Stability of the marine nitrogen cycle over the past 165 million years

Domain: earth_science
Published: 2025-10-09
Editorial outcome: minor_revision

Abstract
Nitrogen and phosphorus are the two macro-nutrients that limit biological productivity in the ocean. While the supply of P depends on geological processes, N is biologically supplied from an inexhaustible atmospheric source, but can be limited by micro-nutrients, especially iron. Here we present a record of N and C isotopes over the past 165 Ma in marine sediments to address feedbacks between the N-cycle and productivity. Over most of the last 165 Myr, the fixed N averaged +3.2‰, (−2 and +9‰), but higher in distal areas of the ocean due to limited vertical mixing. Using an isotope box model and a coupled climate model we show that this is caused by winds that induce upwelling changing due to continental meander. Upwelling along low latitude east-west orientated Tethyan coastlines result in low δ15N, while upwelling along narrow N-S coastlines as it does today, result in high δ15N due to denitrification.

Introduction
In aquatic ecosystems, the availability of two macronutrients, nitrogen (dissolved inorganic N, nitrate and ammonium) and phosphorus (dissolved inorganic P), exerts control on the productivity and biomass of primary producers1,2. These two elements have contrasting biogeochemical cycles. Phosphate is released and consumed on land by rock weathering and soil formation, and transferred to the oceans by rivers, and to a lesser extent, windblown dust3. P is lost from the ocean through burial associated with biological activity as organic phosphates, adsorption to mineral surfaces, primarily Fe and Mn oxides, or by incorporation into phosphatic minerals such as Ca fluorapatite4. While many of these processes are abiotic, there is a clear and important role for biology through weathering and burial processes. In contrast, atmospheric N2 is the largest surface reservoir of N, and its supply is virtually infinite. It enters biological cycles by microbial reduction to NH3, and the majority of the fixed nitrogen in the oceans is returned to the atmosphere by microbial denitrification in the water column or in sediments5. N2 is relatively inert, and its strong triple bond is broken during a reaction catalysed by the oxygen-sensitive enzyme nitrogenase6. Nitrogenase requires 38 atoms of iron per molecule of the protein megacomplex, which is the highest concentration of iron of any enzyme in nature7,8. Hence, N2-fixation in the oceans maybe controlled as much by soluble iron in the upper ocean as by an excess of P9.

Along-debated question has been whether primary production is limited through the supply of N to the oceans, which is potentially controlled by iron limitation of nitrogen fixation, or if it is controlled by weathering and riverine fluxes of P9–12. The modern oceanic dissolved molar N:P ratio of 14.3 is lower than the planktonic N:P ratio of ~16.1, indicating N limits productivity on a global scale1,13. This is further cemented by the ability of N2-fixers and phytoplankton to access dissolved organic P, which can exceed inorganic P by up to an order of magnitude in surface oligotrophic regions and represents a greater fraction of total dissolved P than that of dissolved organic N to total dissolved N (excluding N2)14–16.

While P is delivered by rivers, the Fe required by nitrogenase is primarily supplied to much of the open ocean by aeolian dust or volcanic ash17,18. Furthermore, since dust and volcanic events tend, at least in the modern ocean, to be sporadic, the flux of Fe can vary independently from that of P19. Over geological time, both the aeolian iron flux and weathering rates (P input) have changed considerably, and not necessarily in concert. The seawater inventory of P is dependent on fluxes into the ocean from global weathering and riverine fluxes and burial in sediments, but productivity depends on the supply of P and N to the euphotic zone, which is determined not just by the amount of N and P in the ocean, but also by vertical fluxes, especially in boundary upwelling zones driven by along-shore winds. It is in the oxygen minimum zones that N can be lost preferentially over P. Given these variables, can the balance between N2-fixation and denitrification maintain a relatively stable N:P ratio or do other factors cause the N-cycle to uncouple from that of P?

The operation of the N cycle is clearly dependent upon global oceanic and orogenic processes, even as biological processes mediate between them. As with most biogeochemical cycles, much of our current understanding of the N cycle is based on the modern ocean. The palaeo-proxy of the N cycle is the record of N isotopes incorporated from dissolved inorganic N (DIN) into planktonic biomass, which is buried and retained in sediments, and reported relative to the atmosphere with differences of parts per thousand (δ15N = (Rsample/RAIR - 1)x1000, where R is the 15N/14N ratio).

In the modern ocean, the value of δ15N of the ocean nitrate DIN reservoir is higher than the near 0‰ value of fixed N supplied through N2-fixation due to the processes that remove fixed N. Localised incomplete denitrification that occurs in the OMZs with in high productivity areas, where water that sank from the surface at high latitudes upwells along narrow shelves, leads to fixed N with high δ15N, whereas denitrification in sediments has a minimal effect on fixed N isotopes. In balancing the modern N isotope budget of the ocean, at least 70% of total denitrification has to occur in the sediments based on best estimates of water column denitrification, burial and source terms20. What then happens in terms of a balanced N cycle and the isotope composition of deep ocean nitrate if processes, such as water column denitrification and burial, have changed over time? Can we assume that the isotope composition of nitrate over geological time solely reflects relative losses of fixed N via denitrification in the water column relative to those in sediments?

To address changes in the operation of the geological N cycle, we present data from a series of cores deposited during the last 165 Myr and two models. The first is an isotope box model which addresses the impact on δ15N of different rates of upwelling at a single site under two conditions: (1) in a setup closed for P without burial to represent biogeochemical cycling in a deep water column where P is completely remineralized, and (2) in a setup open for P that allows for exported material to be buried when productivity is dominated by shallow-water regions. The second model provides a set of fully coupled atmosphere-ocean general circulation model (AOGCM) simulations at different geological time slices with different continental configurations and CO2 concentrations21 which we use to estimate the total upwelling flux integrated over all coastal regions in 10 Myr time slices. The model uses Scotese continent configurations and global mean surface temperatures (GMST) reconstructed by Scotese and Wright22 and Scotese et al.23.

Results
The location of each core and its location when sediment accumulated is presented in Fig. 1; the N and C isotope data are presented in Fig. 2. Data for sea level and P accumulation rates are included in Fig. 24,56. The δ15N record is supplemented by published data57–63.

Sedimentary N isotopes since the middle Jurassic
Tethys was an established E-W oriented low-latitude ocean separating Gondwanaland to the south from Eurasia to the north when our δ15N record starts64,65. Changes in continent configurations have altered both the position and fluxes of upwelling zones (Fig. 3). During the Mesozoic, the long southern shore of Tethys provided the potential for high coastal upwelling fluxes of intermediate depth water that circulated within the tropics. Paleobathymetry suggests that deep and mid-depth water in the Tethys were likely formed within and confined to the Tethyan basins, closer to locations of upwelling than occurs today66–68.

Multiple cores were used to create each record, and while the cores are from different oceans, there was no offset in δ15N when their records were spliced (Fig. 2). The temporal resolution of the core sampling does not allow us to capture any periodicity on orbital frequencies, or geologically brief phenomena such as ocean anoxic events (Supplementary Fig. S1). Based on over 400 analyses, over the past 165 Myrs, δ15N DEEP averaged 3.2±1.6‰ (1SD) while δ15N DISTAL averaged 7.0±1.8‰ (1SD). Over this period, the δ15N DEEP (deep water nitrate) varied between −2 and +9‰, while the δ15N DISTAL varied between +3 and +11‰ over the last 90 Myr (Fig. 1) (Supplementary Information). δ15N DEEP and δ15N DISTAL were the same at the start of the late Cretaceous and since the middle Miocene, while the rest of the time, δ15N DISTAL has been higher than δ15N DEEP, and by as much as 5‰ in the Paleocene.

Our data indicate that, with the exception of two relatively brief excursions to low values at 165 and again at 140 Ma, δ15N DEEP has been fairly constant at 3.2±1.6‰. Exceptions to this occurred 165 and 135 Ma when δ15N DEEP was very low, and slightly elevated signals around the end Cretaceous to early Paleogene (75-55 Ma). The two negative excursions coincide with the opening of the Hispanic Corridor in the Western Tethys 165–160 Ma69 and the Central American Seaway 140-130 Ma67, which could have disrupted circulation patterns. δ15N DISTAL has not been as uniform as δ15N DEEP. During the latter half of the Cretaceous and first half of the Paleogene, δ15N DISTAL exceeded its 90 Myr average by as much as 4‰. Since we only have data from one core before 100 Ma, the comparison of the difference between δ15N DISTAL and δ15N DEEP, Δ15N, is limited to the last 100 Myrs. Δ15N was highest in the early Paleogene, indicating weak vertical mixing of deep nitrate to the surface ocean in the gyres. During the Miocene, Δ15N decreased to 0‰ even as both proxies increased abruptly (Fig. 2). This change indicates that vertical mixing increased during the Cenozoic. N isotopes in material bound in foraminifera (δ15N FB) are within 1‰ of δ15N DISTAL except for an excursion lasting less than 10 Myr around 60 Ma in the centre of the Pacific59. δ15N FB captures the δ15N signature of nitrate below the mixed layer, but tends to neglect contributions from N2-fixation. Thus, the extremely high δ15N FB relative to δ15N DISTAL indicates a highly stable water-column structure in the Panthalassa Ocean at that time, with little vertical mixing59 (Fig. 1). Similarly to δ15N DISTAL and δ15N DEEP, δ15N FB also abruptly increased around 10-8 Ma63.

Organic carbon isotope data from the Exmouth Plateau (ODP site 763) off NW Australia overlap with those from open ocean sites70, except for site 516 on the Rio Grande Rise, which is higher by ~2‰ in δ13C ORG. From δ13C ORG, we derived εP-Δ2, the term that reflects the demand for available C, and can be linked to productivity71. The maximal isotope fractionation associated with CO2 uptake is reduced when C demand is high relative to available CO2, driving down εP-Δ2. Changes in εP-Δ2 are largely the inverse of δ13C ORG, with the highest values occurring at the end of the Cretaceous into the Paleogene, and the lowest in the last 10 Myr (Fig. 2). There is a slightly greater range in εP-Δ2 (9‰) compared to that of δ13C ORG (7‰) due to changes in δ13C CARB72. Changes in Δ15N and εP-Δ2 are similar (Fig. 2), which indicates that the contrast between δ15N of OM produced in the gyres and margins (from deep water nitrate) was greatest when C demand versus C availability was lowest, occurring around the Paleocene-Eocene boundary when Earth’s climate was particularly warm73.

Organic C accumulation rates were calculated using measured TOC concentrations and reported age models72,74. Accumulation rates of C ORG in margin sites during the latter half of the Jurassic and Cretaceous were between 0.003 and 0.20 g C/kyr/cm2 and decreased over the Paleogene to a minimum of 0.001 g C/kyr/cm2 during the middle Miocene, at which point they began to increase rapidly. C ORG accumulation rates in the distal areas from which δ15N DISTAL is derived were lower during most of the Cenozoic than at margin sites with a broad minimum throughout the Paleogene. Around 20 Ma, they increased to converge with the margin site values at the start of the Neogene (Fig. 1). Low C ORG accumulation rates correspond to times when δ13C ORG is low (εP-Δ2 high).

Coastal upwelling and nitrogen isotopes
Today, the greatest losses of N in the water column, and where δ15N of the ocean is defined, occur in the cold eastern boundary upwelling zones along the west coast of the Americas, Africa and the northern Indian Ocean75. Coastal upwelling occurs when the wind blows parallel to the coast, with the ocean to the right-hand side of the wind direction in the Northern hemisphere and to the left-hand side of the wind direction in the Southern hemisphere. In such configurations, the near-surface Ekman transport is offshore, forcing deep water to rise and replace surface water. Thus, coastal upwelling depends on both continental configuration (coastline orientation and location) and wind patterns. Upwelling can therefore change when the positions of the continents have shifted throughout geologic history, and when the wind patterns changed due to climate warming or cooling over geologic time.

The climate model run at different time slices using the Scotese continent configuration22 suggests upwelling may have varied significantly over the past hundreds of million of years, maybe double modern values over much of the Cretaceous (refer to Supplementary information for global distributions of coastal upwelling mass fluxes for each of the 26 simulations). The calculation of the total coastal upwelling flux is described in the supplementary material and shown in Fig. 3 and the upper panel of S2. The results suggest that the upwelling flux can indeed change by factors of 5 over different geological periods due to the realigning of wind patterns and coastal regions, as depicted in the default simulation. We repeated the calculation twice more, first by varying the continental configuration using the actual wind pattern at each geologic time slice, and second by fixing the winds to pre-industrial values and using the continental configuration from each time slice. These sensitivity tests indicate that continental configuration has the most impact on upwelling fluxes between 250 and 100 Ma. During this time period, the simulation with the preindustrial wind field combined with changing continent configuration approximately reproduces the global upwelling in the default simulation that includes changes in both the wind field and the continental configuration. In contrast, the simulation that used a modern continent configuration and wind fields derived from the different time slices does not reproduce the variability in upwelling generated by the default simulation between 250 and 100 Ma. Over the Cenozoic, the simulation using the modern continent configuration and changing wind fields reproduces the global upwelling in the default simulation better than the simulation with preindustrial winds and shifting continental configuration. It is important to note that coastal upwelling occurs in narrow bands near the coast at a much smaller scale than the climate model’s resolution. Nonetheless, the calculation shows how upwelling responds to changes in both climate and continent configuration.

To first order, the nitrogen isotopic composition of marine sediments reflects the rate of denitrification in the water column, which is a function of O2 concentration relative to its demand by heterotrophs as they remineralize OM76. For the model, O2 concentrations are determined by O2 solubility in surface water. As we kept the atmosphere’s O2 concentration and sea surface temperature (SST) constant, the only mechanisms that change subsurface O2 concentrations are physical transport and aerobic respiration70. Transport also delivers nutrients to the surface water, which fuel productivity, and the consumption of productivity is the largest sink of O2.

Intense upwelling creates OMZs, which forces denitrification and the remaining nitrate to acquire a high δ15N signature. While residual nitrate is found at the surface above OMZs, its concentration is both low relative to that at the OMZ depth and much less enriched in 15N77. The 15N-enriched nitrate mixes into the deep-water inventory, which means that changes in upwelling rate are transmitted to deep water δ15N. This is what we aim to capture from near-margin sites which do not themselves host OMZs, rather than measuring δ15N at a site which hosted an OMZ, which may be subject to site-specific characteristics of upwelling and productivity intensity. Today, upwelling occurs adjacent to narrow N-S orientated margins. Our model shows that changes in continent configuration have a profound effect on upwelling (Fig. 3) and that these areas ran E-W adjacent to wide shelves of Tethys (Fig. 1). Consequently, it is important to understand the response of the N-cycle not only to increased upwelling and productivity, but to increased burial of that productivity. The final set of models addresses the response of the N cycle to a change in the P inventory.

To investigate the impact of upwelling on δ15N, we varied the upwelling rate in the box model. The model (described in detail in the Supplemental Material S1) resolves an intermediate ocean box, in which the O2 minimum develops, the overlying surface box, and a box representing the rest of the ocean (both surface and deep ocean). The surface and deep parts of the rest of the ocean are combined because the isotope composition of exported production is the same as the deep ocean. Since upwelling rates dictate productivity and the severity of the O2 drawdown and increase in δ15N, we analyse the export and δ15N associated with the 2 boxes representing upwelling zones.

We simulated upwelling rates between 0 and 0.25 Sv, which are typical values for one individual upwelling region. We used a model setup in which P is in a closed system to represent deep-water regions where P burial is relatively low (Fig. 4, panels A and C). To represent sites which are sufficiently shallow to allow significant burial of P, we subsequently modeled a system open to P (Fig. 4, panels B and D). In this setup, there is a P source due to weathering and a P sink through burial, consistent with our understanding of the natural P cycle78. The δ15N of the surface ocean is 5‰ higher than the export production, which reflects the fractionation associated with biological utilization of nitrate.

In both the closed- and open-P systems, increasing upwelling transport leads to increased export production (Fig. 4a, b). In the closed-P system, δ15N generally increases with increasing upwelling (Fig. 4c), since the enhanced export production leads to lower oxygen concentrations in the OMZ. In the open-P system, the increased export production leads to enhanced burial of organic matter, and a steady state is reached with a lower nutrient inventory. As a result, the oxygen transport and hence its concentration in the OMZ increases and δ15N decreases (Fig. 4d). This is because (i) the δ15N of DIN in both the deep ocean and the OMZ is determined by denitrification occurring in the OMZ, which makes the deep ocean entirely dependent on the OMZ in terms of its δ15N; (ii) almost all the exported N is supplied by upwelling from the deep ocean and almost all the upwelled N is exported. In the simulations for Fig. 4b, d, we assumed α=0.25, i.e., 25% of the exported organic P that is not remineralized either aerobically or through denitrification is buried. To investigate the sensitivity of the trend in Fig. 4d to model parameters, we varied the burial fraction α and the N:P ratio of burial. Furthermore, we included an increasing P burial efficiency with increasing oxygen concentration, a feedback that has been hypothesized to have played a role in Ocean Anoxic Events79. Although these changes affected δ15N quantitatively, the trend of decreasing δ15N with increasing upwelling remained. Thus, this qualitative result appears to depend solely on whether there is significant burial of organic matter. For shallow sites where organic matter burial is important, our model results suggest that increasing upwelling tends to increase δ15N. By contrast, our model results suggest that increasing upwelling in deep-sea regions tend to decrease δ15N.

Unsurprisingly, in the closed-P system, export production is determined by the P inventory (Fig. 5a). More specifically, export production increases with increasing P inventory up to about 2.3 Pmol (for comparison, the P inventory of the current ocean is ~3 Pmol) due to increasing P availability. Toward higher P inventories, the export production decreases again due to N limitation. In the open-P model setup, export production is essentially independent of the P input (Fig. 5b), as the higher input is compensated for by enhanced burial. There is a strong relationship between δ15N and export production in the closed-P setup (Fig. 5c) but not in the open-P setup (Fig. 5d). Although export is constant, δ15N decreases as a function of P input due to the increasing burial.

Overall, δ15N behaves rather differently in the open P setup compared to the closed P setup. In the closed P condition, δ15N is determined primarily by export production through its impact on oxygen concentrations in the OMZ and associated water-column denitrification. Export tends to decrease oxygen concentrations also in the open P setup. However, enhanced export leads to enhanced burial in this setup, both directly and as a result of decreased remineralization due to the lower oxygen contractions. The enhanced burial then decreases the nutrient inventory, which eventually leads to an increase in the oxygen concentrations in the OMZ. This in turn decreases water-column denitrification, which then leads to lower δ15N values. Furthermore, the N burial itself tends to decrease δ15N. Although primary producers preferentially take up the lighter N isotope, there is essentially no fractionation due to export in the model because almost all the N in the surface box is consumed. As a result, exported N has approximately the same isotopic composition as the ocean average, which is isotopically heavier than N lost to water-column denitrification. Hence, the more N is lost due to burial (compared to water-column denitrification), the lower the oceanic N inventory’s δ15N becomes. Figure 6 highlights the essential differences between the closed (A) and open (B) models, as well as the differences between δ15N in total OM and δ15N FB.

Methods
Materials
Sediments from a series of cores, described in the online supplement, deposited during the last 165 Myr were used to give bulk sediment N isotopes and C isotopes in organic matter. Data from different sites provide N isotope data representing different aspects of the ocean N cycle. DIN incorporated into planktonic biomass is buried and retained in sediments, providing the geological record of δ15N2,48,49. With high rates of burial, organic N deposited at the outer shelf-upper slope of wide margins capture the δ15N composition of deep nitrate42,49 and can create a record of deep water δ15N (δ15N DEEP)42,49,53. Because organisms residing in the photic zone may not acquire their N solely from the deep ocean, the geological record can differ from that of deep water DIN, and we refer to it as δ15N DISTAL. Our record of δ15N DISTAL is obtained from sediments deposited far from the margins.

We define the difference between δ15N DEEP and δ15N DISTAL as Δ15N. The value of Δ15N reflects mixing of deep water into the surface in distal areas of the ocean, approaching 0 when the ocean is well mixed. We also include planktonic foraminifera-bound nitrogen isotopes, δ15N FB, reported by Kast et al.59. δ15N DEEP and δ15N DISTAL should be similar, given the sample locations used for the δ15N record. However, analyses of particulate and bulk sediment δ15N and δ15N FB do not always match. For example, in the Sargasso Sea, δ15N FB reflects the δ15N of nitrate (δ15N NO3) in the upper thermocline92–94 (+3‰) which differs from deep water δ15N (~5‰)49,54,92–94. In the South China Sea, the range in δ15N of both foraminifera-bound and all bulk sediment for all South China Sea cores are similar (+4 to +8‰) over the last 40 kyrs, although the difference between δ15N BULK and δ15N FB for individual cores ranges from −2 to +3‰9558. A large component of terrestrial N in the bulk record was thought to be the cause of the discrepancy, which is possible given the lack of change in δ15N BULK not typically seen in other locations, e.g.95.

Organic C isotope (δ13C ORG) data from a core retrieved from the Exmouth Plateau off NW Australia74 supplement C isotope data reported previously70,72. Since δ13C ORG depends on the isotope composition of inorganic C, the value of δ13C DIC needs to be accounted for in order to address productivity. Hayes et al.71 defined the relationship εP-Δ2 = εTOC-ΔCARB, which can be calculated from our data: εP is the difference between δ13C CARB and δ13C TOC; and Δ2 is the isotope difference between dissolved CO2 and carbonate minerals72. The isotope composition of dissolved CO2 was estimated using temperature estimates from Song et al.96 and a δ13C value of pre-industrial atmospheric CO2 of -5‰, and equilibrium fractionation factors for hydration of CO2 and the formation of CaCO3 from Mook97. While the preindustrial value of CO2 has likely changed, we assume it is responsible for a small component of the total change in sedimentary δ13C. Δ2 accounts for secondary biological processes that cause primary production to differ from sedimentary organic C, such as trophic enrichment of 13C or its depletion by chemotrophy. For oxic systems, Δ2 is typically 1.5‰ and is not thought to have changed over Phanerozoic time71. Further description of this is given in Freeman and Hayes98 and Hayes et al.71.

Analytical methods
Samples were homogenized and analyzed by CF-IRMS (Eurovector 3000 coupled to a GV Isoprime 100). Samples were analyzed separately for δ15N and δ13Corg. Samples were not pretreated for δ15N SED, and a CO2 trap was used to increase sample throughput due to a potentially long CO2 bleed. For δ13C org, carbonate was removed with 25% HCl and the residue washed with deionized water. All samples were loaded in tin capsules. Nitrogen and organic C concentrations were determined from the area of the major ion (28 or 44) area and calibrated with acetanilide. Isotope standards (IAEA N-1 and N-3 for δ15N, NIST 22 and IAEA CH6 for δ13C99,100) were included in every run, separating 8 samples, with an in-house sediment standard included, which was core-top material from a metalliferous carbonate-rich sediment from the eastern low latitude Pacific.

We evaluated the potential for inputs of terrestrial N using C/N ORG and C accumulation rates using the following approach: Sediments deposited on the continental margins and perhaps in less than 3000 m water depth, as well, accumulate rapidly enough that OM quickly becomes isolated from the effects of oxic diagenesis on N isotopes that occurs on the seafloor42,101. Sediment in deep-water areas accumulates at about one-third the rate or less and has lower C ORG, and they are more susceptible to diagenesis and changes in δ15N SED101,102. While δ15N of slowly accumulating sediments can be higher than sediment-trap or deep-water NO3-, this offset is considered to be constant, so that temporal variations are not a function of changing preservation at one location but reflect changes in the water column processes that determine initial δ15N101.

Sedimentary δ15N data from either margin sites or open ocean carbonate-rich sites seamlessly splice to give a record with no breaks as data switch between different cores. This indicates that diagenetic changes were minimal, or data from each core was similarly affected, even though the sites are distant from each other, but importantly, water column conditions overlying each site were the same at any one point in time. At any one point in time, there may be as much as a 2‰ spread, which may be due to short (sub-millennial) variability which has been recorded throughout the late Pleistocene46. However, our intent is to address long-term changes where variations are larger, and this degree of variation is acceptable and consistent with other studies42,101.

The δ15N SED average of 6.7‰ for our Pleistocene to recent samples is the same as the global average reported by Tesdal et al.42, and about 1.5‰ higher than deep water nitrate. This offset may arise from a trophic increase in δ15N of exported N relative to primary production103, or diagenesis at the seafloor under oxic water42,101,104. In a series of experiments, Lehmann et al.104 suggested that even under oxic conditions, 14N-enriched bacterial biomass could restore δ15N to initial values following early increases in δ15N relative to settling organic matter, while under low O2 conditions, organic matter degradation led to minor, <1‰ increases in δ15N. Rather than explaining changes in δ15N as a reflection of microbial-induced change within sediments, we assume ocean nitrate δ15N changes over time.

A test was performed to determine whether margin sites distal to upwelling systems or major (i.e., Mississippi-size) rivers record deep-water δ15N due to onlapping of mid-depth water onto the shelf and the inner shelf is effective at trapping terrestrial material. Core-top sediment from a multicore, which causes minimal disturbance to the sediment surface, deployment across the shelf and slope at Cape Hatteras (South Atlantic Bight) was obtained (Dr Yair Rosenthal, Rutgers U) and analysed for total δ15N and organic δ13C using the methods as described above. Water depths ranged from 410 m to 2997 m. From each of the 6 sites, samples were taken at 0-1 cm and 1-2 cm intervals (Fig. 8, online data). The average δ15N for 0-1 cm was +5.24±0.34‰ and for 1-2 cm +5.21±0.34‰. The average δ13C ORG for 0-1 cm was −21.92±0.30‰ and for 1-2 cm −22.13±0.31‰. The average C/N TOTAL for 0-1 cm was 8.94±0.36‰ and for 1-2 cm 8.90±0.30‰. There is no change in δ15N with depth at the 95% confidence level, though there is a minimal drop in δ15N for the samples at 2000 m, which corresponds to the maximum depth of the Gulf Stream (Andres, 2021). Depth related changes in δ13C ORG are slightly more pronounced, and are slightly lower at the 1-2 cm depth than the top 1 cm. The only sample exhibiting a notable difference is the shallowest 1-2 cm sample, with δ13C ORG less than −22.5‰, which could indicate a minor terrestrial C contribution.

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_1": "The authors present new nitrogen and carbon isotope data from marine sediments spanning from 165Ma to the modern and use these data, along with a computational box model, to assess linkages between coastal upwelling, biological productivity, and P and N cycling. The results reveal previously undocumented feedbacks between physical oceanographic conditions and biogeochemical cycling that help explain patterns in the data that were previously not well understood. I have spent a lot of my time thinking about linkages between nitrogen isotopes, redox and productivity, and I am excited to see how these parameters can be linked to global oceanographic and orogenic processes. Many patterns in paleoenvironmental proxy data have always been difficult to explain by biogeochemistry alone, and so this linkage to physical and geological phenomena that operate on a global scale is refreshing. I could imagine that these findings will lead to new hypothesis about biogeochemical cycles even further back in time. I do, however, have some comments that should be taken into account to strengthen the conclusions. 1) Despite the extensive effort to accumulate such a large dataset, I worry that the data are not globally representative, given limitations of availability. According to Fig. 1, several of the sites appear to be located in possibly restricted basins. In the modern ocean, restricted basins can be distinct in d15N from open marine margins. The supplementary file needs a more detailed description of the major sampling sites to resolve this concern. 2) I’m not entirely convinced by the assumption that d15N along coastal margins captures deep marine nitrate. Tesdal et al. 2013 (Biogeosciences) show that the highest d15N values in sediments tend to coincide with upwelling zones. Here, denitrification rates are locally high, causing dissolved nitrate to be locally enriched in d15N (up to +12permil, in fact consistent with some of the model results in Fig. 3), but this is likely not representative of the global deep marine nitrate pool. It would help if modern data could be used to illustrate the overall concept of comparing marginal to gyre sediments as a proxy for nitrate advection. 3) It makes a significant difference in the model results whether P is treated as static or dynamic, but it is not made clear how these two scenarios can be gleaned from the paleo-record. When discussing the model results later on, more information (ideally quantitative) is needed for how the state of P can be constrained. Minor points: ll. 74-75: “We explore whether productivity followed P input to the surface ocean” – please explain on which timescales you are exploring this and by which means. This sentence actually seems to be out of place. Maybe delete it or move it further down where you transition to describing the aims of this study. l. 78: Measured N:P ratios in what? I assume in seawater, but it could also be in biomass. Please clarify in this instance. L. 121: Are δ15NGYRE and δ15NFB are similar when the foraminifera are obtained from gyre regions as well? Or do foraminifera from any part of the ocean match δ15NGYRE? Please clarify. l. 123: “in the upper thermocline” – this presumably depends on the species of foraminifera and their preferred habitat, or not? Fig 1 and associated text (ll. 144-153): The text states that both marginal and gyre sites are shown in Fig. 1; however, the figure’s legend lists margin sites, carbonate sites and foraminifera bound samples. Gyre samples are not mentioned in the legend. Please highlight those. Carbonate samples have not been mentioned in the text until now. It would be good to explain how those compare to the margin and gyre sites. Amendment: With further reading, I get the impression that the carbonate sites are the gyre sites. That confuses me, because a lot of carbonate precipitates in shallow waters. So some clarification is needed. Fig. 1 C-accumulation: Change the axis labels into a more readable notation instead of Excel’s version (e.g. 10^-4 instead of 1.E+04). Also, should the units not have a surface area in them? (e.g., g/kyr/m^2 or something like that?). If this is a global C burial rate, then the values seem very small. ll. 236-237: something is wrong with this sentence. Please rewrite. l. 361: demand for CO2 instead of demand for C? ll. 304-399: This review section seems a bit out of place. It made sense to have the modelling after the presentation of the data, but after reading about the model, I expected to see the model results linked to the data presented above. But that’s not the case. Instead, the manuscript continues with a more general review of other topics, and the linkage between the data and the model does not occur until l. 400 onwards. I found that confusing. Please consider reorganising the text. The review portion between ll. 304-399 could probably be shortened and perhaps move up or merged with later parts of the discussion. L. 423: How does one know if sediments play an important role in nutrient storage? This requires explanation. ll. 448-450: This sentence seems to contradict the previous one, according to which upwelling over deep water caused efficient remineralization of OM before settling on the seafloor (and thus presumably low OM accumulation). If that was the case, then the P inventory must not necessarily have been lower to explain low OM accumulation. l. 469: It would be good if quantitative temperature thresholds could be provided for N-fixers and for the inferred water conditions. Methods: State the reproducibility of samples and quality control standards Which software was used to set up the model? It would be ideal if the code could be shared in the appendix. Please share an Excel spreadsheet with all the new sedimentary N and C data. Eva Stüeken", "reviewer_2": "This study aims to analyse the relationship between the nitrogen and carbon cycles over the last 165 Myrs. It presents new nitrogen and carbon isotope data from a series of cores. It combines it with a global climate model to reconstruct ocean upwelling and a box model to characterise the dynamics between the nitrogen isotopes, upwelling and production. This study presents some interesting and potentially important results, including the role of organic matter burial, upwelling and iron on the nitrogen isotope values and the implications for long-term nitrogen and carbon cycles. However, the paper covers many aspects that need to be better connected, making it challenging to identify the key findings. The paper has the potential to have significant results for Nature Communications. It presents the first long-term record of nitrogen and carbon isotopes and combines modelling to examine the controlling processes. However, as previously mentioned, the manuscript requires polishing. Currently, it contains too many undefined terms, unclear parts, and disjointed sections, with little visibility on the main objectives and results. This makes it difficult to follow and could be problematic for Nature Communications, which aims at a non-expert audience. Therefore, I strongly recommend that the authors polish the manuscript before further consideration. I have provided some suggestions below on how it can be improved. A lot of the critical terms are not defined: N, P, fixed nitrogen … The same is true with key concepts (e.g., N:P ratio, P excess, the effect of upwelling on d15N, increase burial decrease 15N, ...). While these aspects needs more descriptions, the manuscript still lacks conciseness, with a lot of concepts introduced but clearly connected to the aim of the paper and the main results. I suggest that the authors to identify more what the key results are and to focus on the elements that directly support these results, making sure that they are well-connected. Also, it is important to justify the aim (why focusing on the last 165 Myrs) and approach (why using models and proxy together?). I also suggest that you make a diagram of the different d15N records (d15Ngyre, d15Nmargin, d15Nno3 ...) and the processes that affect them. There is a lot of references to geological periods, but without giving the dates, which is difficult to follow as most figures refer to dates and not time periods. Can you indicate dates each time you give a new time period? Similarly, you discuss the evolution in paleogeography, but do not show it. It would help to be able to see map with the different ocean basins through the geological time. I suggest that you show the climate model upwelling outputs at the same time (at least in the SM). One of the most interesting results is the effect of burial on d15N when upwelling increases. At the moment, you present it as a close-open system difference. It would be interesting to determine the level of OM burial required to change the trend in d15N (going from decrease to increase with increasing upwelling). Specific comments: The abstract needs polishing, as disjointed and unclear. Also it needs to clear state why this study is important (reporting N and C isotopes over the last 165 Myrs), and what the method is. It is also hard to tease apart what you find and what you speculate. Please make this more clear. Also, there seems to have a series of key results, that are not well connected. Replace “remote areas” and “NGyre” by “open ocean” Need to justify more the assumptions to represent open ocean versus coastal regions in the box model (close versus open system for P), Also what about river inputs? P24: Is 3.2 the modern ocean value? Please specify P26-27: Not clear P27-28: Is that one of your findings or a speculation. Which evidence do you provide for this? P29-28: Not clear P30: Say if the model has N cycling P31-32: If the paleogeography is key, you need to introduce this concept more strongly and describe how it has changed over the last 165 Mys. P37-39: This seems key, but not well introduced. Can you provide more elements to get to this conclusion? P39-40: No real discussion about iron in the abstract. Can you expand on this? P72-74: Not clear for non-experts - explain the concepts of global versus regional sources P78: Explain why N:P ratio is an important metrics for your study P78-79: That seems important. Can you explain it more? I am not sure I fully understand the relationship between change in climate, water formation, wind and the N:P ratio. P93-94: Can you give the bigger implication of this aim, relating it to the iron cycle, and the ultimate nutrient? P109-111: Can you comment on what the geological records might be under scenario of high or low N2 fixation/denitrification? P114-118: Not clear, too long sentence. Can you explain more? This seems crucial to your approach. P119: Delta15N not define P121: Replace from by “measured by Kast et al.” P121-124: Not clear why NFB Ngyre and NNO3 are different. Can you provide a schematic of the different processes, areas and isotropic signature to help? P127-128: Awkward P135-136: Not clear why you make this assumption as without burial you probably assume remineralisation of P. P145: Can you show the data and define SD? Fig.1: Cannot see NMarg, Ngyre clearly - is carbonate sites Ngyre? What about foram? Aslo, “very quick discussion” in the figure caption does not make sense. Beside, need to say more aboud d15N. Why AIR? Which data did you measure and what is the difference between marginal and carbonate site? Finally, can you show which one are the new data (at least in the supplemental material)? P148-150: Not clear. Please explain more P154-155: Except for the drop at about 140 Myrs. Can you comment on this? Fig P158-159: I cannot see that. The values at 42 look more or less 3, so the same and not lower P162: Not clear P162-163: Need to introduce this concept better P167-168: Show data Fig.2: Give the equation of delta15N (at least in the SM). Also, the scale for the changes in sea level is too large, hard to see P172: not clear P197: Need to justify why focusing on coastal upwelling (and ignore equatorial upwelling or deep water mixing) P228-229: The ocean interior circulation will also influence the O2 level and distribution in the ocean, which will affect dysoxic region and denitrification. P235-236: Not clear P237-238: Would be good to show the climate model surface upwelling to show the values regionally (in the SM) P239: Replace conserved by P cycle is in a closed system. Replace left-hand panels with A and C … P241-242: Is that always the case or an assumption in your model? P243: Say close and open P systems Fig.3: Why A, B show upwelling and C/D show Transport. Can you be consistent or explain the difference? Also, say how you estimate global coastal upwelling flux (sum or average). P254: Presumably in an open system, this would not be the case if river input from weathering is higher than upwelling. Can you comment on this? P257: Can you show that as this is not intuitive? Also, is it because of enhanced burial (and not just increase EP)? P277-278: Why do you get N limitation if there is N2 fixation to compensate the N supply? P290: Can you explain this concept? I thought primary producers would take the lighter isotopes so burial would tend to remove it from the system, resulting in an accumulation of heavy N in the water column. P292-293: another coupling that you don't mention is that remineralisation should depend on oxygen level, reduced with lower oxygen concentration. There should then be a feedback where increasing upwelling causes less remineralisation then more burial. P305-308: you keep referring to it, can you show maps of the evolution of continents/ocean configuration over time P324-325: say why P304: not clear what the main point of this section is. Can you expend? P330-340: Not clearly explained the interplay between sedimentary denitrification, sea level rise and nitrogen fixation and 15N P342-343: not clear P344-345: Need to link this part better with your previous results P358-368: This paragraph does not fit well here. You could move it with the early section detailing 13C record. P386-395: Link this comment better with your key results P399: what about the OM burial? This seems as important P401: say when + show on the map P477: limited by iron?", "reviewer_author_response": "Response to reviewer comments\nReviewer #1 (Remarks to the Author):\nThe authors present new nitrogen and carbon isotope data from marine sediments spanning from\n165Ma to the modern and use these data, along with a computational box model, to assess\nlinkages between coastal upwelling, biological productivity, and P and N cycling. The results reveal\npreviously undocumented feedbacks between physical oceanographic conditions and\nbiogeochemical cycling that help explain patterns in the data that were previously not well\nunderstood.\nI have spent a lot of my time thinking about linkages between nitrogen isotopes, redox and\nproductivity, and I am excited to see how these parameters can be linked to global oceanographic\nand orogenic processes. Many patterns in paleoenvironmental proxy data have always been\ndifficult to explain by biogeochemistry alone, and so this linkage to physical and geological\nphenomena that operate on a global scale is refreshing. I could imagine that these findings will\nlead to new hypothesis about biogeochemical cycles even further back in time.\nI do, however, have some comments that should be taken into account to strengthen the\nconclusions.\n1) Despite the extensive effort to accumulate such a large dataset, I worry that the data are not\nglobally representative, given limitations of availability. According to Fig. 1, several of the sites\nappear to be located in possibly restricted basins. In the modern ocean, restricted basins can be\ndistinct in d15N from open marine margins. The supplementary file needs a more detailed\ndescription of the major sampling sites to resolve this concern.\nWe acknowledge this is a concern studying marine sediments when much of the oceanic crust has\nbeen subducted, but the paleogeography indicates that the sites were not located in small shallow\nbasins, but large ones, even as Tethys opened.\n2) I’m not entirely convinced by the assumption that d15N along coastal margins captures deep\nmarine nitrate. Tesdal et al. 2013 (Biogeosciences) show that the highest d15N values in sediments\ntend to coincide with upwelling zones. Here, denitrification rates are locally high, causing dissolved\nnitrate to be locally enriched in d15N (up to +12permil, in fact consistent with some of the model\nresults in Fig. 3), but this is likely not representative of the global deep marine nitrate pool. It would\nhelp if modern data could be used to illustrate the overall concept of comparing marginal to gyre\nsediments as a proxy for nitrate advection.\nThe large OMZs of the ocean do occur at margins due to upwelling, but not every margin is an\nupwelling zone. The reviewer highlights that a better way of describing the nutrient processes of the\npre-industrial outer shelf is nutrient onlapping from the open ocean (see added reference Fennel,\n2010). Shelf sediments act as filters for nutrients associated with run-off, even in the industrial era,\nso that balancing the N budget today requires large onlapping fluxes of N. Due to the proximity of\nthe coast, the availability of P and micronutrients mean that N is the limiting nutrient and it will\nrecord the isotope composition on the fixed N. Sediment denitrification does not have associated\nisotope effect on the water column, and relatively rapid burial makes these sediments less prone to\ndiagenetic effects of oxidation near the sediment water interface. Tesdal et al., 2013 also provide a\nmap of surface sediments showing that away from the anoxic water columns of the major upwelling\nzones, margin sediments are between 4 and 6 per mil, the value of the deep ocean fixed N. I also\nprovide data in the Appendix for a transect of core top material at Cape Hatteras which shows that\nwhile organic C bears some trace of land-derived organic C, the N isotope data are invariant from\n400 to 3000m water depth. This is all more described in the text.\n3) It makes a significant difference in the model results whether P is treated as static or dynamic,\nbut it is not made clear how these two scenarios can be gleaned from the paleo-record. When\ndiscussing the model results later on, more information (ideally quantitative) is needed for how the\nstate of P can be constrained.\nAlthough there are time periods and ocean basins within which P is more conserved than in others,\nthere will always be some input and output of P. In other words, a dynamic P cycle is simply more\nrealistic than a static ocean P inventory, regardless of the paleo-record. The reason why we\nincluded simulations with the static P model is to illuminate causes and effects. In particular, the\nstatic P model includes only one key mechanism for changing ocean 𝛅15N: water-column\ndenitrification. Thus, the static-P simulations allowed us to focus on this mechanism in isolation.\nThe dynamic P model includes both water-column denitrification and burial as mechanisms for\nchanging ocean 𝛅15N. Hence, the reversed trend in the dynamic P model has to be caused by\nburial. We have included this explanation in the revised manuscript.\nMinor points:\nll. 74-75: “We explore whether productivity followed P input to the surface ocean” – please explain\non which timescales you are exploring this and by which means. This sentence actually seems to\nbe out of place. Maybe delete it or move it further down where you transition to describing the aims\nof this study.\nWe agree, so one sentence is deleted and the other modified.\nl. 78: Measured N:P ratios in what? I assume in seawater, but it could also be in biomass. Please\nclarify in this instance.\nThis has been clarified\nL. 121: Are δ15NGYRE and δ15NFB are similar when the foraminifera are obtained from gyre\nregions as well? Or do foraminifera from any part of the ocean match δ15NGYRE? Please clarify.\nYes, it is related to sampling locations, this has been clarified in the text.\nl. 123: “in the upper thermocline” – this presumably depends on the species of foraminifera and\ntheir preferred habitat, or not?\nTrue, but most foraminfera are located where there is food, so the ones studied feed at this depth.\nFig 1 and associated text (ll. 144-153): The text states that both marginal and gyre sites are shown\nin Fig. 1; however, the figure’s legend lists margin sites, carbonate sites and foraminifera bound\nsamples. Gyre samples are not mentioned in the legend. Please highlight those. Carbonate\nsamples have not been mentioned in the text until now. It would be good to explain how those\ncompare to the margin and gyre sites. Amendment: With further reading, I get the impression that\nthe carbonate sites are the gyre sites. That confuses me, because a lot of carbonate precipitates in\nshallow waters. So some clarification is needed.\nThe figure has been corrected. We renamed the carbonate sites gyre, but this figure legend did not\nget updated.\nFig. 1 C-accumulation: Change the axis labels into a more readable notation instead of Excel’s\nversion (e.g. 10^-4 instead of 1.E+04). Also, should the units not have a surface area in them? (e.g.,\ng/kyr/m^2 or something like that?). If this is a global C burial rate, then the values seem very small.\nThis figure has been replotted.\nll. 236-237: something is wrong with this sentence. Please rewrite.\nWe have removed this confusing sentence, which did not add much useful information.\nl. 361: demand for CO2 instead of demand for C?\nyes\nll. 304-399: This review section seems a bit out of place. It made sense to have the modelling after\nthe presentation of the data, but after reading about the model, I expected to see the model results\nlinked to the data presented above. But that’s not the case. Instead, the manuscript continues with\na more general review of other topics, and the linkage between the data and the model does not\noccur until l. 400 onwards. I found that confusing. Please consider reorganising the text. The review\nportion between ll. 304-399 could probably be shortened and perhaps move up or merged with\nlater parts of the discussion.\nWORKING ON IT\nL. 423: How does one know if sediments play an important role in nutrient storage? This requires\nexplanation.\nWe address this by the org-C, P and to a lesser extent, N accumulation rates. While a sink for N\nmaybe the atmosphere, the only sink for P is burial. The importance of burial is considered through\nthe use of 2 models.\nll. 448-450: This sentence seems to contradict the previous one, according to which upwelling over\ndeep water caused efficient remineralization of OM before settling on the seafloor (and thus\npresumably low OM accumulation). If that was the case, then the P inventory must not necessarily\nhave been lower to explain low OM accumulation.\nRemineralization depths for P and N are different you’re right, globally more efficient recycling – but\nwe talking about local effect so we cannot address inventory. We removed the sentence.\nl. 469: It would be good if quantitative temperature thresholds could be provided for N-fixers and\nfor the inferred water conditions.\nMethods: State the reproducibility of samples and quality control standards\nThis is in the appendix\nWhich software was used to set up the model? It would be ideal if the code could be shared in the\nappendix.\nThe model was coded in FORTRAN. We have now included the source code including instructions\nas online Supplementary Material. Furthermore, the source code is available through Omta’s\nGitHub page.\nPlease share an Excel spreadsheet with all the new sedimentary N and C data.\nThe file should have been transferred with the manuscript, it is submitted here.\nEva Stüeken\nReviewer #2 (Remarks to the Author):\nThis study aims to analyse the relationship between the nitrogen and carbon cycles over the last\nwith a global climate model to reconstruct ocean upwelling and a box model to characterise the\ndynamics between the nitrogen isotopes, upwelling and production. This study presents some\ninteresting and potentially important results, including the role of organic matter burial, upwelling\nand iron on the nitrogen isotope values and the implications for long-term nitrogen and carbon\ncycles. However, the paper covers many aspects that need to be better connected, making it\nchallenging to identify the key findings.\nThe paper has the potential to have significant results for Nature Communications. It presents the\nfirst long-term record of nitrogen and carbon isotopes and combines modelling to examine the\ncontrolling processes. However, as previously mentioned, the manuscript requires polishing.\nCurrently, it contains too many undefined terms, unclear parts, and disjointed sections, with little\nvisibility on the main objectives and results. This makes it difficult to follow and could be\nproblematic for Nature Communications, which aims at a non-expert audience. Therefore, I\nstrongly recommend that the authors polish the manuscript before further consideration. I have\nprovided some suggestions below on how it can be improved.\nA lot of the critical terms are not defined: N, P, fixed nitrogen … The same is true with key concepts\n(e.g.", "reviewer_n": "P ratio, P excess, the effect of upwelling on d15N, increase burial decrease 15N, ...). While\nthese aspects needs more descriptions, the manuscript still lacks conciseness, with a lot of\nconcepts introduced but clearly connected to the aim of the paper and the main results. I suggest\nthat the authors to identify more what the key results are and to focus on the elements that directly\nsupport these results, making sure that they are well-connected. Also, it is important to justify the\naim (why focusing on the last 165 Myrs) and approach (why using models and proxy together?).\nI also suggest that you make a diagram of the different d15N records (d15Ngyre, d15Nmargin,\nd15Nno3 ...) and the processes that affect them.\nThere is a lot of references to geological periods, but without giving the dates, which is difficult to\nfollow as most figures refer to dates and not time periods. Can you indicate dates each time you\ngive a new time period?\nWe use dates rather than periods in the text now, but the period is included with date in figure 2.\nSimilarly, you discuss the evolution in paleogeography, but do not show it. It would help to be able\nto see map with the different ocean basins through the geological time. I suggest that you show the\nclimate model upwelling outputs at the same time (at least in the SM).\nWe created a new Figure 1, which is more clear than the maps that had been part of fig 1 in the first\nversion.\nOne of the most interesting results is the effect of burial on d15N when upwelling increases. At the\nmoment, you present it as a close-open system difference. It would be interesting to determine the\nlevel of OM burial required to change the trend in d15N (going from decrease to increase with\nincreasing upwelling).\nYes indeed. I think for such an exercise to produce precise numbers, more cores would need to be\nincluded do to the heterogeneity of accumulation. However, rather than strictly accumulation rates\nthat switch between open and closed behaviour, it is the geometry of the ocean basins, where\nupwelling occurs in relation to where new N can be added (N-fixation). This is discussed.\nReviewer 2 makes important comments that we address as follows.\nAs with Reviewer 1’s comments the discussion is kept on point by unifying the model with the data\nplus paleoenvironment. We give a more thorough description of the terms based on a non-\nspecialist reader, and lay them out earlier in the paper.\n165Myr was chosen based on the availability of continuous core, and that this study follows from\nearlier ones (Katz et al., Falkowski et al) using virtually the same material from DSDP/ ODP/IODP\ncollections.\nDates and time periods are provided.\nThe world ocean basin evolution is shown in Fig 1., the evolution of the different basins with core\nlocations are provided in the supplement.\nSpecific comments:\nThe abstract needs polishing, as disjointed and unclear. Also it needs to clear state why this study\nis important (reporting N and C isotopes over the last 165 Myrs), and what the method is. It is also\nhard to tease apart what you find and what you speculate. Please make this more clear. Also, there\nseems to have a series of key results, that are not well connected.\nReplace “remote areas” and “NGyre” by “open ocean”\nDone\nNeed to justify more the assumptions to represent open ocean versus coastal regions in the box\nmodel (close versus open system for P), Also what about river inputs?\nThe open model just adds P and is agnostic as to where it originates from.\nP24: Is 3.2 the modern ocean value? Please specify\nIt’s the 165 My average, text has been changed\nP26-27: Not clear\nA sentence was added earlier, and this sentence has been clarified.\nP27-28: Is that one of your findings or a speculation. Which evidence do you provide for this?\nWe add a qualifier, but discuss more fully with evidence in the text.\nP29-28: Not clear\nAddressed\nP30: Say if the model has N cycling\nThere are 2 models, the one that determines the relative strength of upwelling is a physical model.\nP31-32: If the paleogeography is key, you need to introduce this concept more strongly and\ndescribe how it has changed over the last 165 Mys.\nThis is addressed in the text, not the abstract.\nP37-39: This seems key, but not well introduced. Can you provide more elements to get to this\nconclusion?\nDone\nP39-40: No real discussion about iron in the abstract. Can you expand on this?\nDone\nP72-74: Not clear for non-experts - explain the concepts of global versus regional sources\nThis is expanded.\nP78: Explain why N:P ratio is an important metrics for your study\nDone\nP78-79: That seems important. Can you explain it more? I am not sure I fully understand the\nrelationship between change in climate, water formation, wind and the N:P ratio.\nThe importance is included here, but the relationships are considered in depth shortly after this\npart.\nP93-94: Can you give the bigger implication of this aim, relating it to the iron cycle, and the ultimate\nnutrient?\nDone\nP109-111: Can you comment on what the geological records might be under scenario of high or low\nN2 fixation/denitrification?\nBy addressing the role of productivity and how N15 will respond if it is open or closed nutrient\nsystem, we can determine when nutrients were conserved (closed) or buried (open). For most of\nthe last 165 Myr, the latter provides a better model of the system.\nP114-118: Not clear, too long sentence. Can you explain more? This seems crucial to your\napproach.\nThis sentence has been rewritten.\nP119: Delta15N not define\nThis is now defined\nP121: Replace from by “measured by Kast et al.”\nReplaced\nP121-124: Not clear why NFB Ngyre and NNO3 are different. Can you provide a schematic of the\ndifferent processes, areas and isotropic signature to help?\nA new figure has been created.\nP127-128: Awkward\nRewritten\nP135-136: Not clear why you make this assumption as without burial you probably assume\nremineralisation of P.\nYes, and this is made explicit in the text.\nP145: Can you show the data and define SD?\nSD is standard deviation. The data is in an accompanying excel file.\nFig.1: Cannot see NMarg, Ngyre clearly - is carbonate sites Ngyre? What about foram? Aslo, “very\nquick discussion” in the figure caption does not make sense. Beside, need to say more aboud\nd15N. Why AIR? Which data did you measure and what is the difference between marginal and\ncarbonate site? Finally, can you show which one are the new data (at least in the supplemental\nmaterial)?\nNitrogen isotiopes are reported relative to the atmosphere which is commonly referred to as “AIR”.\nThe marg and gyre terms were renamed and are consistent now with the text. The caption has been\nrewritten, it seems to have notes to myself on it.\nP148-150: Not clear. Please explain more\nThis is clarified in the text\nP154-155: Except for the drop at about 140 Myrs. Can you comment on this?\nThere are two times when N15 was low, around 162 and again 140 Myr. These are discussed in the\ndiscussion section rather than the presentation of the data and model, but these drops are now\nnoted here.\nFig\nP158-159: I cannot see that. The values at 42 look more or less 3, so the same and not lower\nI agree, this is deleted.\nP162: Not clear\nRewritten.\nP162-163: Need to introduce this concept better\nWe rewrote the description of this concept P140-158\nP167-168: Show data\nIt is included on Figure 1.\nFig.2: Give the equation of delta15N (at least in the SM). Also, the scale for the changes in sea level\nis too large, hard to see\nWe have endeavoured to expand the sea level scale. The equation for delta notation is now written\nin the text P116-117\nP172: not clear\nExpanded.\nP197: Need to justify why focusing on coastal upwelling (and ignore equatorial upwelling or deep\nwater mixing)\nThe denitrification that affects the N isotope composition of the ocean occurs along areas of\nboundary upwelling which have greater water flux than equatorial upwelling. Consequently we\nfocus on these areas. However, the isotope model is not dependent on where denitrification\noccurs.\nP228-229: The ocean interior circulation will also influence the O level and distribution in the\n2\nocean, which will affect dysoxic region and denitrification.\nThat is true, we have corrected this.\nP235-236: Not clear\nWe have removed this confusing sentence, which did not add much useful information.\nP237-238: Would be good to show the climate model surface upwelling to show the values\nregionally (in the SM)\nP239: Replace conserved by P cycle is in a closed system. Replace left-hand panels with A and C …\nWe have incorporated this.\nP241-242: Is that always the case or an assumption in your model?\nThis is a model assumption that we made to approximate the real P cycle. That is, weathering is the\nmain source and burial is the main sink of oceanic P (Filippelli, 2002). We have included this\nmotivation in the revised manuscript.\nP243: Say close and open P systems\nWe have implemented this.\nFig.3: Why A, B show upwelling and C/D show Transport. Can you be consistent or explain the\ndifference? Also, say how you estimate global coastal upwelling flux (sum or average).\nThe horizontal axes in panels A, B, C, and D all indicate the same quantity, our apologies for the\nconfusion caused by the different labels. We have made the labels consistent. The coastal\nupwelling mass flux in the upper panel of Fig. 3 represents the globally spatially integrated\nupwelling transport, i.e., the sum. We have specified this in the caption of Fig. 3.\nP254: Presumably in an open system, this would not be the case if river input from weathering is\nhigher than upwelling. Can you comment on this?\nEven if upwelling accounts for only a minor fraction of the P input to the ocean surface, increasing\nupwelling will lead to increased export production (even if only marginally).\nP257: Can you show that as this is not intuitive? Also, is it because of enhanced burial (and not just\nincrease EP)?\nOnly burial can remove nutrients, EP does not.\nP277-278: Why do you get N limitation if there is N fixation to compensate the N supply?\nburial would tend to remove it from the system, resulting in an accumulation of heavy N in the\nwater column.\nAlthough primary producers preferentially take up the lighter N isotope, there is essentially no\nfractionation due to export in the model because almost all the N in the surface box is consumed.\nAs a result, exported N has approximately the same isotopic composition as the ocean average,\nwhich is isotopically heavier than N lost to water-column denitrification. Thus, the more N is lost\ndue to burial or sediment denitrification, the lighter the oceanic N inventory becomes. In contrast,\nthe more N is lost due to water-column denitrification, the heavier the oceanic N inventory\nbecomes. We have included this explanation in the revised manuscript.\nP292-293: another coupling that you don't mention is that remineralisation should depend on\noxygen level, reduced with lower oxygen concentration. There should then be a feedback where\nincreasing upwelling causes less remineralisation then more burial.\nEnhanced upwelling increases export, which decreases the oxygen concentration in the OMZ. This\nwill indeed enhance burial due to decreased remineralization. We have included a discussion of\nthis effect in the revised manuscript.\nP305-308: you keep referring to it, can you show maps of the evolution of continents/ocean\nconfiguration over time\nThese are shown in Figure 1, but maps specific to the core locations are now in the SM\nP324-325: say why\nP304: not clear what the main point of this section is. Can you expend?\nThis section had importance in describing the changing physical conditions, but we have shortened\nand moved up it into the initial description of the data.\nP330-340: Not clearly explained the interplay between sedimentary denitrification, sea level rise\nand nitrogen fixation and 15N\nP342-343: not clear\nP344-345: Need to link this part better with your previous results\nP358-368: This paragraph does not fit well here. You could move it with the early section detailing\n13C record.\nP386-395: Link this comment better with your key results\nThese comments are addressed by a significant rewrite and re-organization of the manuscript\nP399: what about the OM burial? This seems as important\nYes, there is a new figure that investigates the role of OM burial (Fig 6)\nP401: say when + show on the map\nThis addresses a part of the paper which has been deleted in an effort to focus the paper on\nmechanisms and not a history.\nP477: limited by iron?\nThe model does not include Fe, but it assumes that Fe, or any other micronutrient, cannot inhibit N-\nfixation. The role of Fe limitation on N dynamics is covered (but not deeply) at the end pf the paper,\nand clearly warrants further modeling, but is beyond the scope of this paper."}, "author_response": ""}, {"round": 2, "reviewer_comments": {"reviewer_1": "The authors have addressed many of my previous comments. I am still intrigued by the overall linkages that the paper uncovers. However, a few concerns or questions remain that need to be addressed: In my previous review, I asked whether the some of the selected sampling sites could have been restricted basins during the time of deposition. The authors replied that this was not the case, which is good. However, the response was not backed up by any references. I would like to see a new section of text in the supplementary material discussing the paleogeographic setting of the cores with a brief explanation of what is known about their connectivity to the open ocean. Adding such a section would significantly elevate the conclusions from this study and pre-empt potential doubt among future readers. I am also still confused by the discussion of oxygen-minimum zones (OMZ). The box model includes OMZs; however, those are seemingly not part of the interpretation of the sedimentary data. The authors’ response to my previous comment about d15N values in OMZs was that their sediment sites are not affected by OMZ effects. This creates a disconnect with the box model, where OMZs feature prominently. I would like to see more information about the sampling sites supporting the notion that OMZ processes (which create d15N values that are not globally representative, Tesdal et al. 2013) are not relevant to the sampling sites. This could also be added to the supplementary material. And/or perhaps the model needs to be adjusted to capture processes that are more relevant to the sampling sites instead. Note that this may also be a misunderstanding, which may be resolvable with a better integration of the box model into the manuscript (see detailed comment below). Line comments: Throughout: I suggest changing N-fixation to N2-fixation, by analogy to CO2-fixation. l. 57: delete the comma before ‘nitrogenase’ l. 83: change inorganics to inorganic l. 99: change ‘on10 Myr’ to ‘in 10 Myr’ l. 106: nutrient-rich l. 117: “Sediments underlying anoxic water are more efficient at retaining N” – a reference is needed at the end of this sentence. ll. 136-137: “The organisms that tend to dominate N-fixation fluxes occur in regions with warm sea surface temperatures” – a reference is needed here. l. 158: change ‘land based’ to ‘land-based’. However, ‘land-derived’ might fit better. l. 161: “indicated by a smaller deficit relative to P (Fennel, 2010).” – provide the N/P ratio of upwelling regions or outer shelf regions as a quantitative reference point. Also correct the format of the reference. ll. 161-163: As noted in the previous round of reviews, areas with active upwelling often have higher d15N values than the global average (Tesdal et al. 2013 Biogeosciences). So this statement here needs to be qualified with additional information. l. 170: change to ‘foraminifera-bound’ ll. 161-170: Please provide modern average values for d15N_DISTAL, d15N_DEEP, d15N_FB and D15N, so that the reader has a modern reference point in their head before reading about the results from the paleorecord. The modern data would provide important context for understanding these concepts. Figure 2: I recommend plotting this figure in color. In the first panel with the d15N data, indicate which samples are deep and which ones are distal. ll. 223-224: ‘indicates that vertical mixing increased’ l. 229: check the last sentence in this line. The structure is grammatically wrong. I think, the word ‘converge’ might need to be deleted. ll. 245-246: is there a unit of area (cm2 or m2) missing in the carbon burial units? l. 252: “Data for sea level and P accumulation rates (Fig. 2)” – this sentence is incomplete. What about those data? Please present them. Fig. 3: What does PI in the figure legend mean? Please provide more information in the figure caption about what each of these models represent. Fig. 3: It seems that the lines in the plot don’t actually end at 0 Ma but instead around 5 Ma. What are the modern values that correspond to 0 Ma? Can those be indicated in the plot? ll. 290-366: This section is not well connected to the previous part of the paper. Figure 4 talks about OMZ versus DEEP sites, although the preceding discussion talked about DISTAL versus DEEP. The d15N behavior of OMZs (which are enriched in d15N compared to the deep ocean, see Tesdal et al. 2013), was not previously mentioned. Throughout this section here (ll. 290-366) it is therefore unclear how the box model is going to be linked to the paleorecord. Please provide a better introduction to this section and state which open questions about the paleodata are going to be addressed with this box model. Explain to the reader how the OMZ and DEEP sites modelled here compare to the DISTAL and DEEP sites inferred from the sedimentary record. l. 371: fall instead of falls. (the word ‘data’ is plural) l. 382: “there are regions where excess P occurs in surface water, suggesting otherwise” – please provide a reference. l. 438: indicate l. 464: d15N_MARG appears here for the first time. Which record is used to reconstruct this, and what does it mean? How does it compare to DISTAL, DEEP and OMZ, which were used earlier? l. 512: Please add a conclusion section that summarizes they key points from this study. The models and the paleodata each reveal new insights and relationships, and it would be nice to see those summarized here, perhaps along with an outlook to broader implications. Eva Stüeken (Remarks on code availability) I'm not able to open the file, because I'm not familiar with FORTRAN. But I appreciate that the code is now available and will be useable by others in the future.", "reviewer_2": "I have reviewed the revised manuscript, and find it has been significantly improved, addressing most of my previous comments. I now recommend it for publication. In particular, the addition of Figures 1 and 6 is effective in illustrating the evolution of paleogeography and conceptualising your systems. The discussion is also clearer and better structured, highlighting key results and providing key context, especially towards the role of iron limitation. I have a few final comments on the reviewed version: • Please define N and P in the abstract and intro. • L252: The sentence is incomplete; please revise. • L379: Typo - “increase” should be corrected to “increase”. • L444: The meaning is unclear; please clarify. Lastly, I apologise for the delay in my review. The response to my comments lacked sufficient detail, in particular in specifying the lines where revisions were made. For future reference, I strongly recommend providing a more detailed response, as this would greatly help reviewers with busy schedule like mine :)", "reviewer_3": "Review for Godfrey et al. Stability of the marine nitrogen cycle over the past 165 million years. Godfrey presented several new and published d15N (FB-d15N) and d13Corg records for the 165 million years. Using marginal d15N record to infer deep nitrate d15N changes, and open ocean d15N record as upper ocean nitrate d15N, they argue that the difference between the two is driven by vertical mixing, which is in turn, as they model exercise show, controled by continental configuration. I appreciate their effort to generate this long dataset and the conduct of the modeling exercise to put these data into understanding. However, I disagree with a few key concepts used in this paper, and I also find that this paper is structually challenging to follow. 1. The mean ocean nitrate d15N (or the deep ocean nitrate d15N) is determined by the ratio of N losses occurring in the sediments vs. in the water column, not by the processes occurring in the water column alone. Continental configuration should not only change upwelling, but perhaps more, to the N losses occurring in shelf sediments. In many places in this paper prior to discussion, the authors emphasized on the influence of water column denitrification on nitrate d15N, which is misleading. 2. I do not agree that d15N measured at the outer shelf equals deep nitrate. In response to the first reviewer, the authors explained that river influence is minimized by processes occurring in the inner shelf, and denitrification is not uniformly occurring. But even if these are the case, the shelf upwelling hardly works like a tunnel where deep nitrate is being directly upwelled and completely assimilated. If we look at modern ocean, places where strong upwelling occurs typically have unutilized nutrient left at the surface, so the degree of biological consumption drives most of the d15N changes over time. In other more oligotrophic places, marginal upwelling is still heavily influenced by upper ocean processes, such as nitrification, N2 fixation, denitrification. And I also think the d15N values of these records speak to a different story. The average d15Ndeep (values measure at the margins) is 3.2, similar to and lower than modern deep nitrate d15N (5.5). If the marginal d15N does reflect lower deep ocean nitrate d15N, then it calls for less water column denitrification comparing to benthic denitrification. But the distal d15N are much higher, averaged around 7 permil, which in the present ocean, can be only explained by water column denitrification. 3. Statistical treatment of these records. How did the authors treat these multiple records with different proxies (foram bound or bulk?), locations, temporal resolutions? The authors state that FB-d15N is higher than bulk because FB-d15N neglects N2 fixation (I disagree, see my comments below), but when calculating the differences among these records, did the authors simply take the average or pick one proxy over the other? Line 77. Clarify the processes that cause N to be lost preferentially over P in the marginal sea. Do the authors mean redfield uptake of N and P and burial in sediments, or denitrification in shallow sediments? Line 87-89. The average d15N of ocean nitrate is determined by the ratio of N losses through water column or sedimentary denitrification. It is not determined by the upwelled nitrate along the margins. I do not know what the authors mean here. the marginal upwelling might affect the mean d15N value if upwelling drives sedimentary denitrification, and assuming that water column denitrification remains constant through time. But the statement here made by the authors is wrong. Line 161-163. Nitrate d15N in the outer shelf should not equal deep ocean even if river influence has been removed in the mid and inner shelf. Line 172-174. Foram-bound d15N may also be influenced by newly fixed N, when the fixed N goes into the food web. Overall FB-d15N shows strong correlation with thermocline nitrate, because insitu N2 fixation is a small flux comparing to vertical supplies. It is the same as sinking PON. The d15N of sinking PON, and thus buried bulk organic N in the sediments, should reflect the d15N of all the new sources of N to the euphotic zone. But comparing d15N of bulk sinking PN with these new sources, there is a stronger influence from vertical supplies, and not from insitu N2 fixation. So I would not say foram-bound d15N and bulk d15N differ in this. Line 255, “where d15N of the ocean is defined”. I guess the authors mean the deep ocean nitrate d15N. However, the deep ocean nitrate d15N is defined by the ratio between N loss occurring in the sediments vs. in the water column, not by the processes in the water column alone. This is a confusing sentence. Figure 1. I think the locations of 1263 and 1209 are wrong. Line 226. D15NFB captures the d15N signature of nitrate below the mixed layer, but tends to neglect contributions from N fixation. See my previous comments. I do not think this is the case, at least there is no evidence for this statement. The authors use d15Ndistal and d15Ngyre to refer to the same thing, and use d15Nmargin and d15Ndeep to refer to the same thing, but need a statement at least when introducing the terms. Line 353. The lighter the oceanic N inventory becomes? I guess the authors mean the lighter the oceanic d15N becomes."}, "author_response": ""}]

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