| 11 Mar 2026
Biogeochemical controls on carbonate dynamics driven by methane and freshwater inputs in shallow sediments of a brackish continental shelf sea
Abstract. Continental shelf seas are essential to the carbon cycle, supporting nearly one-third of global marine primary production and significantly contributing to the burial of organic and inorganic carbon. Processes such as organoclastic sulfate reduction (OSR), methane production or anaerobic oxidation of methane (AOM), occurring in coastal sediments, have a significant impact on the carbon cycling in the marine environment. That impact may be modified by an increased organic matter (OM) supply or freshwater input. In the present interdisciplinary study, we investigated carbonate dynamics in three benthic environments of a brackish continental shelf sea: (1) anoxic sediments dominated by OSR; (2) nearshore sediments with high terrigenous OM input and active methanogenesis; and (3) sediments influenced by groundwater infiltration and pore-water freshening, coupled with methanogenesis. We analyzed pore-water chemistry (DIC, total alkalinity, major ions, nutrients), sediment geochemistry (CH4, total organic carbon, total nitrogen, total sulfur), and mineralogy, including authigenic carbonates and iron sulfides. We used stable isotopes of DIC (δ13C-DIC), methane (δ13C-CH4, δ2H-CH4) and organic matter (δ13C, δ15N) to trace carbon transformations. We also determined rates of OSR and AOM experimentally. Based on these data, we have proposed conceptual models of carbon cycling in the three sedimentary environments. At the methane-free sediment, organic matter degradation was primarily governed by OSR, producing 53.6 mmol m-2 d-1 of DIC within the top 100 cm, accompanied by limited carbonate burial and dominant pyrite accumulation. In contrast, methane-bearing sediments displayed markedly enhanced carbonate dynamics. The role of methane-related processes became increasingly important in sediments influenced by freshwater input, where pore water freshening reduces sulfate availability, shallows the sulfate-methane transition and stimulates exceptionally high AOM rates reaching up to 1077 μmol dm-3 d-1, resulting in a DIC production rate of 331 mmol dm-3 d-1, more than fivefold higher than OSR. This environment facilitates significant authigenic dolomite burial (ranging from 467 to 994 μmol m-2 d-1), illustrating efficient inorganic carbon sequestration within these sediments. Our study provides the first quantitative estimate of authigenic dolomite burial rates in Baltic Sea sediments.
Interactive comment on “Biogeochemical controls on carbonate dynamics driven by methane and freshwater inputs in shallow sediments of a brackish continental shelf sea” by Łukawska-Matuszewska et al.
General
This paper presents an extremely comprehensive analysis of sediment biogeochemistry at three locations in the Gdansk Deep. The authors should be commended for the integrated approach to study solid-phase and porewater chemistry, which yields valuable insights into coupled primary and secondary diagenetic processes. In particular the work focuses on the factors controlling the rates of diagenetic mineral formation and burial (especially dolomite and pyrite) but touches on many other topics due to the breadth of the data.
I agree with most of the conclusions of the study but there are some interpretations that I would suggest to modify because their implications may be misunderstood if taken at face value. For example I do not think it is justified to state unilaterally that methanogenic sediments favor authigenic carbonate formation. I would also like to see some clarification of the separate measurements of del13-DIC and del 13C-CO2 included in the porewater analysis and how these results should be interpreted, and some more details about the incubation experiments and connected data processing. Overall I would say that the breadth of the approach introduces some difficulties to maintain coherence in the manuscript. Some rewriting of the introduction would help to guide the reader towards the rationale of the study in a more logical way. My Line by Line comments contain all the relevant points to be addressed. I wish the authors success in their revisions.
Line by Line
Line 24: “In” rather than “At” the methane-free sediment
Lines 25 and 29: DIC production rates are given here in two separate units. For the sake of readability it would be sensible to use the same unit.
Lines 34-80 (general comments on Introduction): Lines 72-80 do a good job of outlining the eventual rationale for the study, but some of the earlier text is harder to read. I suggest to try to introduce the key biogeochemical processes to be studied in a more consistent way, e.g. treat primary and secondary diagenetic processes separately, then introduce the effects of salinity and submarine groundwater discharge, and finally focus on those processes that control alkalinity production as a driver of carbonate precipitation. The current flow jumps between these concepts and is not always consistent.
Lines 45-48: OSR should not lower pH or enhance carbonate dissolution because there is 2:1 production of HCO3- vs. H+. Please check and rephrase.
Line 91: Does this mean 7 cores in July 2023 and another 7 in February 2024? Please be specific.
Line 94: This should read "CH4, CO2 and their stable isotopes..." (but see later comments about needed clarifications about this methodology).
Line 99: How was the rhizon sampling performed under anoxic conditions, was the setup placed in a glove bag?
Line 107: At what stage was a headspace injected into the methane sample vials? This should be stated.
Line 160: The term IG in equation (2) is not defined.
Line 163-172: this section concerns porewater analyses so it is not clear why it is placed here in the sediment analyses section.
Line 168: What was the detection limit in terms of CH4 concentrations to obtain reliable delC13 data? Was a pre-concentration unit used?
Line 178: How were thin sections produced? Was the sediment embedded and if so with which resin?
Line 186: Clarify that d in equation 3 is the wet bulk density.
Line 190: Was the PXRD quantification achieved using the Rietveld method? Please comment on the uncertainty for estimates of dolomite and pyrite content in the ranges calculated in this study.
Line 198: If the measured product is H2S, how does this method to determine OSR exclude H2S produced by SO4-AOM?
Line 237: 3.2 has the same heading as 3.1 (!)
Line 286: This clarification of the incubation approach should also be stated in the Methods.
Line 296 (Table 1): The raw data used to calculate the rates needs to be included in the Supplement. Also it is interesting to note that MET-2 and ZGG are very similar in terms of experimentally-derived process rates. This does not seem to match with the porewater profiles, in which AOM appears much more important at MET-2.
Line 308: Can this variable volume of "sediment matrix" be related to changes in water content downcore? The images imply so, but it depends partly on how the thin sections were prepared, see earlier comment and adjust accordingly.
Line 328: Where are the SEM-EDS results?
Line 334 (Fig. 4): "c" appears to be pyrite and not calcite as stated in the caption.
Line 398: The diagenetic reactions are given different codes (e.g. R1, R2) in the main text and in the supplement. Please be consistent throughout.
Line 426-427: Is this a reference to the incubation results of the present study? If so please be clear.
Line 435: For completeness should denitrification be considered here?
Line 439: Refer to Table 2 again showing the low values of dolomite at this site.
Line 446-447: This logic is not quite correct, because as stated earlier in the manuscript, carbonate alkalinity, as HCO3- + 2(CO3 2-) is not quite equivalent to DIC. I am not against using these type of approximations to derive useful information from the dataset, but all assumptions should be made clear.
Line 499: Should the reference to Fig. 4 actually be to Fig. 5?
Line 544-545 (important): I think the interpretation is more nuanced. Generally the formation of carbonates will be a function of the overall rate of the primary diagenetic reactions producing DIC and thus raising the IAP of dolomite and calcite. There is no mechanistic reason why methanogenic sediments (in the absence of sulfate) should favor carbonate precipitation; on the contrary OSR-dominated systems would be expected to have higher rates of diagenesis generally, due to greater energy yield of OSR. However, in systems where both process occur but overall diagenesis rates are so high that sulfate is exhausted in the uppermost decimeters (e.g. MET-1, MET-2 here), DIC will be observed to be higher overall (thus favoring carbonate formation), and by coincidence a methanogenic zone will be observed in short sediment cores that would otherwise be confined to deeper horizons. So I would suggest that one of the main outcomes of this study is to highlight how topographic features such as pockmarks influence the sedimentation regime such that demand for electron acceptors is concentrated in specific areas, leading to knock-on effects in secondary processes such as mineral formation (with contrasting outcomes for sulfides and carbonates).
Line 973: Whiticar (1999) is missing from the bibliography. Check all references.
Supplement Fig. S3 (important): This point concerns the methodology for stable carbon isotopic analysis of dissolved inorganic carbon species used in the study, and how the data should be interpreted. Samples appear to have been taken in two separate ways: 1. in connection with the CH4 sampling, for which wet sediments were stored in 2.5%NaOH and then headspace gas was extracted for del13C-CO2; and 2. in connection with the DIC sampling, for which extracted porewaters were acidified with phosphoric acid and all DIC converted to CO2 for determination of del13C-DIC. A couple of queries here:
Supplement Fig. S9: There is no legend so the color coding is not clear.