The manuscript by Schnabel et al. reports geochemical and microbiological analyses of sediment cores from an area with known subseafloor hydrocarbon reservoirs. The authors collected the cores on a grid and performed some geostatistical mapping.

I believe the manuscript has great potential based on the large number of investigated cores but the authors should work more on finding a novel aspect as well as implications.

I have some concerns that can be grouped into three categories:

1) the term “seepage” is improperly used throughout the manuscript. Hydrocarbon seepage refers to areas where hydrocarbons are emitted from the seafloor. From what I read, the authors did not find any seepage (and the pore water profiles also show low gas fluxes and deep SMTZ) but rather show diffusive fluxes above the SMTZ (not intercepted) which are indirect evidence for diffusive fluxes of gas from deeper strata. That term is therefore, misleading, as I was looking for some water column “flare” or other evidence of seepage which I could not find. Moreover, in the text it is always mentioned the term  “hydrocarbon” without defining whether it refers to just gas or oil. This must be clarified.  The term “inconspicuous” is not explained, does it refer to ephemeral fluxes? or just to low fluxes?

2) From the highlights, I see that all the bullet points are actually well-known processes, so there is no novelty or insights. We already know the biogeochemical processes associated with hydrocarbon oxidation and the consequent precipitation of minerals at or around the SMTZ. Also the spatial heterogeneity in those processes and pore water fluxes is common in gas charged sites.

3) some methodological issues for pore water fixation

Detailed comments:

Line 65: add reference after “coastal areas”

Line 122: seeps can be classified, instead of “are classified”. The classification in table 1 based on Judd and Etiope’s works cannot be applied worldwide, for example the Arctic fauna present much less diverse ecosystems, pockmarks are not “per se” proof of ongoing seepage but can be fossil structures now inactive.  Te methane fluxes reported in the table, do they refer to fluxes at the sediment/water interface or what? I suggest removing this table and related terminology.

Line 125: actually, we see in the Arctic that low-intensity seepage (emissions) can be associated with widespread chemosynthetic habitats (mats), e.g. HMMV

134: please clarify what you use to distinguish between low-intensity seepage and unaffected zones.

137-140: implications? This is already known

187: define how many hours after retrieval

191: why have you also filtered at 0.22 um? The rhizon mesh is already 0.15 um so that would be useless. But it does not affect the data.

194: why haven’t you acidified the pore water sample for metals? That’s an important preservation step to avoid scavenging onto newly-formed precipitated particles. The metals data can be altered.

232: 3% is referring to a RSD or what parameter?

240: measurement uncertainty , what metrical parameter does it refer to? Repeatability or what? Please check the guidelines by the International Association of Geoanalysts.

467-469 and 495-496: so no seepage

520-523: low-Mg Calcite? Strange, generally methane-derived carbonates are aragonite or high-Mg calcites.

558: please add ref to the sentence “…SO3 concentrations in the solid phase,”

669: variable seepage intensity, again this is not what you are referring to, which is diffusive fluxes within the sediment

This study investigated the impact of low-intensity hydrocarbon seepage on the geochemistry of the solid phase and porewater in organically impoverished sub-seafloor sediments of the Southwest Barren Shelf. By analyzing 50 gravity cores, the research combined organic and inorganic geochemical analyses. It found that while seepage areas lacked significant organic geochemical signals, inorganic indicators (e.g., the formation of carbonate and sulfide minerals) and porewater profiles (e.g., gradient changes in sulfate, alkalinity, and calcium ions) exhibited clear seepage imprints. The results suggest that even if hydrocarbons are completely degraded in deeper layers, shallow sediments can retain evidence of authigenic mineral precipitation driven by redox processes, providing complementary indicators for identifying past and present seepage activities. The significance of this study lies in revealing the subtle impacts of low-intensity seepage on the biogeochemical cycling of marine sediments, holding academic value for understanding carbon cycling, microbial activity, and hydrocarbon exploration. Overall, the study design is sound, the data is rich, and the conclusions support the research hypotheses. However, there are some methodological and interpretational shortcomings that need to be addressed before publication. I believe the manuscript is worthy of publication after appropriate revisions, as it offers novel insights, especially for seepage detection in organically impoverished environments.

Major issues:

The main problems in the manuscript are concentrated in methodological limitations, depth of data interpretation, and statistical processing of some results. For example, the organic geochemical analysis failed to effectively capture the seepage signal, the sampling depth might not have covered key biogeochemical zones, and the statistical methods are somewhat simplified in explaining spatial heterogeneity. These issues affect the comprehensiveness and persuasiveness of the results.

Deficiencies and suggested revisions:

1)Limitations of organic geochemical analysis (Lines 30-31):

The manuscript states that "organic geochemistry analysis provided limited insights" (Lines 30-31) but does not fully explain why FT-ICR-MS failed to detect seepage-related compounds. This could lead readers to question the applicability of the method.

Suggestion: In the discussion section (e.g., Lines 495-504), deeply analyze the reasons for failure, such as whether the degradation products of hydrocarbons had too low molecular weights or were affected by background signal interference. Compare with successful cases in similar environments from the literature to enhance critical thinking in the methods section.

2)Potentially insufficient sampling depth (Lines 39-40 and 533-534):

The manuscript acknowledges that microbial hydrocarbon degradation may occur below the sampled interval (Lines 39-40) and mentions the fluctuation of the SMZT (Sulfate-Methane Transition Zone) in the discussion (Lines 590-597). However, it fails to assess whether the sampling depth (maximum 3 meters) was sufficient to capture key processes, which limits the representativeness of the results for active seepage.

Suggestion: Add a discussion on the rationale for sampling depth in the methods section (Lines 132-135), for example, by citing regional SMZT depth data. In the discussion (Lines 610-617), recommend future studies using deeper sampling or model inference to compensate for spatial limitations.

3)Insufficient detail in statistical method descriptions (Lines 263-286):

The statistical section (e.g., PCA and Mann-Whitney U test) is described very briefly. Lines 273-286 mention the use of R software but omit crucial parameters (e.g., criteria for selecting variogram models), which could affect the reproducibility of the results.

Suggestion: Supplement statistical details in the methods section (near Line 286), such as PCA loadings or the goodness-of-fit for kriging models. Include code snippets in the supplementary materials to enhance transparency.

4) Linearity assumption in porewater data Interpretation (Lines 352-355 and 392-393):

The manuscript assumes linear changes in porewater profiles (e.g., sulfate and alkalinity) (Lines 352-355), but mentions non-linear manganese concentration profiles (Line 392-393). This has not been adequately addressed in the statistics, potentially leading to biases in flux calculations.

Suggestion: Add a comparison of non-linear models (e.g., exponential fitting) in the results section (Lines 350-355). In the discussion (Lines 587-590), explain the limitations of the linearity assumption and suggest the use of more complex diffusion models.

5) Overly general conclusions (Lines 655-665):

The conclusions reiterate the main findings of the results but fail to highlight the novelty of the study (e.g., the significance of spatial heterogeneity). Lines 661-662 mention that "the FT-ICR-MS-based approach was unsuccessful" but do not elaborate on the methodological implications.

Suggestion: Rewrite the conclusion section to emphasize the innovative aspects of this study in detecting low-intensity seepage.

Additionally, please cite the following literature to enhance the logical flow of the study's background and discussion.

Lines 63-70: When introducing microbial activity controlling sedimentary cycles, you can cite this literature (Yang et al., 2025a) to support the role of organic matter input. When outlining the sedimentary carbon cycle, cite literature (Wang et al., 2025) as background.

Lines 81-85: When analyzing the contribution of hydrocarbon seepage to methanogenesis pathways, cite literature (Cai et al., 2025) to explain the key role of substrate availability in regulating microbial responses.

Lines 480-487: When comparing hydrocarbon seepage with background organic matter mineralization, cite literature (Wang et al., 2025) to support the influence of substrate characteristics on temperature sensitivity.

Lines 510-517: When explaining how the anoxic conditions caused by hydrocarbon seepage enhance carbon mineralization, cite literature (Zhang et al., 2025) as supporting evidence.

Lines 184-189: When discussing how hydrocarbon seepage might induce a priming effect through methanogenesis, you should cite literature (Yang et al. 2025b) to strengthen the conclusion.

Lines 132-137: When comparing the priming effect of different organic matter sources, you can cite literature (Yang et al. 2023) to highlight the uniqueness of hydrocarbon seepage.

Lines 498-502: When speculating on the fate of hydrocarbon degradation products, you can cite literature (Yang et al. 2020) to illustrate the potential for microbial utilization of allochthonous DOM.

Refs suggested:

Yang et al., 2025a Bacterial biomass-derived organic matter triggers nitrous oxide production and positive priming effect in lake sediments. Geochim Cosmochim Acta 408: 190-200, https://doi.org/10.1016/j.gca.2025.08.030

Cai et al., 2025 Substrate Availability Controls the Temperature Sensitivity of Methanogenesis in Lake Sediments. Water Research 289: 124836, https://doi.org/10.1016/j.watres.2025.124836

Wang et al., 2025 Substrate chemistry trumps mineral protection in governing temperature sensitivity of organic carbon mineralization in saline lake sediments. Geochim Cosmochim Acta 407: 81-90. https://doi.org/10.1016/j.gca.2025.08.040

Zhang et al., 2025 Increased anoxia promotes organic carbon mineralization in surface sediments of saline lakes. Journal of Earth Science 36: 2240–2250, https://doi.org/10.1007/s12583-024-0155-4

Yang et al. 2025b Methanogenesis rather than carbon dioxide production frives positive priming effects in anoxic sediments of saline lakes. Chemical Geology 678: 122680, https://doi.org/10.1016/j.chemgeo.2025.122680

Yang et al. 2023 Predominance of positive priming effects induced by algal and terrestrial organic matter input in saline lake sediments. Geochimica et Cosmochimica Acta 349: 126–134, https://doi.org/10.1016/j.gca.2023.04.005

Yang et al. 2020, Potential utilization of terrestrially derived dissolved organic matter by aquatic microbial communities in saline lakes. The ISME Journal 14(9): 2313-2324. 11.217 https://doi.org/10.1038/s41396-020-0689-0