Benthic phosphorus cycling in the northern Benguela upwelling system: excess P supply and altered pelagic nutrient stoichiometry

Kraal, Peter; Ungerhofer, Kristin A.; Rush, Darci; Reichart, Gert-Jan

doi:https://doi.org/10.5194/egusphere-2025-1870

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https://doi.org/10.5194/egusphere-2025-1870

Preprints

08 May 2025

| 08 May 2025

Benthic phosphorus cycling in the northern Benguela upwelling system: excess P supply and altered pelagic nutrient stoichiometry

Peter Kraal, Kristin A. Ungerhofer, Darci Rush, and Gert-Jan Reichart

Abstract. The northern Benguela upwelling system (NBUS) off Namibia is one of the most productive marine regions globally, with intense biogeochemical cycling and burial of essential elements such as carbon, nitrogen and phosphorus. Element cycling is strongly impacted by temporally and spatially variable degrees of oxygen depletion, both in the water column and the sediment; a perennial oxygen minimum zone (OMZ; minimum O₂ ~ 50 µmol L^-1) impinges on the slope while the shelf is seasonally oxygen-depleted and even euxinic (i.e. free sulphide in the water column). Areas such as the NBUS are not only significant in regional and global marine element cycles and budgets but can also help predict the impact of globally increasing eutrophication and deoxygenation. Here, we combine biogeochemical water-column and sediment data to explore the (de)coupling of pelagic and benthic nitrogen and phosphorus cycling as function of depositional conditions, particularly deep-water redox. We show major shifts in N:P stoichiometry in deep waters as a result of pelagic nutrient-N (NO₃^-, NH₄⁺) loss as N₂ and supply of excess P from the sediment into the bottom water. Notably, benthic P supply contributes strongly to the pelagic N deficit (PO₄^3-*16 − ∑(NO₃^-, NO₂^-, NH₄⁺)), which is commonly considered to reflect only the strength of anaerobic N loss. Our results further reflect strong differences in benthic nutrient cycling between depositional environments. The seasonally anoxic shelf hosts organic-rich, strongly reducing sediments with large pools of labile P and high effluxes of DIC and total alkalinity, NH₄⁺, PO₄^3- and HS^-. Chemical analysis indicates that a large proportion of the highly reactive sedimentary P pool consists of (i) P supplied in fish debris rather than marine algal biomass and/or (ii) P accumulated intracellularly by sulphide-oxidizing bacteria (SOB). These SOB modulate benthic phosphate and sulphide fluxes, while iron (Fe) redox cycling plays a minor role as the shelf sediments are depleted in reactive ferric iron phases. In contrast to the shelf, slope sediments including those underlying the OMZ are much less organic-rich and show patterns of coupled N and P cycling, the latter coupled to Fe redox cycling. Overall, we show how the distinct environmental conditions on the highly productive and seasonally anoxic shelf drive the decoupling of pelagic and benthic N and P cycles. This results in strongly altered nutrient dynamics and stoichiometry compared to oxygenated marine systems. Such perturbations are then likely to occur at wider (global) scale in the ocean under conditions of intense oxygen depletion either in the geological past or in the anthropogenic future.

Received: 21 Apr 2025 – Discussion started: 08 May 2025

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Peter Kraal, Kristin A. Ungerhofer, Darci Rush, and Gert-Jan Reichart

Status: final response (author comments only)

RC1:
'Comment on egusphere-2025-1870', Anonymous Referee #1, 12 Jun 2025

This is a rich study that explores how oxygen depletion shapes carbon, nitrogen, and phosphorus cycling in the northern Benguela Upwelling System (NBUS). What stands out most is the way the authors weave together multiple strands of evidence, from sediment chemistry to porewater gradients, incubation fluxes, and water-column data to build a cohesive picture of benthic–pelagic interactions across a redox gradient. It’s a relevant contribution, especially given the growing interest in how ocean deoxygenation might reshape nutrient stoichiometry and microbial dynamics in coastal and upwelling systems. One of the strengths of this paper lies in how it brings to light less commonly discussed phosphorus pools, like those tied to fish debris and sulphur-oxidizing bacteria — and connects them to shifts in N:P ratios that challenge some classical Redfield-based thinking.
That said, I’d encourage a bit more caution in how some findings are framed. The N deficit is widely used as a shorthand for identifying deviations from Redfield ratios, but it’s not necessarily meant to trace mechanistic pathways like denitrification or anammox without further support. The data here don’t invalidate the metric, but they offer a reminder that benthic P inputs can skew its interpretation. Reframing this not as a correction of the metric, but as a call for more nuanced use under certain benthic conditions, would make the authors message more balanced to a broader readership.
I also think the paper would benefit from more explicit acknowledgment of temporal variability. While the authors do a good job highlighting spatial differences across the shelf and slope, it’s worth underscoring that processes like P release, redox fluctuations, or fish debris deposition can vary a lot seasonally or even episodically. Since the dataset comes from a single cruise, it’s important not to overgeneralize to long-term OMZ dynamics.A brief acknowledgement of this limitation, coupled with suggestions for future time-series studies, would guard against over-generalisation.
Given the extreme, near-permanent hypoxia/euxinia on the Namibian shelf, not deeply addressing bioturbation is reasonable. On the upper slope, some residual fauna and irrigation likely occur; the paper could have acknowledged that. So while bioturbation isn’t underestimated in the sense of missing a major driver, a statement such as “macro-faunal bioturbation is assumed negligible on the hypoxic shelf and minimal on the upper slope …” could close that narrative gap.
A concern is the apparent mismatch between diffusive flux estimates calculated with Fick’s law and the considerably larger whole-core incubation fluxes, especially for DIC, which at two sites exceed one mole per square meter per day. Do authors think that it raises the possibility of incubation artefacts (e.g. over-stirring, boundary-layer collapse) or uncertainties in porosity? Perhaps providing core geometry, stirring rates, and an uncertainty analysis (for example, how a ±10 % error in porosity or gradient might shift the calculated fluxes) would bolster confidence in the flux comparison.
The causal link between SOB activity and enhanced P release supports much of the paper’s narrative, yet the evidence remains inferential. The authors should note explicitly that the SOB mechanism remains a hypothesis to be tested with future cell counts, FISH, metagenomics or poly-P assays.
Overall, I think this is a strong and well-argued paper. My suggestions are meant to sharpen some of the framing. I’ve included below a list of more specific and technical comments that I hope will be useful as the authors move toward a final revision.
Introduction
Line 25: I suggest authors to specify which chemical analysis in “Chemical analysis indicates that a large proportion of the highly reactive sedimentary P pool consists of (i) P supplied in fish debris rather than marine algal biomass and/or (ii) P accumulated intracellularly by sulphide-oxidizing bacteria (SOB).”, to make the statement more robust and with stronger geochemical constraints.
Line 39: I recommend authors to change “...oxygen depletion boosts anaerobic N transformation processes in the water column and sediment that represent a net sink for N…” to “…oxygen depletion enhances anaerobic nitrogen transformation processes in the water column and sediments, which represent a net sink for nitrogen…”. The change of “that” to “which” works better for a non-restrictive clause.
Line 53: I suggest authors to change “relevant to study” to “"relevant for studying" or "suitable for study"
Line 87: add the date to Kuster-Heins et al.
Line 105: substitute “The” by “the”
Line 108: the sentence with “productivity” and “and oxygen depletion” is separated by Figure 1 caption.
Line 128: I suggest authors to substitute “holding with” by “equipped with”
Line 130: I suggest substituting: "Immediately after the CTD/rosette with sampling bottles was back on deck..." to "Immediately after recovery of the CTD rosette..."
Line 132 and 143: I suggest substituting “filtered over a 0.8/0.2 µm syringe filter” with “"filtered through a 0.8/0.2 µm Pall Acropak syringe”
Line 133: I suggest substituting “After sampling all bottles..." by “"Once all bottles had been sampled..."
Line 137: The sentence “Samples for HPO4 2- and Si were acidified to pH ~1” seems a bit vague. I suggest authors to changed to something like "Samples for HPO₄²⁻ and Si analysis were acidified to ~pH 1 before storage."
Line 145: The phrasing “digestion of (particulate) organic compound” could be improved to something as “"preceded by digestion of particulate organic matter"
Chapter 2.2: I am missing references to procedural blanks, analytical replicates performed and/or certified reference materials (CRMs) analysis. Could flux calculations propagate ±10 % in pore-water gradients and flip flux direction for NO₃⁻ at low concentrations?
Line 151: I suggest authors to substitute “were otherwise undisturbed” to ““and showed no visible signs of disturbance”
Line 154: I recommend authors to substitute “Profiles were aborted when O₂ reached 0.” To “Profiling was stopped once O₂ concentrations approached zero.”, to avoid colloquial language.
Line 167: “sea salt from seawater” reads redundant. I recommend authors change it to “sea salt content” or other.
Line 247: You write that OMZ stations are “better oxygenated (65 µmol L⁻¹)” than shelf stations (3–10 µmol L⁻¹), which is accurate but might confuse readers, since OMZ is normally low-O₂ by definition. I suggest clarify that the OMZ here refers to intermediate depths within the perennial OMZ, but bottom waters were more oxygenated than on the shallow shelf.
Line 249: I suggest authors to better precise the sentence “that were the lowest of the investigated transect”, perhaps changing it to “surface sediment with the lowest TOC contents”
Line 250: add “the” before “lowest”
Line 263: I recommend authors to substitute “(much)” to “considerably” or “significantly”, if statistically based.
Line 278: There is a mismatching parenthesis here.
Line 280: “Fetot/Stot » should be consistent with the previous notation.
Line 281: “PR-Fe” (poorly reactive Fe) is used appropriately but without defining it clearly until later. Perhaps include a brief clarification upfront, e.g., “...dominated by poorly reactive (PR-Fe; e.g., silicate-bound or crystalline) iron...”
Libe 335: “We first note that DOP calculated as total dissolved P minus P…” This sentence equals to: ““...calculated as the difference between total dissolved P and HPO₄²⁻”?
Line 336: You rightly flag that DOP often results in negative values. Could there be error sources such as analytical uncertainty in total dissolved P, precipitation or adsorption of HPO₄²⁻ during sampling or the presence of colloidal P not fully removed by filtration? Maybe briefly acknowledge these limitations to reinforce confidence in your interpretation.
Line 354: by “scaled” you mean “correlated “?
Line 436: There is a grammatical error after “10 cm of” (incomplete phrase).
Line 464: Here, the logical connections between observation and interpretations are implied but not explicitly stated. I suggest authors change “In an alternative process of sink switching, this additional accumulation of pore-water HPO₄²⁻ then drives authigenic precipitation…” for “This accumulation of pore-water HPO₄²⁻ may instead promote authigenic precipitation…”
Line 478> You acknowledge heterogeneity in P content due to patchy fish debris, which raises an important issue: the spatial variability in fish bone deposition is poorly constrained and a source of bias in P budgets. Could be interesting to mention that sediment imaging, bone counts or other techniches which might help constrain this in the future.
Line 479: Here it should be “heterogeneous”, as well as in line 620.
Line 503: If exploratory data (NMR or genetic results) are used to support an interpretation, I suggest they are shown.
Line 528: I suggest authors review the text for opportunities to remove redundant modifiers such as "relatively high," "very low," "generally small" where precise values are already provided.
Line 532: remove the repeated "st"
Line 584: However, it would help the reader if the authors could briefly clarify how they distinguish this signal from alternative processes such as nitrate diffusion from overlying water or residual nitrate from incomplete denitrification. Even a short sentence acknowledging these possibilities.
Line 704: The authors write that “This calls into question how accurate the term ‘N deficit’ is in the NBUS and perhaps more broadly in upwelling regions…” While this is provocative and potentially important, maybe it lacks sufficient framing. The N deficit is commonly defined as a diagnostic proxy, not a mechanistic metric. It reflects deviations from Redfield stoichiometry but does not inherently imply anaerobic N loss unless this is clearly demonstrated through isotopic, process-rate, or mass balance data. I recommend you clearly distinguish between "apparent N deficit" (i.e., deviation from expected N:P) and the mechanistic N loss processes (denitrification, anammox) often inferred from it. Avoid suggesting the metric is "inaccurate"; rather, emphasize that its interpretation requires careful evaluation of benthic P sources.
Linbe 678: Authors assume that 2 umol/L would have been the concentration of HPO42- in bottom waters at stations 5, 6 and 10 as well in the hypothetical absence of the sediment-derived bottom-water HPO4 2- enrichment. I suggest them to better justify this or acknowledge more explicitly that the value is a conservative estimate to illustrate potential P-driven contribution to the N deficit, not a precise background level.

Citation: https://doi.org/10.5194/egusphere-2025-1870-RC1
- AC2:
  'Reply on RC1', Peter Kraal, 22 Oct 2025
  Firstly, we thank the reviewer for their careful and supportive review. The reviewer raises various important aspects that require improvement in the paper, which we will incorporate in our revision:
  With regard to "more explicit acknowledgment of temporal variability": Indeed, our sampling was performed during the period of seasonal anoxia on the shelf, during which benthic exchange is affected by extreme but transient bottom-water conditions. We will better consider (i) the sampling season with regard to depositional conditions (particularly important in light of seasonal changes in benthic microbial communities) and (ii) the potential episodic nature of deposition of OM and other P pools, specifically in Discussion sections 4.2-4.4.
  
  With regard to the impact of bioturbation/irrigation: Faunal activity on the slope, where food is abundant and O2 is present, could play a role in shaping sediment records and possibly benthic exchange. During core slicing, a few worms were observed in sediments from the deeper stations in and below the OMZ. An in-depth investigation on the role of fauna is beyond the scope of this study, but we will take it into consideration when interpreting the fluxes at stations outside the anoxic shelf, possible using calculated diffusive fluxes and measured whole-core fluxes.
  
  With regard to the mismatch between measured and calculated diffusive benthic fluxes: We are used to (large) differences between measured at calculated fluxes, because measurement resolution of discrete samples used for diffusive flux calculation is usually inadequate to capture processes in the uppermost sediment (here, first sample represents 0 – 5 mm sediment depth). O₂ and DIN species compare reasonably well and errors for replicate incubations are not excessive, which to us suggests there are no major incubation artefacts. The mismatch is most apparent for DIC and HPO42-. For HPO42-, we believe this reflects P retention in the uppermost sediment. For DIC, we triple-checked measurements and calculations and we struggle to explain the extreme fluxes at station 6 and 7, so we flag these but keep the data in because the concentration increases are reproducible between cores. We will include more information about the incubation setup (round 10-cm diameter cores were used; stir rate was about 60 rpm with a small stir bar and no visual sediment surface perturbation occurred in this highly unconsolidated and easily resuspended material). Because the calculated flux scales linearly with parameters such as porosity and dC/dz, errors as described by the reviewer will not affect the outcomes in a way that might explain the large differences in calculated and measured fluxes for some species.
  
  With regard to the limited evidence for SOB: The abundance of SOB and associated P phases can indeed be further investigated with the proposed methods; such additional analyses unfortunately lay beyond the scope of this work, which already incorporates elaborate chemical analysis of sediments and bottom waters. We did attempt to identify poly-P with 31P-NMR as described, but to no avail. We visually observed abundant SOB in the surface sediments at shelf stations as described in the SI, together with the chemical data we therefore are of the opinion that it is reasonable to argue for an important role for SOB, despite lacking more advanced microbiological analyses. We will take care to highlight that the role of SOB remains a hypothesis with the available data.
  
  In response to the more specific and technical comments: We have carefully considered all these suggested edits and will incorporate them in the manuscript. Substantive points of a non-technical nature that we will address in the revised discussion section: consider the impact of spatially variable fish bone deposition on P budgets calculated from sediment analysis; better frame the role of P in the calculated N deficit by distinguishing between 'apparent' N deficit (deviation from Redfield N:P) and actual anaerobic N loss processes.
  
  Citation: https://doi.org/10.5194/egusphere-2025-1870-AC2
CC1:
'Comment on egusphere-2025-1870', Gwénaëlle Chaillou, 02 Oct 2025

This study investigates nitrogen (N) and phosphorus (P) cycling in the northern Benguela upwelling system (NBUS) off Namibia, one of the world’s most productive coastal upwelling regions with a large OMZ. The research combines water-column measurements, pore-water chemistry, and sediment analyses across a redox gradient, from the highly oxygen-depleted continental shelf to oxygenated slope waters. The findings challenge the classical view that oxygen depletion enhances pelagic “N deficit”. Instead, the authors proposed that alternative P cycling mechanisms (fish debris burial, SOB activity, Ca–P mineral formation) can sustain high sedimentary P effluxes. This alters how we interpret C/N/P ratios and nutrient feedback under ocean deoxygenation, both in the past and in the context of ongoing climate change.
The paper is very dense, containing a large amount of data from various sources, and offers a deep exploration of numerous major and alternative diagenetic mechanisms within the natural redox gradient imposed by the OMZ. However, the novelty could be more clearly defined. Currently, the paper is difficult to read, despite its relevance to the topic and solid conclusions. It would benefit from significant revisions and extensive methodological clarifications before publication. Additionally, a more explicit statement of its novelty is needed in both the abstract and the introduction. Here are my main concerns.
My initial concern is about the clarity and relevance of specific content. Some parts of the introduction, methods, and discussion are too long, repetitive, or not directly related to the study’s objectives. They need to be condensed. Certain general statements, like those connecting deoxygenation and eutrophication, require more nuance or clarification. I suggest presenting the study's objectives more clearly. In my view, the introduction is overly extensive and does not align well with the methods and discussion that follow. For example, explaining the roles of Fe and S in the P cycle before presenting the analyses might help justify methodological choices.
My second concern relates to the analytical methods. I have several requests for technical details, including the instruments used, analytical errors, detection limits, and calibration protocols (e.g., O₂ sensors, DIC, HS⁻). Redox conditions and oxygen concentrations are central to this paper. However, there is no information on the calibration or the measurements of dissolved oxygen, for example. The structure of the methods section should be revised to help the reader follow the flow of information. The sampling section needs to be separated from analytical methods and calculations for clarity. Missing references should be added to support the protocols (e.g., Viollier 2000, Cline 1969, etc.).
Finally, the discussion is quite lengthy and could be shortened, especially sections 4.2 and 4.3, which contain notable redundancy. Sections 4.1 and 4.4 are well aligned with the objectives (and the abstract), but the other two, despite their interest, could be condensed and clarified. The role of macrofaunal activities should be introduced in the methods section and discussed to clarify the difference between total and diffusive fluxes. Bioturbation could also be used to explain the particulate profiles. On the other hand, redox conditions on the shelf are transient in space and time, and the presence of SOB could indicate the time since the last redox change (or oxic / anoxic transition).
My specific comments are in the document.

Citation: https://doi.org/10.5194/egusphere-2025-1870-CC1
- EC1:
  'Reply on CC1', Edouard Metzger, 14 Oct 2025
  
  Dear authors,
  Gwen Chaillou posted a comment as a referee for the manuscript. Please, take her comments and comments from anonymous referee #1 to make replies in order to close the discussion round ands start the revision stage of the edition processing.
  sorry for the long delay and thank you for your pacience.
  best regards,
  edouard metzger
  
  Citation: https://doi.org/10.5194/egusphere-2025-1870-EC1
  - AC1: 'Reply on EC1', Peter Kraal, 15 Oct 2025
    
    We thank the reviewers and the editor and will compose and post final responses as soon as possible.
    
    Citation: https://doi.org/10.5194/egusphere-2025-1870-AC1
- AC3:
  'Reply on CC1', Peter Kraal, 22 Oct 2025
  We thank the reviewer for their careful and constructive review of our manuscript. We have carefully read and considered the concerns:
  With regard to the clarity and relevance: we will incorporate the feedback of the reviewer and make sure to condense the various sections of the manuscript, particularly discussion section 4.2 and 4.3. For the latter sections, we will make sure the topics are properly aligned with more clearly defined research objectives in the abstract and introduction. Additionally, parts of the methodology and results can be moved to the Supplementary Information.
  
  Regarding the analytical methods: we will revise the manuscript to include instrument descriptions, analytical errors, detection limits and calibration protocols where appropriate. For clarity of the experimental approach, we will restructure the Materials and Methods section for a clear flow of information.
  
  Regarding the roles of fauna and SOB: it’s nice to see comments from reviewer 1 about these aspects of the manuscript echoed by reviewer 2, which underscores the importance of better addressing these in the revised manuscript. We will consider differences between measured and calculated diffusive fluxes to infer the role of fauna in benthic exchange. With regard to SOB, we will better place their presence/absence in the context of the temporally highly variable redox conditions on the Namibian shelf.
  
  Regarding the novelty of the work: reviewer 2 mentions that a link between P release and redox oscillations in itself is not particularly novel. We agree with this, and with the suggestion of the reviewer that the (quantitative) insight into sedimentary P-cycling processes presented in our manuscript should be better highlighted.
  
  With regard to the specific comments in the annotated manuscript uploaded by reviewer 2: we have carefully considered the points and will incorporate them into our revised manuscript. Substantive points not mentioned above that we will address: (1) we will condense the introduction and align it better with the rest of the manuscript; (2) we will include a transect of the shelf OMZ and the sampling stations (possibly part of the figure will be moved to SI); (4) we will improve the discussion of the benthic DIC and TAlk fluxes in relation to processes such as aerobic respiration (source of DIC but not Alk) and CaCO3 dissolution (source of DIC and TAlk in 1:2 ratio).
  
  Citation: https://doi.org/10.5194/egusphere-2025-1870-AC3

Peter Kraal, Kristin A. Ungerhofer, Darci Rush, and Gert-Jan Reichart

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https://doi.org/10.5194/egusphere-2025-1870-supplement

Peter Kraal, Kristin A. Ungerhofer, Darci Rush, and Gert-Jan Reichart

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Short summary

Element cycles in oxygen-depleted areas such as upwelling areas inform future deoxygenation scenarios. The Benguela upwelling system shows strong decoupling of nitrogen and phosphorus cycling due to seasonal shelf anoxia. Anaerobic processes result in pelagic nitrogen loss as N₂. At the same time, sediments are rich in fish-derived and bacterial phosphorus, with high fluxes of excess phosphate, altering deep-water nitrogen:phosphorus ratios. Such alterations can affect ocean functioning.


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