General comments
The manuscript “Anomalous oxygen concentration increases in benthic experiments from the Clarion Clipperton Zone are not related to polymetallic nodules” by Webber et al. (The Metals Company- competing interests are clearly stated) deals with an aspect of a previously published peer-reviewed article by Sweetman et al. (2024). In their manuscript, the authors re-analyze the original dataset used by Sweetman et al.. They investigate a correlation between variables that describe a polymetallic nodule occurrence vs. the reported oxygen concentration change. Webber et al. include three additional stations in their re-analysis, and find that the correlation for polymetallic nodule cover and oxygen is not present with the added data included. From this lack of correlation and from the oxygen increase found in a control station, they conclude that a causality between nodule presence and oxygen increase is impossible (see manuscript title).
The new data are a relevant addition to the discussion around “dark oxygen production”, and a re-examination of the Sweetman et al. findings in many aspects is required and welcome. The pressure on science to be quick on this subject is very high, given the economic interest in exploiting polymetallic nodules. Still, maintaining established scientific standards and aiming for a careful, objective analysis is important, particularly given the potential scientific impact of the Sweetman et al study. In the current form, I see a need for improvements in organization, referencing, reasoning and phrasing for this manuscript to enter the peer reviewed literature.
Regarding recommendation for approval, I would also consider that any statement made here that is exclusively based on preprints, not on own data and arguments, would become citable as peer-reviewed after acceptance.  
I should add that I did not download the provided data package as it would have required downloading >2 GB of data as two zip files with unknown content, to be extracted on the local computer.

Detailed Comments (I have numbered the sentences for each paragraph in many instances because I found no line numbers to refer to.)

Abstract – background
1^st sentence: The original paper addresses benthic chamber experiments, but also an ex-situ incubation.

Abstract – results
1^st sentence: “…indicating that there is no link between the abundance or size of polymetallic nodules and rising oxygen concentrations.” If this is maintained as a conclusion, it should be moved to conclusions.
3^rd sentence, “Furthermore…” This is a mix of results and conclusion. The result is the observation of increasing oxygen concentrations in the absence of visible nodules at the sediment surface.

Abstract- conclusions

1^st sentence: The original paper also reports instances of decreasing oxygen concentrations. The complete absence of polymetallic nodules, which is essential for this conclusion, is not well supported by evidence (see comments below referring to the main text).

Reasoning of the authors: The absence of a correlation is not the same as an absence of a relation. To give an example: Even if fifteen measurements of oxygen production/consumption vs. tree number in a forest might yield a wide range of positive and negative numbers (trees produce, but also consume oxygen, and some oxygen might be produced/consumed by moss), a poor correlation would not mean that trees are not related to oxygen production. (Vice versa, a correlation alone would also not prove the relation). Correlation is not a proof for causality, the absence of correlation is not a proof for the absence of causality.

Introduction
3rd sentence “…the work has attracted criticism from the scientific community, detailing many methodological concerns and issues relating to experimental design, reporting and interpretation of the data.^7-13” While the number of citations would suggest strong support in the scientific literature, a detailed look (see commented references at the end of the review) reveals that none of these seven references is a peer-reviewed research article that substantiates the claim. One is a self-citation of an opinion article, most of them are unreviewed pre-prints, partly self-citations, and one is a peer-reviewed article, but only with a marginal reference to the subject that differs from the claim made (it refers to ocean chemistry 4 billion years ago and it mentions the paper in a different context and does not raise “methodological concerns and issues relating to experimental design, reporting and interpretation of the data”.
5^th sentence: The sentence “However, Sweetman et al. (2024) failed...” is neither supported by references here, nor has it been demonstrated yet in the manuscript. This would be a statement for conclusions, if proven, not for an introduction. If this was the hypothesis that the authors intend to test in their reanalysis of Sweetman’s data, it might be placed at the end of the introduction and introduced as a hypothesis to be tested- ideally in a phrasing that is less personal, but rather focusing on the specific claim the authors wish to challenge. This also applies to the following statements (“fail…”, “fail…”, …), which are neither placed well in an introduction, nor are they phrased as neutrally as required for an objective scientific examination.
The section starting from “Contrary to the finding in Sweetman et al. (2024), we find no significant correlation between oxygen concentration increases and average nodule surface area...” is a result, not an introduction.
The entire following text:
“We also find no significant correlation between total nodule surface area, nodule weight or average nodule weight and oxygen concentration increases. We therefore reject the claim that the magnitude of oxygen concentration increase is related to the size or abundance of polymetallic nodules present. These findings are consistent with the chambers and control experiment without nodules, which indicate that oxygen increased regardless of whether nodules were present or not. We therefore conclude that there is no link between polymetallic nodules and the observed rises in oxygen concentration in the benthic chamber [… ] These observations preclude the possibility that polymetallic nodules have any role in oxygen concentration increases in those experiments, and are incompatible with the stated correlation with nodule surface area.[…] respirometer experiments.”
is a mixture of results and conclusions, and the conclusions remain to be supported at this stage. This should all go to results and conclusions, respectively, if it can be substantiated in the following text.
Irrespective of the correct place in the text and the phrasing, in the sentence “Furthermore, Sweetman et al. (2024) fail to report that chambers from the western CCZ that recorded increasing oxygen did not contain any nodules,14,15”, the references are not fully supporting the statement. Reference 14 states actually “No nodules were collected as they were either not present or in form of manganese oxide granules”, which is not really the same as “no nodules were observed”. Reference 15 is a doctoral thesis that could not be retrieved online and no source was given. Given that the authors state themselves below that “It is highly pertinent to the discussion to note that chambers collected in the western CCZ on cruise KM1808 of the R/V Kilo Moana did not contain manganese nodules.14,15”, this is a substantial missing piece.

Methods
Penultimate paragraph: “Although O2 flux and total O2 production in these chambers was not previously published, we have used available data¹⁷…”. Reference 17 is a generic reference (“SciPy 1.0: fundamental algorithms for scientific computing in Python”) that does not provide available data as suggested by the text.

Discussion, end of ^3rd paragraph
“Collectively, these results clearly demonstrate that oxygen production is not related to the size or number of nodules in the chamber” This is inaccurate. It demonstrates the absence of a correlation for these variables in this dataset. Not more, not less.

Discussion, 3^rd sentence of 4^th paragraph
“These results preclude the possibility that oxygen production in those chambers was due to the presence of polymetallic nodules, because no nodules were present”. The available reference does not rule out the presence of manganese oxide granules. Even if the observed oxygen production was related to another component of the deep-sea floor, this would not touch the central part of the paper by Sweetman et al. (2024), since the scientific change of paradigm that led to its prominent publication is the production of dark oxygen at the seafloor, not the direct production of oxygen by polymetallic nodules.

Discussion, last paragraph:
“…would be extraordinary, and likely violate the established laws of thermodynamics.^7,9”
This is another citation of an opinion piece and an unreviewed preprint in support of a statement that is not directly related to the dataset shown. Thermodynamic conditions were not tested here. The system in a benthic chamber or within a polymetallic nodule is not homogenous, and it contains bound oxygen as well as energy. Stating that the observed oxygen release is thermodynamically impossible (which may or may not be the case) requires a sound scientific assessment, especially in such a central aspect.

Conclusion, penultimate sentence: “There is now a substantial body of evidence^{7-13, 20} that challenges the observations and claims reported in Sweetman et al. (2024)”. The only peer-reviewed research paper addressing this question in the list is reference 20.

Conclusion, last sentence: “Furthermore, examination of the experimental timeline suggests that the authors should have been aware that their primary hypothesis was untenable years before further experiments were conducted”. This sentence could be understood as an allegation, implying that data were intentionally misrepresented. The manuscript here explores one aspect of the Sweetman et al. paper, which is composed of various lines of evidence. While all of these lines of evidence can and should be tested with sound methods, the dataset shown here is no sufficient foundation to allow such far-reaching claims. It could be understood as a personal criticism, not a scientific argument, and should be removed. 

Commented references with peer review status:
1.  Sweetman AK, Smith AJ, De Jonge DSW, et al.: Evidence of dark oxygen production at the abyssal seafloor. Nat. Geosci. 2024; 17: 1–16. Publisher Full Text

2.  Smith KL, Laver MB, Brown NO: Sediment community oxygen consumption and nutrient exchange in the central and eastern North Pacific. Limnol. Oceanogr. 1983; 28(5): 882–898. Publisher Full Text
             

3.  Khripounoff A, Caprais JC, Crassous P, et al.: Geochemical and biological recovery of the disturbed seafloor in polymetallic nodule fields of the Clipperton-Clarion Fracture Zone (CCFZ) at 5,000-m depth. Limnol. Oceanogr. 2006; 51(5): 2033–2041. Publisher Full Text
             

4.  Stratmann T, Voorsmit I, Gebruk A, et al.: Recovery of Holothuroidea population density, community composition, and respiration activity after a deep-sea disturbance experiment. Limnol. Oceanogr. 2018; 63(5): 2140–2153. Publisher Full Text
             

5.  Vonnahme TR, Molari M, Janssen F, et al.: Effects of a deep-sea mining experiment on seafloor microbial communities and functions after 26 years. Sci. Adv. 2020; 6: eaaz5922–eaaz5914. PubMed Abstract | Publisher Full Text | Free Full Text
             

6.  An SU, Baek JW, Kim SH, et al.: Regional differences in sediment oxygen uptake rates in polymetallic nodule and co-rich polymetallic crust mining areas of the Pacific Ocean. Deep-Sea Res. I Oceanogr. Res. Pap. 2024 May; 207: 104295. Publisher Full Text
             

7.  Downes P, Cuesta A, Denny A, et al.: Extraordinary claims require extraordinary evidence: Evaluating nodule-associated dark oxygen production. Front. Mar. Sci. 2025; 12. Publisher Full Text

8.  Downes P, Marsh L, Bento J, et al.: Contributions to the discussion of novel detection of dark oxygen production at the abyssal seafloor.2024. Reference Source
             

9.  Cuesta A, Jaspars M: Is abyssal dark oxygen production even possible at all?.2025 Mar 10 [cited 2025 Jun 10]. Reference Source
             

10.  Nakamura K: Questioning Dark Oxygen Production in the Deep-sea Ferromanganese Nodule Field.2024 Oct 4 [cited 2025 Jun 10]. Reference Source
             

11.  Tengberg A, Hall P, Kononets M: Rebuttal of Sweetman, A.K., Smith, A.J., de Jonge, D.S.W. et al. Evidence of dark oxygen production at the abyssal seafloor. Nat. Geosci. 2024 Oct 4 [cited 2025 Jun 10].Publisher Full Text Reference Source
             

12.  Trellevik LK, Denny A, Svellingen W: Critical Review of the Article: “Evidence of Dark Oxygen Production at the Abyssal Seafloor” by Sweetman et al. in Nat. Geosci. 1–3 (2024). Geochemistry. 2024 [cited 2025 Dec 4]. Reference Source
             

13.  Trost K, Gennis RB, Allen JF, et al.: Oxygen reductase origin followed the great oxidation event and terminated the Lomagundi excursion. Biochim. Biophys. Acta Bioenerg. 2026 Apr 1; 1867(2): 149575. Publisher Full Text

14.  Cecchetto MM, Moser A, Smith CR, et al.: Abyssal seafloor response to fresh phytodetrital input in three areas of particular environmental interest (APEIs) in the western clarion-clipperton zone (CCZ). Deep Sea Res Part I Oceanogr Res Pap. 2023; 195: 1–12. Publisher Full Text
             

15.  Cecchetto MM: Benthic Ecosystem Functioning of the Western Clarion-Clipperton Zone, Pacific Ocean, and the West Antarctic Peninsula [Doctor of Philosophy]. Edinburgh: Heriot-Watt University; 2022.
             

16.  Pedregosa F, Varoquaux G, Gramfort A, et al.: Scikit-learn: Machine learning in Python. J. Mach. Learn. Res. 2011; 12: 2825–2830.
             

              17.  Virtanen P, Gommers R, Oliphant TE, et al.: SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods. 2020; 17(3): 261–272. PubMed Abstract | Publisher Full Text | Free Full Text

18.  Vallat R: Pingouin: statistics in Python. J. Open Source Softw. 2018; 3(31): 1026. Publisher Full Text
             

19.  Hall P, Welsh AH: Limit theorems for the median deviation. Ann. Inst. Stat. Math. 1985 Dec 1; 37(1): 27–36. Publisher Full Text
             

20.  Harrison D, Kolbusz JL, Bond T, et al.: Seafloor surficial sediment variability across the abyssal plains of the central and eastern pacific ocean. Front. Earth Sci. 2025 Apr 22; 13. Publisher Full Text
             

21.  Webber AP: Respirometer Data. Zenodo. 2026 [cited 2026 Apr 23]. Publisher Full Text Reference Source

22.  Webber AP: SegmentAKS. Zenodo. 2026 [cited 2026 Apr 25]. Publisher Full Text Reference Source