ocean was anoxic with 1% PAL\natmospheric oxygen, and thus the calculated denitrification effect in sediments has been\nenhanced (Fig. R2-1). The threshold of O concentration that the reviewer mentioned\n2\nis 0.1 μmol/L in the model setting. The reduction of iron oxides, an electron acceptor\nfor organic matter respiration, has also been involved in the model, but in a relatively\nsimplified way. In the sediments, BEC explicitly calculates the consumption of oxygen\nand nitrate, while other oxidants (including iron oxides, manganese oxides, and\nsulphate) are lumped into one variable (denoted as “other_remin” in the model) because\nthe anoxic remineralization of 1 mole carbon by each of them would remove 1 mole\napparent oxygen demand unit (Soetaert et al., 1996). The value of “other_remin” in O -\n2\ndepleted sediments has been formulated as the total carbon flux at the ocean floor minus\nthe POC settled into sediments and organic carbon consumed by denitrification\n(Soetaert et al., 1996). This straightforward treatment has also been widely employed\nin other biogeochemistry models too (Arndt et al., 2013; Soetaert et al., 2000), though\nthis strategy cannot generate the profile and relative contribution of each lumped\nspecies. We have clarified this part in the revised manuscript as shown below.\nFig. R2-1. Simulated sedimentary denitrification effect in the preindustrial condition\n(A), warm (pCO =2240 ppmv, B), and cold (pCO =280 ppmv, C) scenarios in the\n2 2\nProterozoic. The grey contour lines in the panels indicate the edges of sea ice defined\nas the location where the gridbox sea-ice fraction is 15%. This figure is added in the\nrevised Supplementary Materials as Fig. S12.\nLine 366-371 (in Methods): These remineralization processes include the direct\noxidation by oxygen in the seawater, the denitrification in both seawater and the\nsediments (Bohlen et al., 2012; Soetaert et al., 1996), and the remineralization by ferric\niron, manganese oxides, and sulphate. The anoxic remineralization utilizing these latter\nthree oxidants is lumped into one process in CESM1.2.2, and its flux is formulated to\nbe equal to the organic carbon flux at the seafloor minus the POC settled into sediments\nand organic carbon consumed by denitrification (Soetaert et al., 1996).\n2. Organic matter burial\nThe treatment of organic matter burial in the model is unclear. It is important to specify\nwhether burial fluxes are turned off or offset by external nutrient sources. If organic\nmatter is permanently buried, the manuscript should explain how this nutrient loss is\ncompensated and how the ocean nutrient budget is closed in the simulations.\nWe sincerely thank Reviewer #2 for mentioning the organic matter burial issue, which\nshould be clarified when using the biogeochemical model. The calculated burial flux\nhas been offset by the external nutrient inputs in the model (Moore et al., 2002; Moore\net al., 2013). At the bottom of the ocean, the burial of organic carbon is estimated based\non the POC flux after being consumed by sedimentary denitrification and other\nremineralization processes (Dunne et al., 2007; Soetaert et al., 1996). The amount of\nburied matters is compensated by the nutrient inputs to close the nutrient budget. Since\nthe BEC does not track the entailing processes in sediments, the buried organic carbon\nwould disappear from the ocean domain instantaneously. We have added more detailed\nexplanations of organic matter burial treatment in the revised manuscript.\nLine 364-366 (in Methods): The organic carbon in the ocean, mainly in the form of\ndissolved organic carbon (DOC) and particulate organic carbon (POC), is consumed by\na few remineralization processes in the model and the rest is permanently buried into\nthe seafloor.\nLine 373-377 (in Methods): A maximum burial efficiency of 80% (Dunne et al., 2007)\nis imposed to this POC flux at the seafloor, and the buried organic matter is lost\ninstantaneously from the ocean domain. To avoid drift of the ocean nutrient inventories,\nan additional input of nutrients is needed to balance the loss of nutrients by this POC\nburial (Moore et al., 2002; Moore et al., 2013). That is, the nutrients lost due to the\npermanent burial of these POC are put back to the ocean also instantaneously.\n3. Marine [NO₃⁻] and [PO₄³⁻]\nIt appears that the simulations are initialized with modern nitrate and phosphate\nconcentrations. If this is the case, it is incompatible with current understanding of the\nProterozoic nutrient inventory. Widespread ocean anoxia would likely have suppressed\nthe marine nitrate reservoir (Kang et al., 2023; Motomura et al., 2023). Phosphate levels\nare less certain, with estimates ranging from below modern values (Laakso and Schrag,\n2014) to up to five times higher (Planavsky et al., 2010). The authors should discuss\nthis uncertainty in the main text and run sensitivity simulations using a plausible range\nof nutrient concentrations.\nWe thank Reviewer #2 for this perceptive comment on the initial nitrate and phosphate\ninventories, which leads us to conduct deeper analyses and additional simulations. The\nreviewer is correct that both marine nitrate and phosphate concentrations are initialized\nat their current levels. However, the equilibrium concentrations would be different due\nto the employed Proterozoic boundary conditions and dynamic calculations. Especially,\nthe nitrate cycle achieves a dynamic equilibrium quickly. In our Proterozoic simulations\nwith anoxic ocean, the final nitrate reservoirs were suppressed by over three orders of\nmagnitude through enhanced denitrification (Fig. R2-2). Such phenomenon has also\nbeen demonstrated by previous field observations and simulation studies (Kang et al.,\n2023; Motomura et al., 2023). The nitrate became the most important limiting factor in\nboth warm and cold Proterozoic simulations, after sunlight and temperature (Fig. 3E-\nF). Thus, we think it is acceptable to initiate the model with the present nitrate level.\nFig. R2-2. Simulated zonal mean nitrate (A-C) and denitrification (D-F) within the\nupper 1100 m ocean in the preindustrial condition (top), warm (pCO =2240 ppmv,\n2\nmiddle), and cold (pCO =280 ppmv, bottom) scenarios in the Proterozoic. The light\n2\ngreen bars at the top of panels indicate the edges of sea ice defined as the location where\nthe gridbox sea-ice fraction is 15%. This figure is added in the revised Supplementary\nMaterials as Fig. S8.\nFor marine phosphate, we have set the initial phosphate concentration to the present\nlevel (1 POL, POL: present oceanic level) since the phosphate cycle is also free to\nevolve in the model, and 1 POL also falls within the plausible range of Proterozoic\nphosphorus levels (Guilbaud et al., 2020; Planavsky et al., 2010). Although we have set\nthe riverine P input based on the calculated Proterozoic weathering rate (see Methods),\nthe initial modern phosphate reservoir is too large to be significantly changed during\nthe relatively short simulations. The total amount of PO 3- in the initial ocean is about\n4\n2×1015 mol. When inorganic P input (we neglected riverine dissolved organic P from\nbarren continents) was lowered from 9.09×1010 mol/yr in the present Earth to 1.42×108\nmol/yr in the warm Proterozoic (Table S1), the time scale for the marine phosphate to\nreach new equilibrium would be ~15 Ma, far longer than the iteration timescale (~3500\nyears). As a result, the simulated reservoir of PO 3- changes mildly in the end, although\n4\nthe spatial distribution changes substantially due to the different ocean circulation\npattern between the Proterozoic and the modern (Fig. R2-3). Another notable difference\nin P distribution between the Proterozoic and modern is that the P level in the upper\nocean (above 1000 m) of the former is much less than that of the latter (Fig. R2-3). This\nis due to the storage of P in planktons which form a large reservoir due to the lack of\nzooplankton (Fig. 1D-F of the manuscript).\nFig. R2-3. Simulated marine phosphate in PI (A), warm (pCO =2240 ppmv, B), and\n2\ncold (pCO =280 ppmv, C) scenarios in the Proterozoic. This figure is added in the\n2\nrevised Supplementary Materials as Fig. S14.\nBecause of the long adjustment timescale of P, we should test the influence of different\ninitial P. Under the low atmospheric O level, the P scavenging by iron might impose a\n2\nlow phosphate level (Laakso and Schrag, 2014), and the PO 3- level might be 2.5% POL\n4\nwhen atmospheric oxygen level (pO ) is 1% PAL during early (warm) Neoproterozoic\n2\n(Guilbaud et al., 2020). Meanwhile, geochemical records indicate that the marine\nphosphate reservoir might be 5 times higher than the present level in the aftermath of\nthe Neoproterozoic snowball Earth (Planavsky et al., 2010). In view of those studies,\nwe have added a series of sensitivity tests as has also been described above in the\nresponse to Reviewer #1's comments. In these tests, the concentration of P is set to be\n500%, 200%, 50%, 25%, 10%, and 2.5% of the present oceanic level (POL),\nrespectively, with all other nutrients remained the same as those in the standard \"warm\ncase\" (see Methods for Sensitivity Simulation Group 5). The model results show a much\ngreener Proterozoic ocean under the higher phosphate levels (Fig. R2-4A-B); the\neuphotic layer becomes even shallower due to stronger self-shielding effect; the total\nNPP increases despite a shallower euphotic zone and its value in the 500% POL case is\neven higher than the PI case (Table S3 in Supplementary Materials). The mid- to low-\nlatitude surface ocean is still greener than PI ocean even if P is reduced to 25% POL\n(Fig. R2-4D and Table S3). Note that the total NPP increases at a slower pace with P\nonce it is greater than 1 POL (Fig. R2-4G-H; Table S3), likely due to the limitation of\nN nutrient. Therefore, the Proterozoic ocean was most likely greener than the PI ocean\nunless the P concentration was lower than today by more than a factor of 4, and the\nproductivity was lower unless P concentration was more than twice the modern level\n(Table S3 in Supplementary Materials).\nFig. R2-4. Simulated annual mean concentration of surface chlorophyll (A-F) and net\nprimary production within the upper 150 m (G-L) under the warm (pCO =2240 ppmv)\nPOL, 50% POL, 25% POL, 10% POL, and 2.5% POL as labeled in the top-left corner\nof each panel, where POL stands for present oceanic level. Both the grey contour lines\nin the A-F panels and light green bars at the top of the G-L panels indicate the edges of\nsea ice defined as the location where the gridbox sea-ice fraction is 15%. This figure is\nadded in the revised Supplementary Materials as Fig. S15.\nLine 252-261: For N, although the initial marine nitrate concentration is set to the\npresent level, it achieves a new equilibrium level quickly with the specified boundary\nconditions. The boundary condition that affects N the most is pO because\n2\ndenitrification using nitrate will be triggered once the O2 concentration in the ocean is\nlower than some threshold (0.1 μmol/L in CESM1.2.2). For pO =1% PAL, used in all\n2\nsimulations presented above (Table S1), the oceanic and sedimentary denitrification is\nindeed much stronger than in PI (Fig. S8D-F and Fig. S12) and the final nitrate\nreservoirs are suppressed by over three orders of magnitude through enhanced\ndenitrification (Fig. S8A-C). Such phenomenon has also been demonstrated by\nprevious field observations and simulations (Kang et al., 2023; Motomura et al., 2023).\nThus, N is expected to be an important limiting factor for the Proterozoic ecosystem\n(Fig. 3E-F).\nLine 266-277: For P, it turns out its initial reservoir is too large to be affected by the\nspecified Proterozoic boundary conditions (Table S1) during the simulations (Fig. S14),\nthus additional sensitivity simulations with different initial P concentration have to be\ncarried out (see Methods for Sensitivity Simulation Group 5). Geochemical records\nindicate that the Proterozoic P could be 500% to 2.5% of the present oceanic level (POL)\n(Guilbaud et al., 2020; Laakso and Schrag, 2014; Planavsky et al., 2010). Simulation\nresults show that a much greener Proterozoic ocean will be obtained if P is increased to\n200% and 500% POL (Fig. S15A-B) with even stronger self-shielding effect and\nshallower productive layer (Fig. S15G-H). The global total NPP at P=200% POL is still\nlower than that in PI; only when P is increased to 500% POL, the total NPP is larger\nthan PI (Fig. S15G and Table S3). On the other hand, even though NPP is reduced to\none sixth of the PI value when P is reduced to 25% POL, the mid- to low-latitude ocean\nsurface remains slightly greener than the PI ocean surface (Fig. S15D and Table S3).\nThus, the Proterozoic ocean would be greener but less productive unless P was more\nthan twice or less than one fourth of the PI level (i.e., 1 POL).\nLine 439-441 (in Methods): Due to the lack of globally gridded reconstructions for\nbiogeochemical variables during the Proterozoic, their initial values are set to the\npresent level, and will evolve to new equilibrium state under the boundary conditions\nabove.\nLine 455-458 (Sensitivity Simulation Groups in Methods): (5) Varying the phosphate\nreservoir. The marine phosphate level has been set to 500%, 200%, 50%, 25%, 10%,\nand 2.5% of the present oceanic level, with other conditions identical to those in the\noriginal pCO =2240 ppmv simulation.\nProterozoic and modern ocean productivity. This one-to-one comparison is problematic.\nIt assumes that both systems operated under similar nutrient baselines, which is not\nsupported by current evidence. Statements such as “less productive than the modern\nocean” imply a universal benchmark that does not account for fundamental differences\nin redox state, nutrient supply, and biological structure. If light availability, rather than\nnutrients, is the primary limiting factor in the Proterozoic scenario modeled here, that\ndistinction should be made clear throughout the manuscript. The authors should revise\ntheir framing to reflect that they are comparing the effect of self-shading on NPP, not\ncomparing total productivity across two fundamentally different Earth system states.\nWe thank the reviewer for this critical comment. We agree that the Proterozoic would\nbe greatly different from the present in many aspects, and have tried our best to account\nfor these differences better in this revision. In the original manuscript, the initial nutrient\nlevels were set to the present-day levels. We now confirm that some of the nutrients\nreach new state in equilibrium with the boundary conditions for the Proterozoic during\nthe model integration (Table S1). For example, the equilibrium nitrate level is over\nthree orders of magnitude lower than the present-day level due to enhanced\ndenitrification in the anoxic Proterozoic ocean (Fig. R2-2 above), making a N-limited\nocean to suppresses NPP (Fig. 3E-F).\nThe near-surface Fe reservoir also equilibrates with the input flux quickly (~100 years).\nThe marine Fe input was set to a higher value than the present day in the original\nmanuscript because of the abundant dust deposition (Table S1; Liu et al., 2020). To test\nthe influence of different Fe input fluxes, we performed five additional simulations (see\nMethods for Sensitivity Simulation Group 6) with P fixed to 1 POL. In the first\nexperiment, only the Fe input from the ocean bottom (with its value the same as today)\nis considered, with the atmospheric and riverine Fe inputs in the original experiments\nremoved (Fig. R2-5B). In this case, the Fe input flux was reduced to ~1% of our original\nwarm Proterozoic simulation but was still ~50% of the present-day total Fe flux. In the\nother four experiments, this flux (referred to as SedFe) is further reduced to 50%,\n25%, 10%, and 0% of its default value (Fig. R2-5C-F). Model results show that the ocean is\nmuch greener than the present even if the Fe flux is only 10% SedFe (Fig. R2-5E),\nindicating that Fe is not a limiting factor for the flourishing of phytoplankton when\nzooplankton is absent.\nThe results above show that under extremely low nutrient levels (e.g., P reduced to ≤10%\nPOL), the biosphere could diminish so that talking about the self-shielding effect\nbecomes meaningless. However, as long as the nutrient level was not drastically\ndeficient compared to the present, as we reasoned in the original manuscript, the\nProterozoic ocean would be greener with strong self-shielding effect and less\nproductive than the present-day ocean.\nWith these new results, we agree with Reviewer #2 that our original statements\nregarding the productivity understated the importance of nutrient availability. The\nProterozoic ocean could be more productive if there were a lot more P than in the\npresent-day ocean, in which case, the ocean would be even greener than shown in the\noriginal manuscript (Fig. R2-4 A/G and Table S3). Understandably, the Proterozoic\nocean could be less green than the present-day ocean if the P was extremely low.\nHowever, we think a greener but less productive ocean is still the most likely situation\nfor the Proterozoic. We have revised our manuscript accordingly, highlighting the\nimportance of nutrients in our conclusions and the effect of the greener ocean on the\nsubsurface productivity. Please see the texts below for the detailed responses and the\nrelevant revisions in the manuscript.\nFig. R2-5. Simulated annual mean concentration of surface chlorophyll under warm\n(pCO =2240 ppmv) Proterozoic scenario. The Fe input from the ocean bottom was set\n2\nto 100%, 50%, 25%, 10%, and 0% of the present level (SedFe) without the Fe input\nfrom the atmosphere and runoff. The grey contour lines in the panels indicate the edges\nof sea ice defined as the location where the gridbox sea-ice fraction is 15%. This figure is\nadded in the revised Supplementary Materials as Fig. S16.\nLine 57-58: denitrification would be enhanced in an anoxic ocean (Kang et al., 2023;\nMotomura et al., 2023), leading to nitrogen limitation to the primary productivity;\nLine 159-161: However, note that the different nutrient levels between the Proterozoic\nand PI, especially the marine nitrate (N), are also important for the Proterozoic oceans\nbeing less productive than PI oceans (see Discussion).\nLine 252-261: (We want to save some space here since those lines have appeared in the\nresponse to major comment 3 above.)\nLine 266-277: (We want to save some space here since those lines have appeared in the\nresponse to major comment 3 above.)\nLine 278-283: For Fe, sensitivity simulations (see Methods for Sensitivity Simulation\nGroup 6) show that even when atmospheric and riverine dust inputs are completely\nremoved, and the Fe from ocean bottom is reduced to 10% of the present strength, a\nmuch greener ocean can still be maintained (Fig. S16E). This means that the uncertainty\nin Fe has almost no influence on our main findings. Therefore, these sensitivity tests\nindicate that the Proterozoic ocean would be greener but less productive for the most\nlikely ranges (25% POL < P < 200% POL, and loose ranges for N and Fe) of nutrients\nlevels.\n4. Atmospheric O₂:\nThe prescribed atmospheric O₂ concentration of 1% PAL is broadly consistent with\nestimates for the Proterozoic. However, when combined with modern nutrient\ninventories, it creates an unrealistic, perpetual disequilibrium. In the scenario discussed\nin the manuscript, I suspect that the surface ocean is oversaturated with O₂ and\ncontinuously outgasses to the atmosphere, while the deep ocean defaults to anoxia. This\ndrives anaerobic remineralization throughout much of the water column, a process that\nmay not be well parameterized in the model to begin with.\nWe thank the reviewer for this suggestion. The reviewer is correct that the ocean surface\ncontinuously outgases O when pO prescribed to be 1% PAL, although the surface\n2 2\nocean was not oversaturated with oxygen (Fig. R2-6), leading to a disequilibrium. The\nreviewer is also correct that the remineralization of BEC is parameterized based on the\npresent marine oxygenation and decoupled with the calculated O concentration\n2\n(Armstrong et al., 2002), such that the anaerobic remineralization in seawater is not\nwell parameterized. Meanwhile, the high oxygen production rate by photosynthesis on\nmodern Earth can be attributed to several functional enzymes, which may not have\nevolved in the Precambrian phytoplankton (Rickaby and Eason Hubbard, 2019; Yee et\nal., 2023). Thus, the oxygen production parameter (Redfield ratios) in CESM for\nmodern Earth would differ from those in the Proterozoic (Planavsky, 2014),\noverestimating the oxygen outgassing rate from the ocean to the atmosphere. Moreover,\non million-year timescale, the refractory DOC should play an important role in the\noxygen cycle (Rothman et al., 2003), but is not considered in the BEC either (Letscher\net al., 2015). This is the reason why we focus more on phytoplankton and NPP in the\nshallow euphotic layer in the current study. We mention those limitations in the revised\nmanuscript as pasted below and do not feel that they affect the major conclusions of\nour study. More explanations are provided below related to the pO sensitivity\n2\nsimulations.\nFig. R2-6. Simulated dissolved oxygen at the sea surface (A-C) and net oxygen flux\n(D-F) at the sea surface in the PI condition (top), warm (pCO =2240 ppmv, middle),\n2\nand cold (pCO =280 ppmv, bottom) scenarios in the Proterozoic. The positive values\n2\nin D-F represent the net oxygen flux from the atmosphere to the ocean. The green\ncontour lines indicate the edges of sea ice with the gridbox fraction of 15%.\nLine 288-297: This excessive O from the model is due to deficiency in both the source\n2\nand sinks. For the source, the oxygen production rate by photosynthesis might be\noverestimated for the Proterozoic by the model because several enzymes for catalyzing\noxygen production have not evolved (Rickaby and Eason Hubbard, 2019; Yee et al.,\n2023). For sinks, both the influence of marine (e.g., SO and H S) and terrestrial (e.g.,\n2 2\nFeS) reducers are absent. The remineralization in the seawater is parameterized with\nthe present marine oxygenation and decoupled with the calculated O concentration,\n2\nso the oxygen sink in the anoxic Proterozoic ocean might be largely overestimated\n(Armstrong et al., 2002). Moreover, the refractory DOC, which may increase oxygen\noutgassing, is omitted in the model we use (Letscher et al., 2015). Fortunately, such\ndeficiency in the modeling of oxygen cycle should not interfere with the primary\nproductivity of the near-surface ocean (Table S3).\nIn a low-O₂ Earth system, atmospheric pO₂ should ideally evolve dynamically based on\nbiogeochemical fluxes, since NPP can influence atmospheric oxygen even on seasonal\ntimescales. Furthermore, oxygen sinks such as the oxidation of reduced gases (e.g., SO₂,\nH₂) may have played a significant role in the Proterozoic, unlike in today’s oxygen-rich\natmosphere. These considerations should be factored into the model setup.\nWe appreciate Reviewer #2 for this considerable suggestion. The atmospheric O level\n2\nshould be calculated dynamically by fully considering both marine biogeochemistry,\natmospheric photochemistry, and land processes (such as oxidation of pyrites;\nHemingway et al., 2020; Liu et al., 2021). The lack of oxygen sinks in both the ocean\n(e.g., SO , H , and H S etc. mentioned by the reviewer) and land (e.g., FeS) in the model\n2 2 2\nwe use prevents the outgassed O from being balanced. However, the development of\n2\nsuch a comprehensive model is clearly beyond the purpose of this work and timescale\nof O equilibration (tens to hundreds million years; Liu et al., 2021) also makes it\n2\nformidable to be investigated using an AOGCM like CESM. Under the current\ndevelopment stage of CESM, the atmospheric oxygen level is always and better be\ntreated as a fixed boundary condition, omitting the feedback of various fluxes to the\npO . In our current modeling approach, the NO deposition input, an important nutrient\n2 x\nfor the ocean, has been set considering the background pO . We borrow the NO\n2 x\ndeposition rate from previous photochemical model results (see Methods), obtained by\nthe first author (Liu et al., 2021).\nThe most physically consistent approach would be to couple the ocean biogeochemistry\nmodel to a dynamic atmosphere in which O₂ and CO₂ evolve over time. While this\nwould require significant model development, it would improve the physical realism of\nthe simulations. As an alternative to a fully dynamic atmosphere, the authors could\nadjust prescribed O₂ and nutrient levels until the net ocean-atmosphere O₂ flux is close\nto zero. This would help avoid the artificial disequilibrium produced in the current\nmodel configuration. Sensitivity simulations using different prescribed O₂ levels would\nalso help test the robustness of the study’s conclusions.\nWe thank Reviewer #2 for this useful suggestion. Although developing a fully coupled\nmodel in which O and CO could dynamically evolve is formidable, we are happy to\n2 2\noperate additional sensitivity simulations with different prescribed pO . Specifically,\n2\npO of 0.1% and 10% PAL under high pCO (2240 ppmv) are tried (see Methods for\n2 2\nSensitivity Simulation Group 4). The model results indicate that dissolved oxygen level\nincreases with pO , and the air-sea flux of O decreases (Fig. R2-7). The air-sea flux is\n2 2\nstill large even when pO is set to 10% PAL, 308 Tmol/yr, enough to double pO in\n2 2\n~17,000 years. This flux remains large (110 Tmol/yr) even when P is reduced to 2.5%\nPOL under pO of 1% PAL (Table S3 in Supplementary Materials). Therefore, without\n2\nconsidering many of the sinks for O described above in the model, it is unlikely to\n2\nbalance the air-sea flux of O unless pO is set to much higher than 10% PAL.\n2 2\nFortunately, both the surface chlorophyll and total NPP are similar among three\ndifferent pO , demonstrating the robustness our major conclusions against pO (Table\n2 2\nS3 in Supplementary Materials). Such discussion has been included in the revised\nmanuscript as shown below.\nFig. R2-7. Simulated dissolved oxygen at the sea surface (A-B) and net oxygen flux\n(C-D) at the sea surface under pCO =2240 ppmv (warm) Proterozoic scenarios, when\n2\natmospheric oxygen level is set to 0.1% (top) and 10% (bottom) of the present\natmospheric oxygen level. The positive values in C-D represent the net oxygen flux\nfrom the atmosphere to the ocean. The green contour lines indicate the edges of sea ice\nwith the gridbox fraction of 15%.\nLine 284-297: Deficiency in the oxygen cycle. The oxygen cycle in CESM1.2.2 suffers\nfrom a few problems which prevent us from letting pO evolve freely but has to be\n2\nprescribed. If we let pO evolve freely, the large oxygen outgassing flux from the ocean\n2\nwould double it in a few thousand years if the initial pO is 1% PAL. This timescale\n2\nwill lengthen to ~17000 years when pO is increased to 10% PAL (see Methods for\n2\ndeficiency in both the source and sinks. For the source, the oxygen production rate by\nphotosynthesis might be overestimated for the Proterozoic by the model because several\nenzymes for catalyzing oxygen production have not evolved (Rickaby and Eason\nHubbard, 2019; Yee et al., 2023). For sinks, both the influence of marine (e.g., SO and\n2\nis parameterized with the present marine oxygenation and decoupled with the calculated\nO concentration, so the oxygen sink in the anoxic Proterozoic ocean might be largely\n2\noverestimated (Armstrong et al., 2002). Moreover, the refractory DOC, which may\nincrease oxygen outgassing, is omitted in the model we use (Letscher et al., 2015).\nFortunately, such deficiency in the modeling of oxygen cycle should not interfere with\nthe primary productivity of the near-surface ocean (Table S3).\nLine 454-455 (Sensitivity Simulation Groups in Methods): (4) Different atmospheric\noxygen levels (pO ). The pO is set to 0.1% and 10% of the present level in the\n2 2\npCO =2240 ppmv simulation.\n2\nunderstanding of the nitrate limitation in the Proterozoic. Although increasing pO by\n2\nten times could halve denitrification and increase marine nitrate level (still N-limitation\nregime), the NPP has only increased ~7% (Fig. R2-8A-D). That is because the self-\nshielding effect would still cause light starvation and prevent the NPP from increasing\nsignificantly (Fig. 2-8E-F), demonstrating that the poor sunlight penetration was the\nimportant limiting factor for marine productivity in the Proterozoic. We have added the\nabove discussion in the revised manuscript and pasted below.\nFig. R2-8. Simulated zonal mean net primary production (A-B), denitrification (C-D),\nand limiting factors for small phytoplankton in the second layer (10-20 m) (E-F) for\natmospheric oxygen levels equal to 1% (left) and 10% (right) of the present level under\nthe warm (pCO =2240 ppmv) Proterozoic scenario. The light green contours in E-F\n2\nindicate the edges of sea ice defined as the location where the gridbox sea-ice fraction\nis 15%. This figure is added in the revised Supplementary Materials as Fig. S13.\nLine 261-263: If pO is increased to 10% PAL (see Methods for Sensitivity Simulation\n~7% compared to pO =1% PAL scenario (Fig. S13)\nacknowledged in the revised manuscript.\nWe appreciate Reviewer #2 for the comments that kindly help us clarify the\nassumptions and limitations in our work. We have incorporated relevant contexts in the\nrevised manuscript as elaborated above.\n5. Figure colorbars:\nThe orientation of the colorbars in Figures 1, 2, and 3 is unconventional, they display\nhigher values on the left and lower values on the right. Typically, colorbars are oriented\nfrom low (left) to high (right). This should be revised for clarity and consistency.\nWe apologize for using an unconventional colorbar format. We have reversed the\norientation of the colorbar as shown below.\nFig. 1. Simulated chlorophyll and plankton carbon in PI and Proterozoic conditions.\nFig. 2. Simulated net primary productivity and light availability in PI and Proterozoic\nconditions.\nFig. 3. Simulated sunlight and other limiting factors for marine productivity in PI and\nProterozoic conditions.\nMinor Comments:\n1. The introduction would benefit from greater detail on the current state of knowledge\nand prior work in this area. A more thorough overview would help contextualize the\nstudy and make the manuscript more comprehensive.\nWe have extended the Introduction by showing more detailed information and adding\na paragraph about the potential limiting factors (e.g., nutrients and light) of\nphytoplankton during the Proterozoic according to previous work.\nLine 38-51: During the Precambrian, nearly all global productivity was generated by\nthe marine biosphere, while roughly half of productivity came from the land biosphere\nafter the mid-Palaeozoic when vegetation colonized continents (Butterfield, 2015). The\nProterozoic marine community would primarily be composed of small phytoplankton\n(e.g., cyanobacteria and green algae), with zooplankton likely absent until the Ediacaran\n(Brocks et al., 2017; Hoffman et al., 2017; Lenton et al., 2014). The oxygen isotope\nrecords indicate that the gross primary productivity during the mid-Proterozoic might\nbe ~40% of the preindustrial level if the atmospheric oxygen level (pO ) was 1-10% of\n2\nthe present atmospheric level (PAL) (Crockford et al., 2018), consistent with\ngeochemical simulation results (Wang et al., 2024). An active marine biosphere in the\nProterozoic could be important for the evolution of different Earth components. The\nbiological processes might affect climate by consuming atmospheric CO , and (or)\n2\ninjecting of organic cloud nuclei into the atmosphere (Feulner et al., 2015; Rothman et\nal., 2003; Tziperman et al., 2011). The marine photosynthesis is critical for the\nevolution of the atmospheric as well as marine oxygenation state (Kump, 2008). The\nincrease in marine productivity and oxygen levels were probably important for the\nevolution of animals (Butterfield, 2015).\nLine 53-63: The primary productivity in the ocean is largely determined by the\nvariations of temperature, nutrients, and light availability. Other than the large\ntemperature variations, the Proterozoic was also characterized by very different nutrient\nlevels from today due mainly to the low pO at that time. For example, the environment\n2\nwas likely iron rich, supplying abundant iron to the marine ecosystem (Liu et al., 2020;\nPlanavsky et al., 2011); denitrification would be enhanced in an anoxic ocean (Kang et\nal., 2023; Motomura et al., 2023), leading to nitrogen limitation to the primary\nproductivity; the phosphorus level could have also been lower due to limited oxic\nrespiration and (or) removal by minerals (Guilbaud et al., 2020; Laakso and Schrag,\n2019), but some geochemical evidence suggested otherwise (Planavsky et al., 2010).\nThe dimmer Sun during the Proterozoic could also affect the productivity. Because\nzooplankton has not appeared during the Proterozoic (Hoffman et al., 2017; Lenton et\nal., 2014), the bloom of surface phytoplankton could block sunlight and suppress the\nsubsurface primary productivity, just as sometimes observed on the present-day Earth\nwhere predators are absent (Cebrian et al., 2006; Estes et al., 2011).\nLine 64-76: Previous studies involving Proterozoic biogeochemical simulations were\nbased mostly on simplified models such as conceptual models (Eckford-Soper et al.,\n2022; Laakso and Schrag, 2019) and box models (Claire et al., 2006; Laakso and Schrag,\n2017; Tziperman et al., 2011). Recently, an ocean general circulation model has been\nused to explain the banded iron formations during a Neoproterozoic Snowball Earth\nevent (Gianchandani et al., 2024). Although the Proterozoic biogeochemical cycle has\nbeen simulated with an atmosphere-ocean general circulation model (AOGCM), that\nstudy mainly focused on the role of ocean in modulating the atmospheric CO\n2\nconcentration (pCO ) and super-greenhouse climate in the aftermath of the Marinoan\nwell, many of the important processes affecting the Proterozoic ecosystem were omitted\nin the approaches employed by these previous studies. The simplified models could not\nreveal the spatial structure of the ecosystem while the complex model (Ramme et al.,\n2024) neglected some of the differences in ecological structure between the Proterozoic\nand the present, for example, the absence of zooplankton. It is essential to employ an\nAOGCM that is adapted to the Proterozoic to systematically study its ecosystem.\n2. The manuscript's language requires substantial revision. Here are some specific\nsuggestions (non-exhaustive):\nWe have edited the language in the manuscript throughout, hopefully the reviewer will\nbe satisfied with the improvements.\nLine 20–21: The first sentence is poorly structured and should be rephrased for clarity.\nWe have rephrased this sentence to ‘Geological records suggest that marine\nphytoplankton might have arisen in the Proterozoic while zooplankton remained absent,\nand marine productivity was not excessively low’.\nLine 25: Use “phytoplankton at the sea surface” instead of “phytoplankton on the\nsea surface.”\nDone.\nLine 26: Similarly, use “chlorophyll at the sea surface.”\nWe have changed this sentence to “Heavier surface chlorophyll in the Proterozoic…”.\nLines 29–30: The phrase “... sunlight was the key limiting factor ...” is misleading.\nA better formulation would be: “... poor sunlight penetration was the key limiting\nfactor ...”\nWe have rephrased this sentence and highlighted other reasons for the less productive\nProterozoic ocean too.\nLine 28-31: Through the combined influence of low nitrate level under a low-oxygen\nenvironment, the absence of diatoms, and self-shielding, the Proterozoic NPP was only\n~60% and 30% of the present level in warm (almost ice-free) and cold (sea-ice reaches\n~30°N/S) periods, respectively.\nLine 37: The word “Such” is unnecessary. Instead of “an active marine\nbiogeochemical cycle,” consider using “an active marine biosphere.”\nDone.\nLine 42: The phrase “has never been investigated seriously” may appear dismissive of\nprevious work. Consider rephrasing to: “... has not yet been extensively investigated\nusing a fully coupled model ...”\nAgree. We have deleted the original sentence and included this information in the\nrevised paragraph (line 64-76) as mentioned above.\nLine 67: Replace “submerged layers” with “subsurface layers” or “abyssal layers,”\ndepending on context.\nWe have used ‘subsurface layers’ as the reviewer suggested here.\nLine 110: The adjective “decent” in “... where a decent NPP ...” is informal and\nunnecessary. Simply use: “... where NPP is ...”\nDone.\nReferences:\n- Planavsky, Noah J., et al. \"The evolution of the marine phosphate reservoir.\" Nature\n467.7319 (2010): 1088-1090.\n- Laakso, Thomas A., and Daniel P. Schrag. \"Regulation of atmospheric oxygen during\nthe Proterozoic.\" Earth and Planetary Science Letters 388 (2014): 81-91.\n- Kang, Junyao, et al. \"Nitrate limitation in early Neoproterozoic oceans delayed the\necological rise of eukaryotes.\" Science advances 9.12 (2023): eade9647.\n- Motomura, Kento, et al. \"The nitrate-limited freshwater environment of the late\nPaleoproterozoic Embury Lake Formation, Flin Flon belt, Canada.\" Chemical Geology\n616 (2023): 121234.\nReviewer #3 (Remarks to the Author):\nReview of Liu et al., NatComm\nIn their contribution Liu et al., explore two interesting mechanisms to throttle global\nprimary productivity in the Proterozoic ocean. The first is to examine the effect of\nremoving all predation from the Proterozoic environment, which the authors simulate\nto increase production in surface waters. A consequence of this increased production is\nthe blocking of sunlight to deeper depths which the authors simulations suggest an\noverall decrease in NPP.\nOverall I found the ideas in the manuscript to be very interesting at a conceptual level,\nbut to lack strong grounding to be considered meaningful in forwarding our\nunderstanding of the Proterozoic environment.\nWe appreciate the recognition of our idea from Reviewer #3 and are happy to make the\nrequested revisions, especially adding more related modern observations and additional\nsensitivity simulations.\nDoes removing zooplankton increase surface production and thus particle density in\nsurface waters? The authors reference observations from the Gulf of Mexico, but is this\na general truth? For this argument to be convincing I would expect a broader\nglobal assessment of how the ratio of zooplankton to phytoplankton impacts NPP across\nmany areas in the modern environment. My hunch is that there is much more complexity in\nsuch interactions than is presented in the current manuscript.\nWe thank Reviewer #3 for this constructive suggestion. And yes, removing\nzooplankton could increase surface production and chlorophyll substantially as\ndemonstrated in the new sensitivity simulation where we added zooplankton back to\nthe Proterozoic ocean (Fig. R3-1A-D; see Methods for Sensitivity Simulation Group 1).\nHowever, the total NPP would decrease in the zooplankton-involved simulation\nbecause zooplankton would consume a large amount of nutrients, leading to a nutrient-\nlimited (in particular, nitrate) ocean and suppressing NPP (Fig. R3-1E-F).\nWe have also added more modern observations about this phenomenon in different\nregions through a broader literature review. In the Aleutian archipelago and Alaska of\nthe North Pacific, the collapse of herbivores (including zooplankton) due to the\npresence of sea otters would enhance kelp abundance and production of autotrophs\n(Estes and Duggins, 1995; Estes et al., 2011). A greener region of Long Lake in\nMichigan with abundant phytoplankton was observed when experimentally removing\nthe largemouth bass. Because this bass preys on smaller zooplanktivorous fishes,\nremoving the bass will decrease zooplankton and thus increase phytoplankton\n(Carpenter et al., 2001; Estes et al., 2011; Fig. R3-2). The predatory spotted bass, eating\nherbivorous minnows, could promote the growth of algae as observed in Oklahoma\nstreams (Power et al., 1985). In the open ocean of the North Pacific, the abundance of\nfish (e.g., salmon and saury) would cause the decline of zooplankton and thus enhance\nthe growth of phytoplankton (Odate, 1994; Shiomoto et al., 1997). The above examples\nare mostly triggered by the apex (large) consumers and could cause the following chain\neffects through feed webs, noted as “trophic cascades” (Estes et al., 2011).\nUnfortunately, no information on the quantitative change of NPP could be found for\nthese events.\nThe reviewer is correct that the interactions listed above are more complex in modern\nEarth with more than two species involved and may include tipping points, around\nwhich abrupt changes in ecosystem structure and function may occur (Scheffer et al.,\n2001). The response of the Proterozoic ocean ecosystem to zooplankton removal is also\nmore complex than thought in the original manuscript. The presence of zooplankton\ndecreases the total NPP with the major reason being that nitrate (N) nutrient is also\nconsumed by this species; the ecosystem became N limited under the Proterozoic low-\nN background (Fig. R3-1E), which itself was due to the low pO and thus enhanced\n2\ndenitrification in the ocean.\nWe now summarize the reasons for the generally lower global NPP in the Proterozoic\nocean as: 1) the absence of diatom reduces the global NPP by ~20% according to the\npresent-day budget. 2) the much lower N nutrient level due to the low O level\n2\nwould drive a low total NPP even if the biospheric composition was similar to today.\n3) without zooplankton consuming N, the productivity would not be limited by N but\nthe self-shielding effect would then prevent the NPP from increasing significantly.\nWe have added the above discussion in the revised manuscript and pasted below.\nFig. R3-1. Simulated concentration of surface chlorophyll (A-B), vertical NPP within\nthe upper 150 m ocean (C-D), and limiting factors for small phytoplankton in the second\nlayer (10 - 20 m) under warm (pCO =2240 ppmv) Proterozoic scenario, when including\n2\nzooplankton (top) and excluding zooplankton (bottom). Both the contour lines in the\nA-B/E-F and light green bars at the top of C-D indicate the edges of sea ice defined as\nthe location where the gridbox sea-ice fraction is 15%. This figure is added in the\nrevised Supplementary Materials as Fig. S4.\nPUBLISHED DATA FIGURE REDACTED\nFig. R3-2. Long Lake (Michigan) with largemouth bass present (right, less green\nsurface) and experimentally removed (left, greener surface) (Fig. 1C in Estes et al.,\n2011).\nLine 125-128: When the zooplankton is added back to the Proterozoic ocean (see\nMethods for Sensitivity Simulation Group 1 and Table S2), surface chlorophyll\ndecreases substantially (Fig. S4), confirming that the absence of zooplankton was the\nkey trigger of the greener Proterozoic ocean.\nLine 204-208: In the open ocean of North Pacific, the abundance of fish (e.g., salmon\nand saury) would graze zooplankton and thus enhance the growth of phytoplankton\n(Odate, 1994; Shiomoto et al., 1997). Green of part of Long Lake in Michigan was\nobserved when the largemouth bass was experimentally removed, because it allowed\nsmaller zooplanktivorous fishes to thrive, reducing zooplankton and increasing\nphytoplankton (Carpenter et al., 2001; Estes et al., 2011).\nLine 446-448 (Sensitivity Simulation Groups in Methods): (1) Inclusion of zooplankton\nin the Proterozoic. The zooplankton has been involved in the ocean simulation with the\nother boundary conditions the same as those in the pCO =280 ppmv simulation.\nthe net effect of decreasing overall global NPP? Maybe, but this appears to again be a\ndistinct question which should be much more thoroughly explored through doing a deep\ndive into modern marine environments and even terrestrial environments. Again,\nperhaps this is true, but it is not clear from the current manuscript.\nWe thank Reviewer #3 for this constructive suggestion. Although we think the\nincreasing surface production (chlorophyll) would have certainly decreased the sunlight\nin the subsurface layer and NPP, there are other complexities. As mentioned above,\neven if zooplankton was present during the Proterozoic, the total NPP would be much\nlower than the oceans of today. This is because the Proterozoic was overall N depleted\n(the nitrate concentration was more than 3 orders of magnitude lower than in the present)\ndue to enhanced denitrification under a low pO background; zooplankton would also\n2\nconsume N, making the whole ecosystem N limited (Fig. R3-1E).\nWe have also added more observations related to the shielding phenomenon in modern\nEarth, following the reviewer's suggestion. The phytobenthic production is known to\ndecrease when the biomass of overshielding plankton increases, even though\nmicrophytobenthos can persist at low light levels. For example, the enhanced shielding\neffect of phytoplankton blooms in the West Florida Shelf from the 1970s to 1990s could\ndecrease sunlight penetration and benthic primary production (Okey et al., 2004).\nSimilarly, with field experiments in estuaries of Weeks Bay (Alabama, USA), the light\nshielding induced by the blooms of surface phytoplankton generally caused a\nsignificant reduction in the sediment primary production (Cebrian et al., 2006). This\nmechanism is also valid for the coastal lagoons. In the highly eutrophicated lagoon\n(Kirr-Bucht), the surface chlorophyll level was ~8 times higher than that of Rossower\nStrom. However, for the subsurface layer (~1 m), the gross and net production of Kirr-\nBucht are about 2 and 10 times lower than those of Rossower Strom due to the light\nlimitation as indicated by in situ and laboratory data (Meyercordt and Meyer-Reil,\n1999). However, little quantitative calculation about the sum of surface and subsurface\nNPP, nor overall global NPP, has been found under the modern self-shielding scenario.\nThus, we can only present the observations for the subsurface NPP for reference. We\nhave added the above discussion in the revised manuscript and pasted below.\nLine 208-212: The shielding effect by surface blooms on the subsurface and benthic\nprimary productivity has also been observed in the modern West Florida shelf and\nWeeks Bay of Alabama (Cebrian et al., 2006; Okey et al., 2004). Based on both in-situ\nand laboratory data, the subsurface NPP in the coastal lagoon near Baltic Sea was\nbelieved to be lower due to light limitation caused by a high surface chlorophyll\nconcentration (Meyercordt and Meyer-Reil, 1999).\nWith the above comments in mind, I also think it is worth noting on whether such results\nare truly relevant to the Proterozoic, a 2 billion year interval of Earth’s past. The authors\nuse a single continental configuration, however, this would have varied considerably\nacross this eon. Moreover, the authors appear to have ignored virtually all geochemical\ndata across this interval in their analysis and instead have opted to take modern values\nand explore how they might change with a different continental configuration and the\nimposed effects of no zooplankton. For example, if productivity was lower globally due\nto P limitation or metal limitation which may have decreased the rate of nitrogenase\nsynthesis, would the self shielding effect still matter?\nWe appreciate Reviewer #3 for these constructive suggestions. Although only the\ncontinental reconstruction for 720 Ma is used in this study, the characteristics of the\necosystem for the whole Proterozoic may be considered fundamentally similar given\nthat the continents were located relatively in the low latitudes for the whole Eon (Cao\net al., 2024; Li et al., 2008). Moreover, we have conducted 17 additional sensitivity\nsimulations in this revision, which should be sufficient to cover the uncertainties due to\ncontinental configurations. For example, the influence of different oceanic dust\ndeposition under different continental configurations should not be greater than that in\nthe sensitivity experiment where all dust deposition was removed (see Methods for\nSensitivity Simulation Group 6). Similarly, the influence of continental silicate\nweathering and the associated riverine nutrient input may be covered by the sensitivity\ntests in which the phosphorus (P) concentration in the ocean was changed (see Methods\nfor Sensitivity Simulation Group 5). The P concentration has been changed from 2.5%\npresent oceanic level (POL) to 500% POL according to geological evidence (Guilbaud\net al., 2020; Planavsky et al., 2010). The results of these simulations show that the most\ncritical driving mechanism for the simulated greener Proterozoic ocean is the absence\nof zooplankton (Fig. R3-1A) rather than other factors, including the continental\nconfiguration.\nThe reviewer is correct that the self-shielding effect would not matter anymore if the\nnutrient level is very low. For example, if P concentration in the Proterozoic was 10%\nPOL or lower, the surface productivity would be too low to trigger the self-shielding\neffect (Fig. R3-3E-F and K-L) and the sunlight was no longer be the key limiting factor\nfor phytoplankton (Fig. R3-4). However, such low P (i.e. 2.5% PAL) concentration is\na lower bound of the available reconstructions (Guilbaud et al., 2020). We may consider\nthat the Proterozoic ocean was most likely greener and the self-shielding effect was\nstrong. We have added the above discussion in the revised manuscript and pasted below.\nFig. R3-3. Simulated annual mean concentration of surface chlorophyll (A-F) and net\nprimary production within the upper 150 m (G-L) under the warm (pCO =2240 ppmv)\nPOL, 50% POL, 25% POL, 10% POL, and 2.5% POL as labeled in the top-left corner\nof each panel, where POL stands for present oceanic level. Both the grey contour lines\nin the A-F panels and light green bars at the top of the G-L panels indicate the edges of\nsea ice defined as the location where the gridbox sea-ice fraction is 15%. This figure is\nadded in the revised Supplementary Materials as Fig. S15.\nFig. R3-4. Simulated limiting factors for small phytoplankton in the second layer (10 -\n20 m) when the marine concentration of phosphate is set to (A) 10% and (B) 2.5% of\nthe present oceanic level (POL) under pCO =2240 ppmv (warm) Proterozoic scenarios.\nthe gridbox sea-ice fraction is 15%.\nLine 266-277: For P, it turns out its initial reservoir is too large to be affected by the\nspecified Proterozoic boundary conditions (Table S1) during the simulations (Fig. S14),\nthus additional sensitivity simulations with different initial P concentration have to be\ncarried out (see Methods for Sensitivity Simulation Group 5). Geochemical records\nindicate that the Proterozoic P could be 500% to 2.5% of the present oceanic level (POL)\n(Guilbaud et al., 2020; Laakso and Schrag, 2014; Planavsky et al., 2010). Simulation\nresults show that a much greener Proterozoic ocean will be obtained if P is increased to\n200% and 500% POL (Fig. S15A-B) with even stronger self-shielding effect and\nshallower productive layer (Fig. S15G-H). The global total NPP at P=200% POL is still\nlower than that in PI; only when P is increased to 500% POL, the total NPP is larger\nthan PI (Fig. S15G and Table S3). On the other hand, even though NPP is reduced to\none sixth of the PI value when P is reduced to 25% POL, the mid- to low-latitude ocean\nsurface remains slightly greener than the PI ocean surface (Fig. S15D and Table S3).\nThus, the Proterozoic ocean would be greener but less productive unless P was more\nthan twice or less than one fourth of the PI level (i.e., 1 POL).\nLine 278-283: For Fe, sensitivity simulations (see Methods for Sensitivity Simulation\nGroup 6) show that even when atmospheric and riverine dust inputs are completely\nremoved, and the Fe from ocean bottom is reduced to 10% of the present strength, a\nmuch greener ocean can still be maintained (Fig. S16E). This means that the uncertainty\nin Fe has almost no influence on our main findings. Therefore, these sensitivity tests\nindicate that the Proterozoic ocean would be greener but less productive for the most\nlikely ranges (25% POL < P < 200% POL, and loose ranges for N and Fe) of nutrients\nlevels.\nLine 455-461 (Sensitivity Simulation Groups in Methods): (5) Varying the phosphate\nreservoir. The marine phosphate level has been set to 500%, 200%, 50%, 25%, 10%,\nand 2.5% of the present oceanic level, with other conditions identical to those in the\noriginal pCO =2240 ppmv simulation. (6) Lower iron input. This group includes five\n2\nsimulations. In the first one, the sources from the atmospheric dust deposition and\nriverine input are removed, so that only Fe input through the ocean bottom is considered.\nIn the other four simulations, the Fe from ocean bottom is further reduced to 50%, 25%,\n10%, and 0% of the present level.\nAgain, I don’t want to be too negative here. The ideas are interesting I just don’t think\nthat jumping from concept to a complex GCM without a lot of work in assessing these\nideas in modern environments helps to forward these ideas. Moreover, jumping to the\nProterozoic without exploring these effects more rigorously using data and insights that\nhave presented for this eon I think is a missed opportunity.\nI’m sorry I can’t be more supportive at this time.\nWe sincerely thank Reviewer #3 for the highly constructive comments, which help us\nimprove the quality of the manuscript. We have added broader observations about the\neffects of the absence of zooplankton on the phytoplankton and production to support\nour findings. Moreover, we have also carried out additional sensitivity tests to clarify\nthe driving factors of the greener ocean and the potential effects of different nutrient\nscenarios in the Proterozoic. 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Primary productivity recovery and shallow-water\noxygenation during the Sturtian deglaciation in South China. Global Planet. Change 241, 104546.\nWatanabe, Y., Tajika, E., Ozaki, K., 2023. Evolution of iron and oxygen biogeochemical cycles during\nthe Precambrian. Geobiol. 21, 689-707.\nResponses to reviewers’ comments\nThe detailed review and constructive comments of all reviewers are greatly appreciated.\nOur point-to-point responses to the reviewers’ comments are shown in red below and\nthe related revisions are also highlighted in red in the revised manuscript.\nReviewer #1 (Remarks to the Author):\nIn response to the initial round of reviews, the authors have conducted a comprehensive\nset of sensitivity simulations that substantially strengthen the robustness of their\nfindings. Additional simulations target the uncertainties around the impact of the\ndimmer sun, the parameterization of vertical mixing, as well as the availability of\nnutrients and oxygen. A further test simulation that puts the zooplankton back into the\nmodel shows the expected reduction in surface greenness, underlining the existence of\nthe proposed self-shielding effect in the Proterozoic. I also appreciate the added modern\nexamples of self-shielding.\nMy only remaining concern is that in the manuscript the authors generally makes quite\nstrong claims seemingly about the whole Proterozoic, where they are actually just\ndescribing their model simulation. I have two suggestions here:\nWe appreciate Reviewer #1 for the supportive comments and kind recognition of our\nefforts in the last revision. In this revision, we have identified certain imprecise\ninterpretations of our findings derived from the simulation results and accordingly\nrevised the manuscript throughout to enhance objectivity, following the comments of\nReviewer #1. Please see the following responses for details.\nFirstly, I would suggest that, especially in the results section, the authors revise those\nstatements. This can be as simple as in the following example:\nl. 141: \"the Proterozoic NPP was limited to a few zonal strips\" (this is a very bold\nstatement for a period that spans around 2 billion years!). What the authors should\nactually say is something like: \"NPP is limited to a few zonal strips in the Proterozoic\nsetup of our model.\"\nThanks for pointing out this inappropriateness in our description, we have modified this\nsentence following the reviewer’s suggestion.\nHowever, there are quite many of such statements, so a careful checking of the whole\nmanuscript is required. Within the discussion it is then okay to draw conclusions from\nthe findings of the model and make statements about the biogeochemistry in the\nProterozoic.\nWe have thoroughly reviewed and revised the manuscript to address this type of\nproblem. For example:\n(1) Line 96-97. We have changed “The total productivity of the Proterozoic ocean was...”\nto “The total productivity of the Proterozoic ocean simulated by the CESM 1.2.2\nwas…”.\n(2) Line 100. We have added “Simulation results show that” before the original\n“without grazing by zooplankton…”.\n(3) Line 180-181. We have used “chlorophyll in the simulated Proterozoic ocean” rather\nthan “chlorophyll in the Proterozoic ocean”.\nPlease see our revised manuscript for all the modifications related to this type of\nissue (e.g., line 111, 119, etc.).\nSecondly, the used continental setup is only representative of the (late) Neoproterozoic.\nI would suggest to discuss this early on, and maybe rather speak of a Neoproterozoic\nsetup generally. It might still be okay to draw conclusions for the whole Proterozoic\nfrom this in the discussion.\nThe reviewer is correct that the continental reconstruction for the late Neoproterozoic\n(720 Ma) is used in this study, largely because of the high computational demand.\nHowever, the characteristics of the ecosystem for the whole Proterozoic may be\nconsidered fundamentally similar given that the continents were located relatively in\nthe low latitudes throughout the Proterozoic (Cao et al., 2024; Li et al., 2008). Moreover,\nthe sensitivity simulations (i.e., for nutrients and vertical mixing) should be sufficient\nto cover the uncertainties due to continental configurations. We have added the above\ndiscussion early before the Results section, following the reviewer’s suggestion, and\npasted the contexts below.\nLine 81-85: Although the continental configuration used here was reconstructed for the\nlate Neoproterozoic (see Methods), the fundamental characteristics of the ecosystem\nacross the entire Proterozoic may have been analogous since the continents remained\nat relatively low latitudes for the whole eon (Cao et al., 2024; Li et al., 2008). Moreover,\nthe sensitivity simulations (see Methods) could have covered the uncertainties due to\nthe evolution of continental configuration.\nApart from that, I find that the additional simulations and the added discussion have\nimproved the manuscript a lot, and I have no further major concerns that would stand\nin the way of publication.\nWe sincerely thank Reviewer #1 for the constructive and positive comments.\nReviewer #2 (Remarks to the Author):\nReview of “A Greener but Less Productive Proterozoic Ocean” by Liu et al. for Nature\nCommunications.\nAfter reviewing the revised manuscript and the authors’ responses to the reviewers’\ncomments, I am encouraged to see that the main scientific concerns raised in the initial\nreview have been addressed. The revisions have improved the manuscript, and the\nresults are interesting and valuable to the community.\nThat said, I believe the manuscript would benefit from another careful pass focused\nspecifically on language and framing. In its current form, the text is often difficult to\nfollow, and some statements read as more definitive than is warranted given the\nuncertainties associated with the Proterozoic. Improving clarity and tone is important\nhere because the conclusions rely on subtle modeling arguments, which risk being\nobscured or misinterpreted when the language is imprecise or overly strong.\nI therefore recommend publication contingent on further language revisions aimed at\nimproving coherence, precision, and appropriate qualification of uncertainty. Below I\nlist several specific examples to guide the authors. This list is not exhaustive, but it\nillustrates the types of changes that are still needed throughout the manuscript.\nWe appreciate Reviewer #2 for the supportive comments and kind recognition of our\nefforts in the last revision. We agree with the reviewer that careful and rational\ninterpretation of results is critical, and have thus modified the manuscript throughout,\nfocusing on the precision and objectivity during the presentation of our results. Please\nsee the following responses to the specific suggestions raised by the reviewer and the\nother related modifications made to the manuscript regarding the diction.\n1. Line 25: The phrase “under the most probable nutrient levels” is too casual for a\nscientific article. Please consider rephrasing to something more explicit, for example:\n“within the expected range of nutrient levels”.\nChanged as the reviewer suggested. Similarly, we have also used “within the expected\nnutrient regimes” in line 92.\n2. Line 27: The sentence appears to be missing a verb. For clarity, revise to something\nlike: “… would block sunlight from penetrating (or reaching) subsurface layers”.\nWe have added “reaching” following the reviewer’s suggestion. Similarly, we have also\nadded “reaching” in line 165.\n3. Line 28: To clarify the origin of the result, consider revising the opening to:\n“Simulations show that, through the combined influence …”.\nChanged as the reviewer suggested. Furthermore, we have also emphasized the model-\nderived origin of results throughout the manuscript to improve the overall clarity and\nobjectivity of our presentation (e.g., line 97, 181, etc.).\n4. Line 38: “considerable” is vague and not very informative. A more precise term such\nas “substantial” would be preferable. It would also help to explicitly state the ranges\ndiscussed in previous studies, for example: “… might have been substantial (between\nA and B in the Proterozoic, compared to C today)”.\nWe have used “substantial” and added “(between ~5% and ~40% of the present-day\nlevel)” following the reviewer’s suggestion. Similarly, the “considerable” in line 318\nhas also been replaced by “substantial”.\n5. Lines 46–47: “could be” should be replaced with “could have been.” More generally,\nI encourage the use of the past conditional tense where appropriate to reflect uncertainty.\nBy the same logic, “might affect” in line 47 should be revised to “may have affected”.\nChanged as the reviewer suggested. Following this logic, we have checked the\nmanuscript throughout and changed the tense accordingly. For example, we have used\nthe past conditional tense in line 62, 106, etc.\n6. Line 53: Use “… variation in temperature …” rather than “of”.\nChanged as the reviewer suggested. Similarly, we have used “Variation in the vertical\ndiffusivity” rather than “of” in line 466.\n7. Line 58: Use “… limitation of primary productivity …” rather than “to”.\nChanged as the reviewer suggested.\n8. Line 61: Use “… zooplankton had not appeared …” rather than “has”.\nChanged as the reviewer suggested.\n9. Line 83: Use “… strategy employed by Gianchandani et al. …” rather than “in”.\nChanged as the reviewer suggested.\n10. Line 104: “Either” is incorrect in this context and should be replaced with “both”.\nChanged as the reviewer suggested.\n11. Line 195: The section title “Supports from modern observation” is awkward.\nA clearer alternative might be “Support from modern observations” or “Present-day\nanalogs”\nWe have used “Support from modern observations” following the reviewer’s\nsuggestion.\n12. Lines 281–283: The phrase “most likely ranges” is too strong and potentially\nmisleading. The analysis does not establish statistical likelihood, and the wording risks\nimplying a level of confidence that is not justified. Please revise to a more cautious\nformulation that reflects expectation or plausibility rather than likelihood.\nWe apologize for the inappropriate statement, and this sentence has been changed to\n“…Proterozoic ocean would have been greener but less productive for the expected\nnutrient ranges…”. Similarly, we have changed “…the most likely range of nutrients”\nto “the expected range of nutrients” in line 261.\n13. Line 285: The sentence should read “… evolve freely and has to be …” rather than\nusing “but.”\nChanged as the reviewer suggested.\nAt last, we sincerely thank Reviewer #2 for the above constructive comments and very\ncareful checking!\nReviewer #3 (Remarks to the Author):\nThis is my second time reviewing the current manuscript. The authors have worked\nhard to address numerous reviewer comments. However, I feel the manuscript suffers\nfrom poor presentation and presenting certain simulations as their preferred scenario to\nattempt to constrain features of the Proterozoic environment such as primary\nproductivity and depths of the chlorophyll max, which does not reflect the full degree\nof the uncertainty that is explored in their simulations. Again, I believe the ideas are\ninteresting in this manuscript, however in it's current form it does not seem to add new\nconstraints, but rather possible consequences of posited nutrient levels across the\nProterozoic. Therefore I am not supportive of the publication of this work in its current\nform.\nWe appreciate Reviewer #3 for the re-evaluation of the manuscript and kind recognition\nof our efforts in the last revision. We apologize for certain imprecise interpretations of\nour findings, which have also been pointed out by other reviewers. To address the\ncomments of Reviewer #3, the following revisions and clarifications have been\nimplemented in the revised manuscript.\n(1) We have widely used the past conditional tense to reflect uncertainty and improve\nobjectivity, especially in the result presentations. For example, we have changed “could\nbe” to “could have been” in line 47; used “may have affected” instead of “might affect”\nin line 48. Please see the revised manuscript for other modifications related to this type\nof issue (e.g., line 62, 106, etc.).\n(2) We have clarified the model-derived origin in the result presentation to avoid\nmisinterpretation of our findings. For example, we have added “Simulation results\nshow that” before the original “without grazing by zooplankton…” in line 100. Please\nsee the revised manuscript for the complete modifications following this logic (e.g.,\nline 111,119, etc.).\n(3) More importantly, we wish to clarify that the ranges of nutrients selected in our\nsimulations (Table S1 and S2) were bounded by geological observations and model\nconstraints. Specifically, the marine phosphorus level might be between 2.5% to 500%\nof the present oceanic level (POL) based on geochemical records (Guilbaud et al., 2020;\nPlanavsky et al., 2010); the marine nitrogen level might have been determined by the\nmarine (de)nitrification, which would have been largely affected by atmospheric\noxygen level (pO ). Thus, we have tested the range of pO from 0.1% to 10% of the\n2 2\npresent level based on geological records and model studies (Lyons et al., 2014). Our\nmodel would dynamically iterate the nitrogen level to the equilibrium state accordingly,\nwhich is also consistent with the Proterozoic situation as demonstrated by previous\nworks (Kang et al., 2023; Motomura et al., 2023); the iron inputs have also been set\nbased on geological records and model simulations (Liu et al., 2020; Watanabe et al.,\n2023). Thus, the selected nutrient levels and characteristics of the ecosystem simulated\nby the state-of-the-art GCM model might be plausible for the Proterozoic.\n(4) After conducting the sensitivity tests, the uncertainty in nitrogen and iron within the\nexpected ranges has almost no influence on the simulated greener and less productive\nProterozoic ocean (Fig. S13 and S16). However, model results would show a more\nproductive (still greener) Proterozoic ocean under high (>200% POL) phosphorus\nlevels, and a less green (still less productive) Proterozoic ocean under extremely low\n(<25% POL) phosphorus levels (Fig. S15). Those simulation results have all been\ndiscussed in the section “Uncertainties in the simulated surface greening and NPP”.\nMoreover, to highlight and reflect the full degree of the simulation results, we have\nadded the following contexts in the summary section of the revised manuscript.\nLine 312-314: It is noted that a less green or more productive Proterozoic ocean might\nbe plausible when the phosphorus level was less than one fourth or more than twice of\nthe PI level, respectively.\nAt last, we sincerely thank Reviewer #3 again for the constructive comments, and hope\nour modifications are appropriate to address the reviewer’s concerns.\nReferences for Reviewers:\nCao, X., Collins, A.S., Pisarevsky, S., Flament, N., Li, S., Hasterok, D., Müller, R.D., 2024. Earth’s\ntectonic and plate boundary evolution over 1.8 billion years. Geosci. Front. 15, 101922.\nGuilbaud, R., Poulton, S.W., Thompson, J., Husband, K.F., Zhu, M., Zhou, Y., Shields, G.A., Lenton,\nT.M., 2020. Phosphorus-limited conditions in the early Neoproterozoic ocean maintained low levels of\natmospheric oxygen. Nat. Geosci. 13, 296-301.\nKang, J., Gill, B., Reid, R., Zhang, F., Xiao, S., 2023. Nitrate limitation in early Neoproterozoic oceans\ndelayed the ecological rise of eukaryotes. Sci. Adv. 9, eade9647.\nLi, Z.-X., Bogdanova, S., Collins, A., Davidson, A., De Waele, B., Ernst, R., Fitzsimons, I., Fuck, R.,\nGladkochub, D., Jacobs, J., 2008. Assembly, configuration, and break-up history of Rodinia: a synthesis.\nPrecambrian Res. 160, 179-210.\nLiu, P., Liu, Y., Peng, Y., Lamarque, J.-F., Wang, M., Hu, Y., 2020. Large influence of dust on the\nPrecambrian climate. Nat. Commun. 11, 4427.\nLyons, T.W., Reinhard, C.T., Planavsky, N.J., 2014. The rise of oxygen in Earth’s early ocean and\natmosphere. Nature 506, 307-315.\nMotomura, K., Horie, K., Ikehara, M., Sano, T., Takehara, M., Kiyokawa, S., 2023. The nitrate-limited\nfreshwater environment of the late Paleoproterozoic Embury Lake Formation, Flin Flon belt, Canada.\nChem. Geol. 616, 121234.\nPlanavsky, N.J., Rouxel, O.J., Bekker, A., Lalonde, S.V., Konhauser, K.O., Reinhard, C.T., Lyons, T.W.,\n2010. The evolution of the marine phosphate reservoir. Nature 467, 1088-1090.\nWatanabe, Y., Tajika, E., Ozaki, K., 2023. Evolution of iron and oxygen biogeochemical cycles during\nthe Precambrian. Geobiol. 21, 689-707."}, {"round": 2, "reviewer_comments": {"reviewer_1": "In response to the initial round of reviews, the authors have conducted a comprehensive set of sensitivity simulations that substantially strengthen the robustness of their findings. Additional simulations target the uncertainties around the impact of the dimmer sun, the parameterization of vertical mixing, as well as the availability of nutrients and oxygen. A further test simulation that puts the zooplankton back into the model shows the expected reduction in surface greenness, underlining the existence of the proposed self-shielding effect in the Proterozoic. I also appreciate the added modern examples of self-shielding.\n\nMy only remaining concern is that in the manuscript the authors generally makes quite strong claims seemingly about the whole Proterozoic, where they are actually just describing their model simulation. I have two suggestions here:\nFirstly, I would suggest that, especially in the results section, the authors revise those statements. This can be as simple as in the following example:\nl. 141: \"the Proterozoic NPP was limited to a few zonal strips\" (this is a very bold statement for a period that spans around 2 billion years!). What the authors should actually say is something like: \"NPP is limited to a few zonal strips in the Proterozoic setup of our model.\"\nHowever, there are quite many of such statements, so a careful checking of the whole manuscript is required. Within the discussion it is then okay to draw conclusions from the findings of the model and make statements about the biogeochemistry in the Proterozoic.\nSecondly, the used continental setup is only representative of the (late) Neoproterozoic. I would suggest to discuss this early on, and maybe rather speak of a Neoproterozoic setup generally. It might still be okay to draw conclusions for the whole Proterozoic from this in the discussion.\nApart from that, I find that the additional simulations and the added discussion have improved the manuscript a lot, and I have no further major concerns that would stand in the way of publication.", "reviewer_2": "Review of “A Greener but Less Productive Proterozoic Ocean” by Liu et al. for Nature Communications.\n\nAfter reviewing the revised manuscript and the authors’ responses to the reviewers’ comments, I am encouraged to see that the main scientific concerns raised in the initial review have been addressed. The revisions have improved the manuscript, and the results are interesting and valuable to the community.\n\nThat said, I believe the manuscript would benefit from another careful pass focused specifically on language and framing. In its current form, the text is often difficult to follow, and some statements read as more definitive than is warranted given the uncertainties associated with the Proterozoic. Improving clarity and tone is important here because the conclusions rely on subtle modeling arguments, which risk being obscured or misinterpreted when the language is imprecise or overly strong.\n\nI therefore recommend publication contingent on further language revisions aimed at improving coherence, precision, and appropriate qualification of uncertainty. Below I list several specific examples to guide the authors. This list is not exhaustive, but it illustrates the types of changes that are still needed throughout the manuscript.\n\n1. Line 25: The phrase “under the most probable nutrient levels” is too casual for a scientific article. Please consider rephrasing to something more explicit, for example: “within the expected range of nutrient levels”.\n2. Line 27: The sentence appears to be missing a verb. For clarity, revise to something like: “… would block sunlight from penetrating (or reaching) subsurface layers”.\n3. Line 28: To clarify the origin of the result, consider revising the opening to: “Simulations show that, through the combined influence …”.\n4. Line 38: “considerable” is vague and not very informative. A more precise term such as “substantial” would be preferable. It would also help to explicitly state the ranges discussed in previous studies, for example: “… might have been substantial (between A and B in the Proterozoic, compared to C today)”.\n5. Lines 46–47: “could be” should be replaced with “could have been.” More generally, I encourage the use of the past conditional tense where appropriate to reflect uncertainty. By the same logic, “might affect” in line 47 should be revised to “may have affected”.\n6. Line 53: Use “… variation in temperature …” rather than “of”.\n7. Line 58: Use “… limitation of primary productivity …” rather than “to”.\n8. Line 61: Use “… zooplankton had not appeared …” rather than “has”.\n9. Line 83: Use “… strategy employed by Gianchandani et al. …” rather than “in”.\n10. Line 104: “Either” is incorrect in this context and should be replaced with “both”.\n11. Line 195: The section title “Supports from modern observation” is awkward. A clearer alternative might be “Support from modern observations” or “Present-day analogs”\n12. Lines 281–283: The phrase “most likely ranges” is too strong and potentially misleading. The analysis does not establish statistical likelihood, and the wording risks implying a level of confidence that is not justified. Please revise to a more cautious formulation that reflects expectation or plausibility rather than likelihood.\n13. Line 285: The sentence should read “… evolve freely and has to be …” rather than using “but.”", "reviewer_3": "This is my second time reviewing the current manuscript. The authors have worked hard to address numerous reviewer comments. However, I feel the manuscript suffers from poor presentation and presenting certain simulations as their preferred scenario to attempt to constrain features of the Proterozoic environment such as primary productivity and depths of the chlorophyll max, which does not reflect the full degree of the uncertainty that is explored in their simulations. Again, I believe the ideas are interesting in this manuscript, however in it's current form it does not seem to add new constraints, but rather possible consequences of posited nutrient levels across the Proterozoic. Therefore I am not supportive of the publication of this work in its current form."}, "author_response": ""}]

Decision letter