This manuscript presents a thorough imaging and modeling study on pore networks in peat samples collected at different depths from a drained peatland, and uses this analysis to discuss implications of peat porosity and pore network characteristics on gas transport and methane production in peatlands. The manuscript is well written and easy to follow. The methods are explained well, although more details of error analyses and impacts of errors on the results, as well as some reconsideration of the statistical analyses would be needed (see specific comments below). My main concern about the presentation is that the results seem mostly intuitively obvious. It makes sense that porosity increases in peat towards the surface just because of how increasing pressure would influence and deform peat structures the deeper one goes in the soil layer. Maybe this has not been shown with the methods used in this study before, but the manuscript fails to communicate the state of the art in this kind of studies. This, combined with that one of the main results, the hysteresis behavior, seems to be just a model result with no verification based on the experiments, and the superficiality of the discussion on the connections between the porosity and network parameters and their impact on methane emissions and gas transport makes it hard to understand the importance and impact of the study. Was the goal to demonstrate what the used techniques can do? Or was it more to showcase a way to understand CH4 emissions? This same unclarity in focus is apparent from the figures. Figure 3 is clearly a model vs. measurement comparison, but it is discussed in the results as a figure presenting characteristics of the peat samples. Figure 4, on the other hand, is presented in a format that emphasizes differences in the peat sample properties, but is discussed in the text as a model-measurement comparison. To improve the presentation, I suggest that the authors clearly define the purpose of the study, and then build the text and presentation of data in the figures to support that goal. For example, to support the statements about Fig 1, the changes in porosity between depths could be more effectively presented as a box or bar plot with appropriate error bars and statistical analyses. And for fig 4, the model-measurement comparison would be presented more clearly by an x-y –plot. For the discussion, I suggest, again, focusing on the goal of the study. If the goal is CH4 production and transport, then some simple calculations about the impact of the parameters measured here on the transport and emissions would be helpful. As it is, the discussion reads like a collection of separate paragraphs where the importance of more complex network parameters such as tortuosity or top-bottom betweenness centrality for CH4 production and gas transport are left unexplained, while some relatively obvious results, like that higher porosity lead to higher connectivity (lines 436-444) are discussed in length.

Specific comments:

Line 14: What was the hysteresis in relation to? What were the parameters that showed the hysteresis behavior?

Line 23: Please be more specific about how peatlands modulate or are modulators of hydrological and biogeochemical cycles. Why are they globally important?

Line 28: The line starts with repetition.

Line 39: Capability instead of characteristic?

Line 96: Why was the diameter of the sample only measured to determine shrinkage? Where the samples all the time in the plastic tubes? Why was the vertical shrinkage not considered?

Line 104: How good is the value of 1500 kg m-3 for particle density for these samples? Does it accurately represent all the sample depths?

Line 106: The assumption that air-filled porosity was zero in the saturated state is probably not quite true. Please give an estimate for how much that might be off in your samples and what kind of an error it would lead to in your results.

Eq 3. Why is this equation needed? Why is not the calculation using eq 1 not enough for the comparisons? How was this equation fitted to data? What were the fitted variables that were measured, and how were they measured?

Line 113-114: Why is it important to tell that the pressure range was so narrow that the fitting procedure needed to be modified? Why was a larger pressure range or a more appropriate fitting algorithm not used?

Line 118: Please move “noninvasively” to the end of the sentence.

Line 123-125: Please give an error estimate for what this darkening might do to your results.

Line 136: How did you deal with that the contrast between air-filled and water containing regions or organic materials was low? How did this affect your results? What kind of and how large an error could it cause?

Line 154: Why did you use the sum of distances? It is hard to visualize how this calculation what performed and what it means.

Line 158-160: Does this mean that the shrinkage of the samples was not taken into account here at all?

Line 164: What does the “largest of these clusters” mean? How was size defined? How does taking this part under analysis solely affect the interpretation of the porosity and connectivity results from the samples? Can this size be somehow standardized between samples to make them comparable? Can there be more than 1 large enough network in a sample that all of them should be considered?

Line 202: See previous comment. How does the defined region affect the connectivity analysis. How can you account for non-connectivity in a standardized sample size?

Line 234: Please explain more clearly how the one-way anova analysis was performed. Were all the depths analyzed simultaneously or did you perform pairwise tests between each. Would a multi-way anova with interactions included or a version of linear models give you more comprehensive results?

Line 242: Figure 3 actually shows a consistent underestimate of porosity by the model.

Line 254: Does water content here refer to the original samples, or saturated samples or dried samples, and at what depth?

Line 260: The hysteresis effect seems to be only a modeling result. Is that a feature of the model, or is there real experimental evidence for that this hysteresis happens?

Figure 6: I think combining the cumulative volume figures to one figure where each depth is described by one average line and error bars (or error shading) would be a mode effective way to present this data. It is not necessary to present data for individual samples here.

Lines 371-380: How do the results of this study relate to this text?

Line 442: Can anything else happen in networks than shorter pathways leading to more alternate routes?

Lines 454-459: How is this related to gas transport of CH4 production?

Line 494-495: How do you get to the conclusion that orientation in diffusion paths does not change transfer towards atmosphere?

The manuscript is a carefully detailed and well described study on pore network analyses of peat soils with a depth differentiated view. The aim is to use results of pore network analyses to help explain methane production potential in these environments. The level of language is very high, the text flow is very good, and it was a great pleasure to review. Although I am not that familiar with micro CT, image analyses and pore network simulations, the results are feasible, while not super surprising, as would be expected from the literature. Still, the manuscript is novel in its approach and comparisons.

I was left a little bewildered, what had happened to the discussion of methane (L371-383 gives some general statements on the importance and general conceptual discussion), in particular, since it was not explicitly modelled nor were the results contrasted against methane flux measurements from the field.

My recommendation is that, now with some distance, the authors re-assess the paper and whether or not the self set aims are fully fullfilled. Perhaps it might be a good idea to focus a little more on the strong technical part of the manuscript and limit the study a little more to the descriptive nature, and then discuss the methane production and diffusion from this vantage points in a more speculative manner. After all, the emerging methane emissions are mostly explaned by a conceptual model.

Major concern

What does this study have to do with methane emissions? This remained unclear to me. Either, the scope of the study should be a more quantitative

Minor concerns

L5 How can the formation of anaerobic pockets be conceptualized in a pore network approach? This is left unaddressed.

L42-43 Here peat specific citations should be made (e.g. Hayward and Clymo (1982), Weber et al., 2017), after all, the suggest a pore size distribution.

L53 like previous comments.

L 90 ff section 2.2: was the VGM model fitted to the averages of the replicates from each depth, respectively? Just a minor information to add.

L94 Sentence not needed, but not harmful, either.

L97 in -> at

L105 This is a rather bold statement. If samples were not saturated under co2 environment of vacuum, my impression is this is not actually correct. Please do not use this assumption.

L118 quantify the sample: What is meant by this? Please specify.

L122 is resolution meant, here?

L122 if this is the resolution, then the real micropores <10micron are not resolved. Thus, much of the area where anaerobia may continue to exist is not covered. Please address this limitation in the discussion. This, alongside the problem of dissecting organic from water.

L191 The resulting image

L198ff you state you exclude the effect of shrinkage (I think you should neglect it in this analyses), but I am not convinced this method does what you say it does. Perhaps elucidate a little more.

L213 relatively? to what?

Figure 3: Are the results shown for 3 samples, only, are there replicate samples included in the data? Potentially, including uncertainties in x might help explain the deviation from the 1:1 line (Table 1). Also, I expect that since the air filled porosity = 0 at saturation assumption is not warranted, the data points would be shifted to the left in x. This could be explored a little more. Also, what would the intercept in Figure 3 represent?

L256: “rather coherent”: what does this mean, specifically? Contrary to this statement, in Figure 4 I see quite some systematic deviation.

Figure 4: exhibits bimodality in the retention curve (i.e. some macroporisity close to saturation) due to sharper drop around 1 cm pressure head. This is visible at the top, and not at the bottom as expected from pedogenesis, again Weber et al. 2017.

Figure 4: It appears that a normalization was done onto one air filled porosity. correct? If so, please specify.

Figure 4: why are these simulations not carried out until a pressure head of -100cm? (Same in Figure 5).

L 290: This pattern can, again, be observed in Weber et al. (2017), but also in other sources in the literature. I suggest adding citations, here.

L384-385 repetition of introduction

L393: a bit of a leap of faith or perhaps a rather general statement: the simulation provide support for the conceptual understanding to be ok. I think these hard earned results should perhaps be discussed a little more in acknowledgement to this (although I detect absolutely no oversell, here).

L425: I see the potential to discuss the obtained pore space characterizing numbers in the light of other peoples results re: methane transport, or any other gas transport in particular. If this does not exist, I suggest to scope this section a little more carefully.

L448 mark you, many of the dead end pores might not have been resolved due to the micro CT technique. Perhaps this should be contextualize, too.

L486: How can a relative quantitative measure (anisotropy) determine the efficiency (a qualitative) absolute measure of gas diffusion.

References

Hayward, P. M. and Clymo, R. S.: Profiles of Water Content and Pore Size in Sphagnum and Peat, and their Relation to Peat Bog Ecology, Proceedings of the Royal Society B: Biological Sciences, 215, 299–325, https://doi.org/10.1098/rspb.1982.0044, 1982.

Weber, T. K. D., Iden, S. C., and Durner, W.: A pore-size classification for peat bogs derived from unsaturated hydraulic properties, Hydrol. Earth Syst. Sci., 21, 6185–6200, https://doi.org/10.5194/hess-21-6185-2017, 2017.