Cyrill Zosso and colleagues present an interesting look into how deep soil warming alters microbial biomass and high-level community abundance in a forest ecosystem. Overall, I think this is a very interesting paper and applaud the authors for their use of lipids rather than getting stuck in the mud with sequencing, as it provides a different perspective on warming impacts on microbial communities than is typically used. The paper is also well-written and flows well, and was enjoyable to read. There are a few areas I think the manuscript could benefit from clarification on. In particular, how and/or why certain comparisons for depth*warming interactions were made, and a better integration and justification for the brGDTs in hypothesis testing.

Main comments:

The scale on which the data are presented does not seem to match the scale on which the analyses were completed. It would be very helpful to post the R scripts with the manuscript. I found it hard to follow what was being included as a random effect (or whether random effects were nested) in the different results. Was a model of form “lipid ~ warming *depth + (1|block/warm)” or “lipid ~ warming *depth + (1|block/depth)” fit? Or something else?

Related, there seem to be a lot of post-hoc tests, but it is not always clear how these post-hoc tests were selected for completion. Why is the top 10cm sometimes compared to the bottom 10cm, and other times some intermediate depth compared to the deep? Or why is the cutoff for depth 30cm in some instances, and 50cm for others (ex. total PLFA vs. Actinobacteria)? Why is there only one p-value reported (ex. L229-230) when looking at all the depths below a certain point, and not one for each of the depths analyzed as show in the figure? Was the total lipid below a certain depth summed for each core to complete this analysis? [I think this would make sense from a statistics standpoint]

Second, please add more justification for why brGDGTs were measured (in terms of specific hypotheses) and how they should be interpreted. The authors mention that they turnover slowly…is this why they were chosen? If so, what does this mean for interpreting the data from a 4-year warming study? Since these are predominantly necromass, is the idea that microbes under heated and control conditions might be preferentially consuming these or warming might accelerate their turnover? Or is the idea to try and see if there is a signal in the brGDGTs that might indicate how microbial communities have overall changed in the past 4 years, which is not visible in the more rapidly cycling PLFAs? Or is the idea to capture predominantly the archaea community, which would not be captured by PLFAs?

Minor comments:

Since the soil is warmed by a smaller degree in the top 20cm compared to below that, why not just discard the shallow soil data since it cannot fairly be compared with the deeper samples? Also, since lipids were extracted from less soil in shallow compared to deep samples, the deep samples could just be more representative of deep soil and therefore easier to detect a difference in.

L135: why add the standard in after lipid extraction, and not directly to the soil so that the authors could get a better idea of extraction efficiency for the different soil depths?

Could figure 4 be presented as an ordination instead? There is a lot to digest here.

Grammar/style

The “gram” in Gram positive/negative should be capitalized, as it refers to someone’s name (Hans Christian Gram)

L177: please mention what kind of post-hoc test was used. 

L281: correlations are generally reported as R (for Pearson) or rho (for Spearman); R^2 is the coefficient of determination.

L300: there are also a lot of unknowns with respect to extraction efficiency of chloroform fumigation extraction. It almost certainly underestimates the C content of high surface area:volume small cells, as it predominantly captures cytoplasm.

Please also make sure to report the F/T/Z statistic and degrees of freedom, preferably in the text, or otherwise in a supplementary table.

Whenever someone says something increased/decreased with depth, it sounds like depth has been treated as a continuous rather than categorical variable. So please try to avoid this.

The article entitled “Whole soil warming decreases abundance and modifies community structure of microorganisms in subsoil but not in surface soil”, address the impact of soil warning in the soil microbial community. The article fits the scope of the journal and it will be of great interest for the journal readers.

The introduction summarized the previous knowledge in the topic in clear and concise way with clear and funded hypothesis.

The material and methods described in detail the laboratory analysis, but the description of the experimental setup is very brief. How was the temperature increase in the soil profile done? The articles you cited would probably describe it in detail and if a reader is interested can go and check those articles; but a short description here (no need to go in deep detail) would help to understand the setup of your experiment.

In the result section, the soils depths shown in your tables and figures is not clear. At some point, looks like you sample the 0-5 cm soil surface, and then you sampled in intervals of 10 cm until 85 cm depth, but that is not what I stated in the material and methods. Maybe including the sampling intervals instead of the middle point of it will be clearer. Secondly, when you describe the results in the section 3.1, 3.2, 3.3 and 3.4 the numbers do not match with the respective tables. Are those numbers an average on control and warm soils? If so, this need to be clarify in the text. Regarding the MBC, this data have been used for another paper that has been resubmitted, in my opinion you could discuss about it but not include as a result.  

Finally, in the discussion section, you mentioned the difference in the heating temperature between the topsoil and the sub-soil in the section 4.2. This should discussed a bit further, since the differences you observed could be easily related to this temperature difference.

Below some specific comments

• Line 21: Gram should start with capital letter
• Line 31: “representative concentration pathway 8.5” this is part of a global model simulation, right? It needs some clarification on the text.
• Line 39: The reference “Fierer et al., 2003b”, it should be a Fierer et al., 2003a before in the text. You need to reorganize the references of this author.
• Line 73-77: You introduce the use of the PLFAs with several examples. You should do the same with the brGDGTs.
• Line 83-93: The hypothesis are clear, but I would suggest rewriting a bit this paragraph. Stating at the beginning that you have two main hypothesis and described them, and then add all the text to back them up.
• Line 103: Why was the soil heated at different temperatures along the soil profile? A short explanation should be added.
• Line 118: Why do you skip some soil depths? I.e. 20-30; 40-50; 60-70; 70-80? A short explanation of why these depths were excluded from the analysis should be added.
• Line 145: This reference is not in the reference list.
• Line 190: Reference of unpublished articles should not be included.
• Line 365-367: This paragraph is hanging loose, try to connect to with the previous one.
• Line 582-584: Please add the DOI number.
• Line 602-603: Please add the DOI number.