General Comments

The study assessed the impact of seasonal freeze-thaw processes on pore structure and their  impact on SOC fractions for soils of the Qinghai-Tibet Plateau, which has large permafrost coverage for its latitude. The specific study objectives were to (1) to quantify changes in pore structure and the SOC fraction content of aggregates in typical alpine ecosystems (shrubland and meadow) during the seasonal freeze-thaw process; (2) to investigate the relationships between them and (3) to clarify the role of pore structure on aggregate functions related to SOC protection during seasonal freeze‒thaw processes. The researchers sampled 18 soil profiles per freeze-thaw period in 3 depth increments and used a combination of dry sieving, XRT/CT scanning, elemental analysis, and soil fractionation to assess aggregate and pore structure, total carbon, particulate carbon, and mineral-associated carbon. Their main results were that 

1. pore characteristics of 0.25-2 mm aggregates were more vulnerable to seasonal FT processes than that of > 2 mm aggregates.
2. The freezing process promoted the formation of > 80 μm pores of aggregates. 
3. The total organic carbon (TOC), particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) contents of macroaggregates were high in the stable frozen period and low in unstable thawing period, demonstrating that freezing process enhanced SOC accumulation while early stage of thawing led to SOC loss. 
4. The vertical distribution of SOC of aggregates was more uniform in stable frozen period than in other periods. 
5. Pore equivalent diameter was the most important structural characteristic influencing SOC contents of aggregates. 
6. In the thawing period, pores of 1530 μm inhibited SOC protection. 

This is an interesting and important research area and is a currently relevant study within the broad realm of soil carbon loss as a function of melting permafrost. However, I have several concerns with the study methods and therefore the interpretation of results. The very low sample size of nine for the comparisons between freezing and thaw period soils raises questions about the assertions of statistically significant differences, particularly when taking the large standard errors into account. The main concerns relate to making multiple comparisons without adjusting for those multiple comparisons that could be quelled if the data and code were provided. The second concern is the soil density fraction method, which is an outdated method from the early 1990s that has proven to be an imprecise method of density separation compared to the more commonly used sodium polytungstate method. Sodium hexametaphosphate solutions can only achieve densities of up to about 1.2-1.4 g/cm3, whereas the commonly agreed upon densities for separating mineral fractions are 1.6 -1.85 g/cm3, which cannot be achieved using sodium hexametaphosphate. Results relating to the density separation are therefore unreliable. 

I recommend removing results related to the density fractions and down-scoping this manuscript to focus on the seasonal differences in pore properties and TOC content, including the correlation table but not the RDA, which is redundant information. The introduction is lengthy and could be revised to include less ancillary information and grammatical structure could be improved throughout. 

Specific Comments

SOC fractionation performed according to 1992 methods using sodium hexametaphosphate. This is an outdated method that should be retired in favor of using sodium polytungstate solutions for more precise density separation. Only in cases where the researcher is building on previous data to form long-term datasets would it still be appropriate to use sodium hexametaphosphate for comparability between studies. 

Figure 2 is excellent!

Table 2 is labeled as correlations between SOC content, soil microbial characteristics. It seems that microbial characteristics is not meant to be included since none of the variables presented fit that category. 

Actual p-values should be provided in the text instead of presenting them as p <0.05. 

Fig. 5: When conducting multiple comparisons with the low sample size of nine, caution must be taken in interpretation of results. Without seeing the data itself, it is difficult to assess the validity of these results, given the high variability and low sample size. It is likely that the proportion of significant results would be relatively low given the sample size and variability. Further scrutiny of the data and statistical tests is necessary.

Table 2 and Fig. 7 effectively present the same information – that is the strength and direction of correlation among different covariates, so only one of the two should be presented. 

The supplementary data table should include standard error for each variable measured. 

Technical Corrections

I would be happy to provide technical corrections for a revised version of the manuscript.

General Comments

This manuscript presents field data of soil aggregate pore structure and carbon content through an annual freeze-thaw cycle. The measurements appear to have been carefully executed, and demonstrate some trends throughout the year for both pore structure and carbon content. The work also demonstrates strong correlations between some pore structure observations and carbon cycling through the year. Most strikingly, POC and MAOC pools strongly are associated with different pore characteristics during the freezing and thawing seasons. The review of soil aggregate FT mechanics is quite extensive.

    Despite extensive literature review, the manuscript struggles to contextualize its findings. Most importantly, the relationships presented are purely correlational, and are difficult to assume as causal. Protection is postulated as the driving mechanism for carbon protection, but the seasonal inputs and outputs are hardly mentioned. Additional drivers like mineralogy, hydrology, and FT intensity are also not discussed. The influence of these factors has already been described in another manuscript by the same authors, where soil water content was found to be a critical factor (https://doi.org/10.1016/j.catena.2023.107359). This highly related study should be more carefully introduced and discussed in the present work. Moreover, the broader significance of carbon protection in aggregate pores is not strongly established by the manuscript. For example, the study region is generously introduced in the introduction, but does not return in any of the results, discussion, or conclusions. The manuscript could also be improved by a smaller number of better integrated citations. Grammar and paragraph structure could be improved and streamlined throughout.

   I would be interested to see a closer look at the data, with increased focus on the seasonal cycle, causality, and other driving factors. I think the value of the annual time series was not fully explored, and suggest that the analysis could look more carefully at the changes in each layer of each ecosystem over time, rather than aggregating all the soil layers and both ecosystems into the same statistical analysis. For the interesting data and contribution to understanding challenging soil processes, I recommend this manuscript to be reconsidered with revisions to the analysis, discussion, and contextualization of the findings.

Specific Comments

• The author’s previous work in the region should be more thoroughly described and integrated into the manuscript. Discussion of mineralogy, soil water content, and inter-aggregate porosity would all aid in the interpretation of your novel findings here.
• The introduction and conclusion could be strengthened by removing extraneous detail, while focusing more on the implications of the work. Climate change and the QTP is a very interesting topic, and the reader would be interested in the implications of your work to understanding the future of the region.
• The data on vertical structure (eg Table 1) has potential to be interesting, but is largely unsupported by the manuscript. I suggest it should either be presented with supporting discussion, or trimmed from the manuscript.
• Table 2 and Figure 7 present some interesting correlations, but I would be interested to see a scatter plot (perhaps color-coded by ecosystem) for some of the key relationships. I’m worried that the seasonal differences reflect different ecosystem behaviors, rather than mechanistic causality.
• The results throughout the paper are presented without much discussion of the physical mechanisms. I think the results in changing pore structure would be much more compelling with thoughtful discussion of the physical mechanisms. The same goes for the mechanisms of carbon protection, taking into account the sources and sinks of carbon.

Technical Corrections

Better paragraph structure and organization will improve the overall clarity and readability tremendously. I would be happy to provide more detailed comments on a revised manuscript.