This study presents a comprehensive dataset to characterize the rates and control of methane production across thermokarst lakes of different ages in interior Alaska. The authors conducted geochemical analyses and incubation experiments with sediment cores collected from a young (BTL) and an older (GSL) thermokarst lake. They observed elevated methane production rates at BTL, which was correlated with higher carbon lability for thermal induced reactions measured by Rock Eval analyses. They discussed how methane production varies with lake evolution and sediment depth, and also the influence of permafrost thawing on microbial activity. By comparing the depth-integrated methane production rates, they propose mechanism of how lake age and thawed talik thickness affect methane production rates and fluxes. The experiments were well-designed and the methods were generally sound. However, I have a few comments that need to be addressed before acceptance of the manuscript. 

Major Comments:

(1)    The stable isotopes of dissolved inorganic carbon in BTL were much more enriched in 13C than GSL, and the authors interpreted this as a result of methanogenesis. However, both methane concentrations and production rates were quite similar at two sites. So I wonder if methanogenesis could lead to such a large difference in 13C-DIC between two sites. Or if this could be related to the source of DIC. I also notice that both data of 13C-DIC and 13C-CO2 were present in Table S1, but I am not sure how were 13C-CO2 measured.  

(2)    Source of methane. The observed δ13CCH4 values from the incubation experiment were mostly >-60 ‰ particularly in BTL, with many of them >-50 ‰. This seems contrary to the biological production of methane with such positive δ13CCH4 values. Any explanation for this? Do you have a parallel killed control sample for incubations and how do they like? 

(3)    Following the above comment, it would be nice if the authors could include more discussion about the importance of different methane production pathways. 

(4)    Similar observations about the control of organic matter on methane production have been reported previously, which can be cited in this work. 

Zhuang et al. 2018. Relative importance of methylotrophic methanogenesis in sediments of the Western Mediterranean Sea. Geochim. Cosmochim. Acta 224: 171-186.

Maltby et al. 2016. Microbial methanogenesis in the sulfate-reducing zone of surface sediments traversing the Peruvian margin. Biogeosciences 13: 283-299. 

Berberich et al. 2020. Spatial variability of sediment methane production and methanogen communities within a eutrophic reservoir: Importance of organic matter source and quantity. Limnol. Oceanogr. 65: 1336-1358.

(5)    It is kind of confusing for the use of methane fluxes in Fig. 7. From my understanding, the production rates did not necessarily mean the emission flux from sediments to the water columns. I did not say the comparison was invalid, but please better justify it. 

(6)    Some figures such as Fig. S1 to Fig. S4 that contain important information should move to the main text rather than buried in the supplementary. 

Minor Comments:

Line 37: Remove the comma.

Lines 54, 317, 412: Revise and format the brackets.

Line 154: What was the purpose of the additional 3 mL sample? Please clarify.

Line 225: Should be "200 ℃".

Figure 2: Please indicate what A, B, C, and D represent in the legend. 

Lines 345 and 351: The term in situ should be used consistently and italicized throughout the text.

Figure 7: The figure is blurred and the resolution needs to be improved.

Lines 403–407: This sentence is vague and confusing. When you talk about significant difference, you need statistical analysis to support it. 

Figure 8: Please adjust the figure layout, as the overlapping text affects readability. 

Lines 485–491: The claimed correlations are not statistically analyzed. Please provide statistics and coefficients in the figure or text. 

This study focusses on the production of methane in a young and an old thermokarst lakes in Alaska and provides a comprehensive data set based on carefully collected, sub-sampled and geochemical analyzed samples. Here they could show that the methane related biogeochemistry in thermokarst lakes change over time as labile carbon stocks are metabolized first but methane production is sustained by the deepening of the talik below the lakes. The study was well designed and sampling as well as analytical methods used were carefully planned and executed. However, the following comments here and in the pdf need to be addressed before acceptance.

• Please add more details to the methods used or provide the respective references where the methods are described in more detail. As it is the analysis could not be reproduced. For example, line 191 and following: which GC was used, at which oven temperature? What length was the column? What was the standards methane concentration for used in the calibration? Furthermore, please provide an overview of the taken cores and their length, either as table or figures. For more detailed comments please see the attached pdf.

• I agree with reviewer 1 that some of the supplementary figures should be moved to the main text, at least figure S1 and S2. Furthermore, I agree that the interpretation of the δ¹³C-CH₄ is incomplete. In addition to the remarks of reviewer 1, the less depleted signal in the incubations could also be due to partial oxidation of methane which can happen in parallel to methanogenesis. This was shown in hypersaline coastal wetlands for the coupling of methylotrophic methanogenesis and AOM (see Krause and Treude 2021, https://www.sciencedirect.com/science/article/pii/S0016703721001873). Additional information on methane production and oxidation might be gained from graphics like δ¹³C-CO₂ vs δ¹³C-CH₄ after Whiticar 1999, as you already have analyzed the δ¹³C-CO₂.

• Regarding Figure 8, the highest production rate at BTL is always topped or at least equal to the highest rate at GSL. This somewhat contradicts your statement in line 492. This should at least be addressed. Furthermore, in the other figures you are distinguishing between center and edge. Please explain why are you showing means from both edge and center in this graph?

I agree with the other reviewers that this is an important, well-conducted study that suits this journal. However, refinement of the figures and conclusion is necessary before publication.

MAJOR Comments:

147-150: After cutting, were the cores returned to the vertical position? Unclear if you sampled in the field or at the University? Was sampling, especially rhizone sampling, performed with the core vertical? These are critical details to understand how mixed your sampling horizons are, and how well sharp geochemical porewater changes can be measured as a result. Currently the text reads as if the cores were transported horizontally to the university and then rhizone sampled on their sides. Please clarify and consider commenting here or in the discussion about how porewater vertical mixing during collection and sampling can affect your results.

326-327: Include the uncertainty as a +- next to the absolute value. If I read the supplement correctly, the BTL center estimate would be 7.4 +- 1.8 mol/m2yr. You kept your uncertainties reasonable under challenging sampling conditions, it’s good to highlight that in the text.

439-442: I don’t follow your logic here. Can this study really tell about methane uptake? Are you assuming your incubation methane production is net between producers and AOM consumers? I think this also relates to another reviewer’s comment about what the d13C values imply, you could move it down to this section. I do think you need to discuss methane consumption in the sediment and water column, but possibly as something you can’t account for here, with the references you have to support your claim that it’s playing a minor role. This would be a great place for future work, especially how AOM rate evolves with age & OM lability.

403/407: directly contradictory statements. A statistically significant difference IS possible to differentiate. Please add numbers and uncertainties to explain what you mean. This paragraph could probably be shortened and combined with the text around it.

572-582: consider moving figure 9 and its description into a last discussion section, at the author and editor’s discretion. I find your first presentation of data of this kind to be an important conclusion and the interpretation (fig 9) not quite as strong, but currently dominates the conclusion section.

Abstract/Conclusions: I am not fully convinced that your results support figure 9. From the current text and figures both the young and old lake have similar methane flux in your study and the previously published work shown in Fig 8 panel C has the younger lake with the greatest flux. As per the previous two comments, if you provide more support in the text and address the Pellerin data in the discussion you could still include fig as a hypothesis. If you really are telling a story where the oldest lake has a higher methane flux, I think there are a few places in the text where it sounds like the young/old is the same and that will need to be checked.

FIGURE Comments:

Much of what is currently in the supplement needs to be in the main text, in particular when showing a rate or isotopic composition the corresponding concentration also needs to be shown on the same figure.

All figure captions need to refer to panel labels, please check throughout manuscript.

Consider the format of Figure 5 and S3: filled icons for edge, open for center (I would swap this personally, but not critical), circles for GSL, diamonds for BTL. Keep this convention for all the figures to make it easy for the reader to follow.

Consider dropping redundant y-axis labels if you want to save space or put 4 panels together.

Fig 1: Consider listing the lake ages in the figure caption. Please move the scalebar so it is not covering the other lake feature.

Figure 2 can have one panel per lake per quantity (allows us to easily compare edge to center). Or you can keep all four cores separate but add a second x-axis with DIC concentration (would match more next to figure ¾). Need DIC concentration!

Figure 3&4 need to be combined, add methane concentrations to the figure, and remove the descriptions from the figure captions into the text. Also add “methane” or “CH4” before “rate” in the axis labels. Possibly 8 panels total: top row with methane in situ concentration and production rate (2 x-axes), bottom row is Figure S2 with d13C of in situ and incubation methane.

Figure 5: Consider putting the equations in the supplement and the legend into the figure caption so you can expand the inset. Currently a busy figure.

Figure 6: what’s the uncertainty of the data in Fig 6? If it’s under the symbols, please add this to the description, otherwise please show error bars or discuss in the text.

Figure 7: Is the 15 m box showing integrated values from 0 to 15 m? Or just from 10 to 15 m? This is confusing in the figure. Perhaps you could write 0-5m, 0-10m, 0-15m, even though it seems a bit redundant. Also need hatch marks on horizontal lines at x-axis values (0,5,…,35): currently too hard to read values in the figure. Consider listing the lake ages as this is a nice summary figure and that could help readers follow your point.

Figure 8: Need Methane in axis labels. What are the numbers in the 400s under the y-axes? Please remove.

MINOR Text Comments:

64-68, do you not argue later in the manuscript that old lakes are still a large source of methane to the atmosphere if you integrate through the talik? If so, please qualify this statement in the introduction.

95-99 Consider moving to methods or shortening.

115: have been described “by” and drop the brackets around Elder et al. (2021).

121-122: Confusing to read, consider rephrasing.

125-143: nice descriptions

154-155 extract sediment for what?

160-164 how long were the DIC samples stored before analysis? Were they killed?

185: is “total profile methane production rate” the biologic methane flux out of the sediment?

331: Need a reference for talik thaw ages.

343: “roughly calculated”

389: drop brackets from all but ref date.

427-428: drop “which we believe to be most realistic”, and make “reflect” plural

436: add “the” before “low but relatively constant”. Please give an example value here, eg for one core, how much methane is produced in the first meter vs. how much in all the meters below? Could be in percentage rather than absolute value but it will highlight your point, which I do think is an important one. You could reiterate here that a low rate over a larger distance can “outcompete” a high rate over a shorter distance.

447-453: rephrase this paragraph. It’s arguably your most important finding but difficult to read at the moment. Try writing it in reverse “This study found that as lakes mature, total thawed talik methane production rates will remain similar or even increase bc….”. Rewrite transition to the next section.

486: Reverse this sentence order so you refer to the in-text figure first and the supplement second (also shallow, then deep).

492: drop “in the top meter of BTL” and replace “driven” with “due to”. Could put “available in the top meter of sediment” at the end of the sentence.

511-516: do you mean that you have to look at age since thaw rather than age since deposition?

533: “shows” not “showing”

537: drop “a shift towards”

541-544: swap these sentences, so your conclusions begin with “This study presents the first empirical data quantifying methane production and organic matter degradation of thermokarst lakes from young to mature” or something like this. Then, “this can be used to test models….

553-557: move to discussion

571-572: “while the highest methane production rates occur in the shallowest sediments of the young lake, the increase in talik depth with age also plays…..”

574: do you mean flux when you say accumulated production rate? Consider having it in brackets? Or use consistent terminology.

582-585: Consider rephrasing, I don’t think it really says what you want it to and people will remember the last sentence.