| 21 Jul 2026
The role of biologically-mediated fragmentation in carbon flux attenuation in a 1-D mechanistic particle model
Abstract. The efficiency of particulate organic carbon (POC) transport through the water column is the foundation of the biological carbon pump’s capability to sequester atmospheric CO2 into the ocean interior over prolonged timescales. However, constraining the magnitude and composition of POC flux reaching ~ 1 km depth remains challenging, due to diverse biotic and abiotic processes that alter particle morphology, composition and sinking speed. Recent studies have highlighted biologically-mediated fragmentation, which breaks up particles into smaller, slower-sinking POC, as a potential primary driver for POC flux attenuation in the mesopelagic zone. Here, we use a vertical mechanistic particle model, based on the SISSOMA mixed-layer model, to assess the role of biologically-mediated fragmentation on diverse aggregates and POC flux attenuation. Our model resolves a spectrum of particles across size and density, incorporating a representation for particle associated copepodsas key agents of fragmentation below the mixed layer. Sensitivity experiments show fragmentation is critical to reproducing the observed initial decrease in particle size with depth. Fragmentation is shown to have a greater contribution to POC flux loss when export is increased and is composed of relatively larger particles, suggesting it is likely to be a more significant process for flux attenuation in more productive regions. We also demonstrate that the initial slope of particle size distribution at the export depth significantly influences the extent to which transformation processes affect particle size profiles and flux attenuation. While our results highlight the necessity of including fragmentation in biological pump models, fragmentation alone cannot fully account for observed profiles in particle size structure and transfer efficiency. We propose that additional sources of POC (e.g., fecal pellets) and transformation processes (e.g., differential remineralisation, ballasting) likely contribute to the discrepancies between our model and observations. Our results highlight the importance of explicitly representing fragmentation and particle diversity in biological pump models to improve mechanistic understanding and predictions of ocean carbon sequestration.
General comment
The manuscript by Naidoo-Bagwell et al. proposes a mechanistic 1-D model to explore the role of biologically-mediated fragmentation in carbon flux attenuation. The authors performed simulations with varying particle properties. Different PSD slope experiments (S = 0, 2, 3, 4) were conducted (following Clement et al., 2022), along with seasonal experiments.
The introduction is well-written and well-referenced, providing readers with access to the fundamental knowledge about the BCP to evaluate the pertinence of zooplankton fragmentation in ocean transfer efficiency.
The idea that the initial particle size distribution slope is a critical factor in POC flux attenuation is very interesting, as it controls the relative abundance of large, fast-sinking particles capable of transporting carbon deeper into the water column. This aspect deserves to be highlighted within our current understanding of the BCP. Zooplankton-induced fragmentation and its effects on size profiles and flux attenuation need to be incorporated into BCP models to better represent POC flux attenuation with depth.
However, I have a few (moderate) concerns about the manuscript in its current state.
One of the main shortcomings of the manuscript is that, given Fig. 1 (bioregions), I was expecting the authors to establish a comparison between bioregions. Which bioregions are the most impacted by zooplankton-mediated fragmentation?
I think the quality of the figures can also be improved (size, resolution, organization, etc.).
The discussion is short (which is appreciated), yet the interpretation of the model outputs is not sufficiently developed. The discussion is somewhat frustrating, as it reads more like a list of model limitations and gaps, which is not particularly compelling. Several aspects (detailed below) can be improved and developed.
Based on these points, I recommend a moderate revision of the manuscript before it can be considered for publication in Biogeosciences.
Abstract
Lines 15-17: Would it also be interesting to mention the re-aggregation processes that can occur in mesopelagic layers, as well as the opposing trend (i.e., increasing POC flux)? This is particularly relevant regarding fecal pellet production and repacking, which can significantly increase POC flux.
Line 20: Why only copepods and not all zooplankton taxa?
Line 29-30: Does it consider a conversion between marine snow POC mass (grazed and ingested) and fecal pellet egestion? (e.g. a fraction of marine snow POC into fecal pellet POC)?
Introduction
Lines 48-49: The way the sentence is written suggests that particle mass and morphology are consequences of acceleration or deceleration, whereas the opposite is true (or mass and morphology dictate particle dynamics). Alternatively, is the relationship bidirectional?
Line 50: More recent publication suggest that the ballasting effect accelerate the velocities (e.g. Laurenceau-Cornec et al., 2020).
Lines 76–78: Fragmentation cannot be observed directly, but can zooplankton-associated particles within marine snow be assessed using UVP6 images? Are there any references for this?
Lines 87-88: Does PAC also consider grazing and POC conversion into fecal pellet?
Methodology
Line 101: a “Fluffy” aggregate should be shortly defined here.
Line 109: Is 0.01 d-1 based on literature? Is it supposed to change with temperature and depth?
Line 123: Why the fraction of ingested POC (ψi) prescribed at 0.3? Can you add maybe a reference about it?
Lines 129: Can you introduce what is a Holling III functional response (what feeding trait does it correspond?) + reference?
Line 151: What “f” prefix standing for?
Table 1: The column Reminerealisation and Fragmentation (tick and exclusion) are not necessary in this table (the first column is explicit).
Results
Fig. 2: The figure resolution is very low. It should be improved for the final submission. The x-axis label (Average Size (µm)) should be visible on the subplot (F) (or on each subplot). The x-axis of subplot (b) and (e) are cropped. Have you also considered showing the aggregates and zooplankton abundance profile? In the same format as Fig. 2.
Lines 265-270: I think it could be relevant to display profiles of vertical PAC distribution (particles abundance and zooplankton abundance input in the model) at this step to figure it out.
Line 285: “as you get deeper” sounds very unformal, prefer “as depth increases”
Fig. 5. Using two subplots might be more appropriate than a dual y-axis in this case. To improve the readability of this graph, I suggest indicating the POC flux loss due to fragmentation directly within the integrated POC flux loss bar (e.g., using a stacked bar plot with two colors).
Does POC flux loss due to fragmentation (%) is still relative to NONE? Does 100% loss (red bar) due to fragmentation mean that all the loss is due to fragmentation? which is expected in FRAG?
Fig. 5. Is a bit confusing.
Lines 318-319: “Fragmentation is the dominant attenuator of flux in the upper mesopelagic, where particle-associated copepod (PAC) and other zooplankton biomass is greatest”, See my previous comment about the addition of zooplankton abundance vertical profile.
Fig. 8. I recommend changing the color scale gradient by a cyclic color gradient (e.g. twilight, hsv…) it would considerably highlight the winter vs summer months influences. Fragmentation (dashed lines) and remineralization (solid lines) could be also presented in the subfigure (d). I recommend splitting this graph into 2 separated graphs (fragmentation and remineralization). Figure size ratio and orientation could be improved for better readability.
Discussion
Lines 426-426: Why don’t present the regional variability of biologically mediated fragmentation in attenuating POC flux?
Lines 445-446: “although no consistent net effect on fragmentation was found, » In Toullec et al. (2019), aggregates were fragmented after 48 hours in the Temora longicornis (cruise feeder) incubation compared to the control, where neither fragmentation nor re-aggregation was observed.
Lines 449-451: If you are referring to the fecal pellet emission and carbon flux boost (higher sinking rate and lower remineralization rate of fecal pellet), I think the idea can be better developed in the discussion, regarding the attenuation effect of PAC-meditated fragmentation.
Lines 465-467: Does this aspect vary with latitude (or bioregions)?
Lines 472-475: Biogenic ballast (opal and calcite/aragonite) are expected to vary regionally and seasonally. This should considerably enhance the sinking rate and remineralization (both seasonally and regionally). This aspect could be also developed in the discussion regarding the model input.
Concluding remarks
Line 496: Once again, you have the possibility to at least present the regional variability.