The manuscript is devoted to the reconstruction of soil responces to the permafrost thaw under climate change during last two centuries in the Western Siberian Arctic based on two peat cores. The investigation is well designed, presents new findings on the realtions of climate change, permafrost thaw and carbon accumulation in soils. The manuscript is clear organised and well written. I suggest to accept the manuscript for publication in current state.

Hopw to see the paper published soon!

Yuri Mazei

General comments

The revised manuscript “Peatland development reconstruction and complex soil biological responses to permafrost thawing in Western Siberia” represents high-quality and original study addressing an important question of permafrost mire dynamics in Wester Siberia of the last two centuries. This scientific question is relevant withing the scopes of BG journal. The authors present new paleoecological data and try to interpret them using original concepts. As a result, authors reach substantial conclusions on the dynamics of the studied permafrost mires revealing complex interactions among permafrost, fire regime, local surface wetness and vegetation. The dynamics is interpreted in the context of climate changes. The applied scientific methods and assumptions are valid and in most cases are clearly outlined. My main concern is that sometimes authors go beyond their results in the interpretations and conclusions (see my specific comments), but this can be easily corrected by more precise phrasing or by removal speculative parts (which are not numerous). The structure and the language of the manuscript can be also improved to more concise (see my specific comments). The same concerns the title and the abstract of the manuscript. I think that the manuscript can be accepted for publication after minor revisions. 

Specific comments

Title “soil” is quite unexpected here. It would be better to stick to one term here permafrost soils or permafrost mires. I think the latter is more relevant to the study. The word "soil" can be completely removed from the title.

Abstract

“an increased abundance of fungal communities” I do not see such data in the ms.

“Our study reveals that thaw-induced terrain subsidence was remarkably subtle, yet it underscores the intricate and multifaceted nature of permafrost degradation, which may potentially lead to dramatic consequences.” This sentence is very general.

Introduction

40 I do not really see the difference between these two ways. I think that you are trying to say that increased temperatures will lead to release of the organic materials either through it leaching/removal or decomposition. Why is this negative impact? Or negative for whom? It seems to be a positive relation, the greater the temperature the greater the loss of organic materials. Moreover, at 45-50 you say that increased temperatures lead to other changes in permafrost peatlands such as greater surface wetness and active layer thickness. Why are these effects are not counted in those “negative impacts”? I think that more precise phrases and structure of the introduction can easily solve the issue.

60 “The surface of permafrost peatlands often consists of microhabitats” It is not clear for what kind of living organisms these microhabitats. Perhaps, it would be better to refer to them here as “complex surface topography”. And then explain why this topography represent different microhabitats.

75 “Studied Khanymei permafrost peatlands are located between greening-dominated and browning-dominated zones of Western Siberia.” It does seem like a right place for this sentence because the readers do not know anything yet about the study site.

Study area

115 “precipitation patterns have altered significantly” perhaps have been altered?

Material and methods

Figure 2. Please give more detained descriptions of the cores, otherwise it is not clear from which part of the mire they were extracted (the reader needs to go back to the text). Please, check the other figure legends as well.

205 How the fresh sample volume was determined?

215 “For the peat core, Kh-K1, four (Kh1-A-D) and for Kh-K2, six zones (Kh2-A-F) were distinguished and used in the result description.” This sentence belongs to the Results section.

225 It is not clear why NMDS analysis was performed for one core only?

Results

240 Perhaps, it would be better to place the images of the unidentified testate amoeba to the supplementary materials, as this is not the main focus of the paper. I would recommend structuring the paragraph from the most reliable to the least reliable statements. It would be better to report the abundance and to interpret the hydrological preferences of well-known taxa first, and then mention the presence of the unidentified species. The reconstructed WTD should be reported after the description of testate amoeba assemblages. The same is for the descriptions of the other zones.

“Wetter conditions favoured bigger TA aperture size, higher shell biovolume, and more spherical shells.” The inversed logic here, because water conditions have been reconstructed on testate amoebae. You can say that the predominance of TA with large and spherical shells also indicate wet conditions.

“A less acidic pH (5.1) was reconstructed at the start of the record.” Less acidic compared to what?

330 “Peat plateaus with lichen-moss-shrub cover have been a characteristic feature of the Khanymei peatlands’ landscape in recent years (Volkova et al., 2019).” This sentence seems to belong to Discussion.

Discussion

410 “During this period, the dominance of Betula pollen in the region confirmed moist conditions. Betula is a pioneer species that prefers wetter environments but is sensitive to both floods and droughts (Beck et al., 2016; Lanta and Hazukova, 2005).” I agree that birch is a pioneer species, but I am not sure that it can indicate moist conditions. Why do you think so?

555 “releases additional moisture” Thawing permafrost can release additional water or increase substrate moisture

565 To my mind this paragraph is quite speculative and vague. I think it can be removed completely

610 “The described critical thawing zone (Fig. 8B) is dynamic and rapidly changing, and occurs in a small area most often perpendicular to the previously thawed and collapsed depression and is about 1-2 meters wide with much influence of lateral hydrological drainage (which is difficult to determine).” I do not any description of the critical zone in the text, it is just marked on the figure. Even from the figure I do not see that the zone is “perpendicular” to anything, so these spatial relationships are not persuasive for me. Overall this paragraph seems to be speculative. Are there any other studies, which would report similar patterns?

Technical corrections

180 Lycopodium should be in italic