The study “Seasonal controls on methane flux components in a boreal peatland - combining plant removal and stable isotope analyses” is an interesting field experiment conducted in a Finish boreal bog which looked at d13C-CH4 composition, CH4 concentration in peat porewater along with CH4 emissions (plant-mediated + diffusion + ebullition). The authors designed an experiment in which they were able to isolate the contribution of CH4 emission or oxidation from different vegetation types. The study was conducted during the growing season 2021 and 2022 using manual flux chamber measurements in 15 different plots (5 spatial replicates of three different treatment plots). The main findings from the study are that methane oxidation in the Sphagnum moss layer decreases total methane emissions by 82 ± 20 % while transport of methane through aerenchymatous plants increases methane emissions by 80 ± 22 %. Although not mentioned in the abstract, the authors also found higher CH4 emission at lower water table levels which raised my attention since it goes against the general consensus that greater CH4 emissions occur at higher water table levels.

The manuscript is coherent and well-detailed. I found the results section a bit lengthy and tedious, however. Removing secondary information might help increase the clarity of the text, if the authors wish to do so. The discussion was clear, well-structured and furnished with relevant references. Despite my overall enthusiasm about the study, I still have some major and minor comments that would deserve to be considered. Please see below.

Major comments:

1. I do not think that the study is directly investigating the effect of climate change on peatlands CH4 emissions. The authors have only conducted manual measurements over the growing season in 2021 and 2022. I would recommend the authors to focus on the methane emission pathways and avoid referring directly to climate change when discussing their results.

1. Although the results and interpretation are clear within the main text (i.e. vascular plants increase CH4 emissions while Sphagnum increase methane oxidation), the overall outcome and implications of the work are confusing. In the abstract the authors wrote “The provided insights can help to improve the representation of environmental controls on the methane cycle and its seasonal dynamics in process-based models to more accurately predict future methane emissions from boreal peatlands.” In the conclusion they recommend that “Better understanding the effect of peatland vegetation on CH4 emissions and its seasonal dynamics and incorporating it into process-based models will therefore greatly improve our estimates of future CH4 emissions from boreal peatlands under the changing climate.” While I agree with the suggestions, I feel that the authors did not fully delivered here since they presented contrasted results without explaining how their findings should be incorporated into models and projections. Moreover, findings from the study suggest that “aerenchymatous plants increases methane emissions by 80 ± 22 %” while “Sphagnum moss layer decreases total methane emissions by 82 ± 20 %”. In other words, the two processes seem to cancel each other. The strength of the paper is that the authors were able to isolate those pathways which helps understand the respective contribution of different vegetation types on methane emissions but I don’t think that the findings presented are fundamentally changing the way CH4 emissions from peatlands are being measured and integrated into models. I would recommend the authors to better link their findings with the needs for the process-based model developments they claim.

1. I was surprised by the statement “higher CH4 emission occurred at lower water tables” which wasn’t supported by any figure or statistical analysis. If this claim were to be true, it would go against the general consensus and would deserve further elaboration from the authors. Here are some global references showing the clear relationship between water table level and CH4 emissions in peatlands and wetlands.

Evans, C. D., Peacock, M., Baird, A. J., Artz, R. R. E., Burden, A., Callaghan, N., et al. (2021). Overriding water table control on managed peatland greenhouse gas emissions. Nature, 593(7860), 548–552. https://doi.org/10.1038/s41586-021-03523-1

Huang, Y., Ciais, P., Luo, Y., Zhu, D., Wang, Y., Qiu, C., et al. (2021). Tradeoff of CO2 and CH4 emissions from global peatlands under water-table drawdown. Nature Climate Change. https://doi.org/10.1038/s41558-021-01059-w

Zou, J., Ziegler, A. D., Chen, D., Mcnicol, G., Ciais, P., Jiang, X., et al. (2022). Rewetting global wetlands effectively reduces major greenhouse gas emissions. Nature Geoscience, 15(August), 627–632. https://doi.org/10.1038/s41561-022-00989-0

1. I am sorry if I missed it but could the authors clearly explain how the respective contribution of aerenchymatous plants and sphagnum moss to CH4 emissions was determined since it is an important part of the study – perhaps by using a conceptual diagram. I also wonder how confident the authors are that the numbers provided and the approach used is relevant and representative beyond their study site? I wonder if a stable isotope mass balance model could help further support their findings by using a second approach that is independent of the first one. For example, previous studies were able to differentiate CH4 loss between ebullition and plant-mediated transport. Please see the reference below:

Corbett, J. E., Tfaily, M. M., Burdige, D. J., Cooper, W. T., Glaser, P. H., & Chanton, J. P. (2013). Partitioning pathways of CO2 production in peatlands with stable carbon isotopes. Biogeochemistry, 114(1–3), 327–340. https://doi.org/10.1007/s10533-012-9813-1

Holmes, M. E., Chanton, J. P., Tfaily, M. M., & Orgam, A. (2015). CO2 and CH4 isotope compositions and production pathways in a tropical peatland. Global Biogeochemical Cycles, 29, 1–18. https://doi.org/10.1111/1462-2920.13280

Below are the minor comments I made while going through the manuscript

General: It would have been easier for the reviewers to have the line number provided for all the lines.

Abstract :

Line 1: The general statement “wetlands are highly vulnerable to climate change” is not clearly explained or mentioned in the manuscript. I wonder if it makes sense to start the abstract with this. How does a study looking at seasonal variability providing insight on an ecosystem response to climate change? The time scales are different. Moreover, the study is about peatlands not wetlands.

Line 5: I am assuming that methane emission means diffusion + ebullition? If not, better to state methane diffusion instead.

Line 7-8: Interesting. This may be true at the plot scale but I think water table level would still play a big role at the ecosystem scale if the authors would have considered the elevation gradient within their experimental design, for example.

Line 9: “Increases” or “Contributes to”?

Line 11-12: I am not sure I understand this sentence correctly. What is left in a peatland if sphagnum and vascular plants are removed? It may be good to rephrase with the word “presence”. Boreal peatlands are by definition occupied by sphagnum moss, aren’t they?

Line 13-14: Care must be taken when linking environmental variables with climate change. The effect of climate change is usually described (and observed) over a decadal time scale or longer…

Introduction:

Line 22: It may be good to add a sentence to explain that while water-saturated peatland soil prevents organic matter oxic decomposition, they also favour anoxic degradation pathways such as methanogenesis. This will help connect the two sentences.

Line 25: Is it accurate to put at the same level vegetation composition, that soil temperature and WTD here? IMHO, the weather and climate directly influence soil temperature and WTD which in turn my affect the vegetation composition.

Line 26-29: How does “a shift in vegetation communities” will “likely result in a widespread drying trend in boreal peatlands”? I understand the hydrological feedbacks part but I don’t know if one can say that vegetation communities directly influence ecosystem’s moisture. Again, I wouldn’t put vegetation communities at the same level than the two other environmental variables.

Line 28-31: Could the author be clearer here? The sentence doesn’t say much. Is climate change going to increase or decrease CH4 emissions from boreal peatlands? Terms like “might considerably affect” or “altering” are very general. If the direction and magnitude of CH4 change from boreal peatlands cannot be clarified or supported by the literature, I suggest removing this part.

Line 31: Net “flux” of CH4 produced by methanogenesis?

Line 34: How can a gas be stored in the peat without evading or being oxidized? Do the authors mean in the peat “pore water” as dissolved gas?

Line 34: I suggest replacing “CH4 flux” by “CH4 diffusion and ebullition”.

Line 38: Environmental or “Environmental and ecological”?

Line 58: I think what the authors mean here is the “carbon stable isotope ratio (δ¹³C-CH₄)”

Line 59: Sine most of the introduction was on understanding the impact of climate change on peatlands, I wonder what kind of answers vegetation removal experiment can provide to answer the stated research question?

Line 60: The authors could mention the term “ombrotrophic” here. Nevertheless, I don’t think the definition of a bog should appear after stating the research objectives.

Line 62: CH4 emission rates.

Line 63: Sorry but I couldn’t find the statement that “hollows are the most sensitive to climate change” in Kokkonen et al., 2019. The term “hollow” is only mentioned once in the document.

Line 83: I haven’t been able to find the microtopography mapping methodology in Alekseychik et al., 2021. I am particularly interested in knowing how the difference between lawns and hollows were made since they usually follow an elevation gradient and are occupied by the same type of vegetation.

Line 89: What was the area of each plot?

Line 90: When saying “vascular plants removed”, do the authors also mean the roots or only the aboveground part? This would mean that the fresh yet dead roots were available for decomposition. For the P plot, how thick (cm) was the removed layer?

Line 93: The root barrier intrusion may have cut the roots. This would mean the fresh yet dead roots were available for decomposition. Was this considered as a possible bias in the study?

Line 112-115: What hypothesis were the authors trying to test here? Is light expected to influence CH4 emission?

Line 154: Was there any statistical threshold (p value, r2) to determine if the diffusion flux was statistically significant or not?

Line 160: By light conditions, do the authors mean transparent or dark chamber or based on the incoming radiation or photosynthetically active radiation?

Line 167: Interesting. How many times did this happen?

Line 176: pore water dissolved CH4

Line 189: Typo: The water samples for analysis of dissolved CH4 were kept cooled. Usually the headspace technique is done on site to avoid oxidation to happen in the meantime. I also wonder if the change of atmospheric pressure between the study site and lab may have affected the manipulation and results.

Line 195: Just out of curiosity, did the authors sometimes got a Chemdetect value of 1 when running they samples? If so, what action was taken to go around this?

Line 207: Where was this reference gas / standard from?

Line 237-238: It may have been good to explain in the introduction how each of these variables are likely to affect CH4 production and emission

Line 259-262: Can this linear relationship be provided as a supplementary material?

Line 265: If I understand correctly, the authors refer to “daily averaged temperature”. It should be explicitly stated as such.

Line 274: OK, this answer the comment made for line 112-115. Maybe good to merge these two sentences for clarity.

Line 297: What the authors mean here is “Ch4 emissions from our dataset”, I believe. The value of 2mgCH4m-2d-1 was only measured at peat + sphagnum moss, for example.

Line 300: Was this difference statistically significant?

Line 305-309: Were all these differences statistically significant?

Line 322: How was the effect of vascular plant and sphagnum calculated? Is it only a subtraction between the flux taken in different plots at the same time?

Line 335-337: Should peat temperature and water table depth “influence the effect of the Sphagnum layer on CH4 fluxes” or simply “influenced CH4 fluxes”?

Figure 3a: The decision to merge pore water data for PA and P seems to go against the research objective…

Line 438-441: Can the author be more specific on how they were able to determine that HM was more important than AM based on Figure A2?

Line 506: One word is missing here. Is it “balance”? If so, storage as dissolved gas and lateral exchange seem to be missing in the “equation”.

Line 547: This is an interesting claim as it goes against most of the papers that have jointly measured WTL and CH4 emissions from peatlands. I am, however, unable to find any figure or relationship that is supporting the claim that the authors are making.

Line 550: Again, I do not think the term “climate warming” is appropriate here .

Line 555: How much warmer and variable were the temperatures between the two periods mentioned?

Figure A2: Why is there only 2 points for emissions? Could the colour code be for the sample depths and the shape code for the plot types? Additionally, the authors could considered give a CH4 concentration weighted-size of the points to show where the highest concentrations are located within the plot.

General comments:

The authors assessed the relative importance of different forcing variables on methane flux in Southern Finland. The main objective was to measure the seasonal variations of methane fluxes and the explaining variables. This study is at the crossroad of ecosystem functioning/climate change/biodiversity. As such, the questions addressed in this paper fall within the scope of BIOGEOSCIENCES.

On the whole, the manuscript is very well written and illustrated.

Although the objectives are clearly stated, the hypotheses are missing in the introduction. The authors manipulated the biodiversity by removing 1) vascular plants and 2) vascular plant and Sphagnum. They don’t mention what are the expected effects of these treatments on methane flux. This information should be stated right from the introduction.

The methods are clearly described and can be reproduced. The methods and the statistical analyses used are adequate.

The discussion is relevant and supported by the results. However, some aspects of the article need to be clarified to reach a wider readership and to acknowledge a key issue in terms of soil physics between treatments.

Specific comment:

First, the readability and the understanding of the discussion on isotopic results would be greatly improved by giving some basic reminder of δ¹³C signature of the different metabolic pathways. Also, some assertions are lacking explanation, such as the sentence of the lines 437/438-page 38. As it is, the discussion on the isotopic results is a bit hard to follow, and it fails to fully convince the reader. The manuscript would be greatly improved by clarifying all the sections dealing with isotopic results.

Second, the Sphagnum removal should not be placed at the same level of vascular plant removal in terms of its effect on methane flux. Vascular plant removal (PS treatment) does not affect (or in a minor proportion) the physical condition compared to the control situation (PSV): same damping of air temperature with depth in both treatments, almost the same water table depth, supposedly. However, in the “P” treatment, the temperature amplitude at the maximum methane producing zone (just below the water table) should be greatly affected compared to the other two treatments, because of the physical removal of matter. Although the effect of a thicker peat layer on methane production and consumption is highlighted, the effect of the physical removal of a Sphagnum layer on abiotic variables and their subsequent effect on biological processes is not fully acknowledged. The “P” treatment is not only about biodiversity, but also about soil physics. It is in this sense that the “P” treatment is not at the same level as the vascular plant removal treatment. This should be more clearly stated and taken into account in the discussion. If the authors have high frequencies time series of soil temperature under each treatment at least one spatial replicate, they should add these data to the manuscript and use them to further improve the discussion.

Technical comment:

Page 15 – line 372 : write “…was more depleted in ¹³C …” instead of “…was more depleted in δ¹³C …”

Page 20 – line 506 : should write “CH₄ flux is the net balance of CH4 production and CH4 oxidation” instead of “CH₄ flux is the net of CH4 production and CH4 oxidation”