Dear Drs. Yafarov and Schaefer,

many thanks for your replies and the revised manuscript which has become much clearer.
One of the reviewers provided a second review. The main point of this review is, that the manuscript requires a strong conclusion, with a clear emphasis on the new findings,
as well as some structural work.

I encourage you to submit the revised version of the manuscript, as well as the point-by-point response letter, in response to the reviewer's comments.

As soon as I get this point-by-point response, as well as the revised version (using tracked changes), I will continue with the review process.

I look forward to the revised version,
Sincerely,
Julia

Dear authors,
many thanks for your revised manuscript.
Please find below the minor revisions recommended by one of the reviewers.
Sincerely,
Julia

Abstract

Thank you for adding some concrete results here. I would make a further suggestion, however: increasing the total amount of simulated carbon can be easily achieved in many ways (for example, change the decomposition rate), however the key thing is that it is simulated in the right places. Therefore I would suggest you also add something along the lines of – the spatial correlation of the simulated and observed distribution of carbon is increased from x to y?

Introduction
Line 22: "and emissions to amplify climate warming" -> "and emissions that amplify climate warming"
Line 40: Typo: Hugeluis -> Hugelius
Line 44-45: Deleted either 'area' or 'extent' Line 71: "an SOL" -> "a SOL"

Last paragraph is much better. One minor comment is that it just says the aim is “to reduce the bias of initial permafrost carbon stocks” - but as you have discussed in the preceding paragraphs, improving the thermal dynamics not only improves the initial carbon stocks but the response to warming. So perhaps change this to “to reduce the bias of initial permafrost carbon stocks and improve the dynamics”

Methods
Move lines 215 - 223 (until end of sentence) to the next section as they are about the roots. Lines 267-270. The following is basically a repeat of the previous paragraph:
"We restricted simulated root growth to occur only in thawed soil layers. In SiBCASA, leaf growth is linked to fine root growth (Schaefer et al., 2008), so this also delays spring leafout until the soil begins to thaw. We first calculated the fraction of thawed roots within the root zone defined by:"

I suggest to change it to
"In order to restrict simulated root growth to thawed soil layers, we first calculated the fraction of thawed roots within the root zone defined by:"

Results

Lines 370-394: Paragraph on vertical profiles. Discusses what the modelled profiles are but does not compare to measured ones. Harden et al. 2012 (which is referenced, but not discussed) shows some observed profiles. I suggest to add one or two sentences along the lines of: The carbon in the active layer below the organic layer is lower than in the observed profiles in Harden et al. This is probably because cryoturbation is not included in the model. The top SOL and deeper carbon match well with the observed profiles (?).

Lines 405-433: Final paragraph of results. Discusses new initialisation. This paragraph is not totally clear. I am a bit confused by this sentence: "However, the NCSCD map (Fig 6B) shows that not all permafrost regions contain a uniform amount of frozen carbon." Would we expect them to? How

discusses the differences between NCSCD and the simulation, but it would be good to indicate actually how much the distribution is improved by initialising with the NCSCD rather than the original method. For this I would suggest to make a spatial correlation of the NCSCD with your simulations. This value can then go into the conclusion and abstract as well.

Discussion

Lines 489-492: Seems to suggest that when the carbon is below the active layer it does not influence the soil thermal dynamics. Does it not still change the thermal properties of the permafrost, and because this part of the soil column is thermally connected to the active layer part above it, it should have at least a small influence on the active layer thermal dynamics?

Line 556: 'SND' -> 'SD'?
Lines 505-561. This is interesting but I'm not sure it is completely relevant. I realise this was added on my suggestion, but the reason I suggested it was because you were saying that permafrost was or wasn't simulated in particular regions due to meteorological variables / snow, and my concern was that those assertions shouldn't be made without showing something more concrete. However, now those original comments are not in the manuscript I think it might be better to remove this paragraph? But I leave it up to you to decide.

Conclusion

As I have mentioned in the comments for the abstract/results, it would be really good to say something about the spatial distribution improving as well as increasing the amount of carbon simulated.
I also suggest that you add a sentence along the lines of 'These improvements indicate the importance of including these developments in all land surface models.'
Line 619 : 'modified' -> 'modify'

Dear authors,
I am pleased with the changes and look forward to the final manuscript.
Sincerely,
Julia