The authors did a good job to respond to all the comments from both reviewers. They changed the figures to clarified their results, and rewritten the discussion delivering a clearer message. I only have few specific corrections and two main point that the authors need to address below.
Thanks for clarifying the methods used for measuring soil respiration and also to show the respiration at day 4 as well as day 13. An important point that need to be added, it is not only a question of the effect of freeze-thaw cycle, temperature and length of the incubation on the samples, but you apparently also sieved the sampled at 2 mm before freezing the samples (L94-95). Sieving the sample will have stronger effect than one cycle of freeze-thaw, releasing organic matter, breaking down soil crust and aggregates and also exposing microorganisms to different level of O2. Coupled with the temperature and length of incubation, this could drastically alter the trends in your results and stimulate activity in some samples more than others. Together, and as you mentioned, you measured potential respiration, but you need to clearly say that these conditions are not in situ, and a potential effect of the incubation procedure (sieving, temperature, thawing) cannot be discarded. You have to mention the effect of sieving (L318-319) which could have a stronger effect on soil biological crust than other soil, and have to conclude that you can’t discard a method effect (L324-326). I stress the fact that this is a requirement to clearly state the potential limitation of your measurement.
Section 4.1 is still too long and mainly describe the site and present results instead of discussing them. The section brings little information. For example, the first sentence is similar than the material and methods, just a site description; L277, this result is already given L199 in the results section. And this is true for most of the section. Unless, you have novel results compared to the literature, or those results can directly explain the microbial results, this section is not useful and could be reduced in few sentences or deleted. This is especially true from L272-285. The sentence L285-287 is unclear and should be rephrased (if kept) and related to the microbial community. Line 287-290 is also detached from the microbial data and miss linking those results together.
The next section (L291-300) is not at his place in section 4.1. This is (Mg) partly discussed L366-380. I would merge both sections and avoid repetition.
Overall, I don’t think you need section 4.1 and 4.2 but just one discussion nicely split in different section without headers.
L12: delete “proceeding”
L18: change in the whole text “basal respiration” to potential respiration”
L20: change “in” by “on”
L32: “play a fundamental”
L39: delete “The proceeding”
L52, 55, 56, 58: this was already in my initial review (reviewer 1); you need to clearly state which ecosystems the articles you site work on. As you said in your reply, the altitude trend for microorganisms does not work like for plants and animals. So, where the study took place is likely to have a strong effect on the results. You have to state which ecosystems the study you site work on, this will help the reader to have a better understanding. As it read, the reader could think that all these studies took place in the Arctic but it is not the case. Please, give the ecosystems. This is also true for the discussion,
L65: delete “alpine”
L65: change “the arctic alpine” to “arctic”
L65 “we conducted a study”
L142: it is difficult to believe there is no significant difference between day 4 and day 13 when figure 2 b and c shows that at day 4 (Fig 2c) potential respiration is around 2 times higher than at day 13 (Fig 2b). Unless what you want to say is that you have the same difference between the altitude regardless of the measurement date? Be more clear.
It is also not true that you only present day 13 as suggested at the end of Line 142, as you present day 4 and 13. Please correct the sentence.
L144: change “defined” by “determined”
L186-187: it is not true that you can’t consider the triplicate as independent. Microbial ecology shows that you can have more similarity in samples taken km away from each other than few cm away. This is especially true for your design when you sample from vegetated area to bare soil, while you clearly show in your study that bare soil are different. So, you could consider your triplicate as independent. This is a general comment, as I am not asking to change the statistics here.
L221: change “Oppositely”, by “In contrast”
Section 3.3: it is worth mentioning that the daily rate is around 2 times higher at day 4 than day 3. Would be also interesting to mention how it compare with day 12. Even if this is not the main message you want to deliver, it is an interesting result which could be briefly presented.
L233: “was significantly positively correlated”
L243: “change “had” by “at”
L258: change “Oppositely” by “In contrast”
L260: delete “an”
L265: change to “The soil with the poorest TOC and richest Mg concentration at the highest site on Tr1...”
L272: “characterised by a four”
L294: delete “In result,”
L316, 327, 328, 329, 330: give the ecosystems the studies are working on
L320: give the days of incubation in brackets with what you define as flush, adaptation, stabilisation
L323: change “accord” by “agreement”
L330: “the majority… was associated with…”
L354: change “at more elevated sited” by “with altitude”
L355: change “typical” by “characterised”
L355: “unfavourable” depends of the microorganisms as you mention, what is unfavourable for one is favourable for the other. It is better to characterise the conditions rather than saying favourable or not.
L357-358: you need to acknowledge here that you did not measure the F/B ratio on the incubated samples use to measure soil respiration. Thus, you can’t be sure that the fungi explain such results. You could have a complete shift of your community as stated L327.
L358: change “prosper” by “grow”
L361: what do you mean by “begign”. Don’t use such word but rather define the type of soil/conditions
L 364: change “likely” by “could”
L370: “Tr1 had higher actinobacteria and phototrophic microorganisms abundance”
L390: delete or rephrase, what does “uniform” mean in that context? Do not use “concurrently”
Figure 2: b and c are both potential respiration, it would make more sense to give the incubation day (4, 13) which is more clear, especially in the caption and y axis. “flush respiration” and “potential respiration” are not self-explanatory in the figure. The caption should not need the support of the text to be understood.