Carbon Stocks and Microbial Activity in the Low Arctic Tundra of the Yana–Indigirka Lowland, Russia

Comments 1: Abstract: 1) Results regarding nitrogen deposition are absent. 2) Key conclusions are lacking. The statement "with continued climate warming, large-scale thermokarst development, an increase in grass-sedge bog proportion, and shrub community reduction could cause net carbon loss from southern hypoarctic tundras" should be emphasized as a critical highlight.

Response 1: 1) We partially agree. In the manuscript, we present materials on the total nitrogen content in plants and soil to show the C:N ratio, the degree of decomposition of organic matter and explanations of microbiological processes. We did not intend to show nitrogen pools and reserves in the manuscript, since the work is structured with an emphasis on carbon. A separate work is being prepared on nitrogen, which is due to the insufficient study of this element in the permafrost landscapes of Yakutia. In our opinion, for this manuscript, it is sufficient to show the nitrogen content. 2) We think that this was clearly stated in the conclusion.

Comments 2: Line 59: Italicize species name.

Response 2: Agree. We have, accordingly revised. We have corrected the remark. The changes are marked in red on line 62.

Comments 3: Line 62-63: Previous studies indicate shrub expansion [3–10], yet this study suggests shrub community reduction. This apparent contradiction requires explanation in the Discussion.

Response 3: Here, the text is written in the form of a polemic. R.E. Petrov et al. (2018, 2020) suggest that the positive trend of increasing carbon sink in the Chokurdakh tundra that they identified is due to climate change and the expansion of the habitat of shrub species. At the same time, they indicate an increase in the abundance of willow thickets only in the floodplain along the river bank, and not in the alas lowland where we conducted our research. In the article, we assume a reduction in the area of shrub thickets in these alas landscapes rich in underground ice, subject to large-scale thermokarst processes with soil failures with further warming.

Comments 4: Line 72: Convert "2" in "km2" to superscript (audit entire text).

Response 4: Agree. We have changed the structure of the manuscript as a result of Reviewer #3's comments and have made revisions accordingly.

Comments 5: Results (Sec. 3.1–3.2): Content is excessive. Subdivide into four or five subsections. Present only core findings; simplify language.

Response 5: Agree. We have, accordingly revised. We have divided subsection 3.1 into 3 sections: 3.1. Geobotanical Analysis and Content of Biogenic Elements in Biomass and Necromass, Line 481; 3.2. Carbon Pools and Stocks by Tundra Type, Line 638; 3.3. Heterotrophic Activity of the Organic and Mineral Soil Horizons, Line 692.

Comments 6: Discussion: Address key findings sequentially using subtitles.

Response 6: We have changed it accordingly. Subsections added: 4.1. Assessment of Above- and Below-ground Biomass and Necromass in the Context of Southern Tundra Ecology and a Changing Climate, Lines 794-795; 4.2. Influence of Permafrost on Biogenic Elements and Microbial Activity, Line 994.

Comments 7: Conclusions: Excessively verbose. Summarize research outcomes and primary discoveries concisely.

Response 7: Agree. We have changed the conclusion, lines 1084-1136.

4. Response to Comments on the Quality of English Language

Point 1:

Response 1: The quality of the English language has been improved. The translation was done by highly specialized and professional translators with the text being proofread by a native English speaker.

5. Additional clarifications

The manuscript was revised taking into account all comments and three reviewers.

Comments 1: 1) Please consider to indicate the methodology used, including methods of analysis of the microbial community, even if the abstract becomes somewhat larger.

2) Line 28. What means —449.48 t C? Is this a negative value? By the way, please change “C” to “ºC”

3) Line 37. The information about the microbial metabolic quotient should be enhanced. The paper clearly sates that A higher qCO₂ indicates a less efficient microbial community, while a lower qCO₂ suggests a more efficient and potentially more developed community. Thus, qCO₂ provides insights into how effectively soil microbes are using resources and converting them into new biomass, making it a valuable indicator of soil health and ecosystem function. Therefore, this parameter could help to assess if the studied site is becoming a net source of carbon due to climate change.

Response 1: Agree. Comments corrected. Abstract revised, lines 18-42.

2) This means tonnes of carbon per hectare (t C ha-1). No, these are not degrees Celsius. Please excuse the confusion. Lines 30, 32 and 33.

3) The abstract has been changed and rethought, lines 18-42.

Comments 2: There are no references for sentences in Lines 42 to 48. Also sentences in Lines 52 to 57 need references. Please, revise the sentence “… and to analyze the microbiological activity within the soil-plant cover”. Are you meaning within the soil? What means soil-plant cover in this context?

Response 2: Agree. We have, accordingly revised. We have corrected the Introduction. Necessary references have been added, Lines 53-60. We meant plant litter, peat and mineral horizons of the soil.

Comments 3: 1) Information about longitude, latitude and altitude of the studied site and also of the studied region is required.

Response 3: Agree. We have, accordingly revised. Added coordinates of the administrative center of Allaikhovsky district and areas, lines 138-149.

Comments 4: 2) Lines 205 and 206. (1) for formula appears two times. One time is OK.

Response 4: Agree. We have, accordingly revised. Section 2. Materials and Methods has been completely revised, lines 132-479.

Comments 5: Similar comment for Lines 226-227, Lines 235-236. Etc.

Response 5: Agree. We have, accordingly revised. Lines 252, 253, 285, 286, 305, 306, 313, 314, 317, 318, 322, 323, 333 and 334.

Comments 6: Results 1) Two subsections are taken into account in the Results section:

3.1. Permafrost-Landscape Conditions and Physicochemical Soil Characteristics at the "Chokurdakh" Tundra Research Station. 3.2. Geobotanical Analysis and the Content of Biogenic Elements in Phytomass and Mortmass. Please, consider to include a third section. This wouls be section 3.3 dealing with activity of microbial community.

Response 6: Agree. We have changed it accordingly. We have divided subsection 3.1 into 3 sections: 3.1. Geobotanical Analysis and Content of Biogenic Elements in Biomass and Necromass, Line 481; 3.2. Carbon Pools and Stocks by Tundra Type, Line 638; 3.3. Heterotrophic Activity of the Organic and Mineral Soil Horizons, Line 692.

Comments 7: 2) Lines 577-479 include a citation. Citations did not belong to the Results section. Please, move to the discussion section.

Response 7: Agree. The results section has been revised. Lines 480-792.

Comments 8: 3) By the way, several other paragraphs of the Results section can be moved to the Discussion section or even to the Introduction.

Response 8: Agree. The results section has been revised. Lines 480-792.

Comments 9: Discussion. I suggest to organize the Discussion section into three subsections, similar to the Results section. This may be useful to clarify the content of the paper.

Response 9: We have changed it accordingly. Subsections added: 4.1. Assessment of Above- and Below-ground Biomass and Necromass in the Context of Southern Tundra Ecology and a Changing Climate, Lines 794-795; 4.2. Influence of Permafrost on Biogenic Elements and Microbial Activity, Line 994.

Comments 10: Conclusions. This section is two long. Several paragraphs can be moved to the Discussion section.

Response 10: Agree. We have changed the conclusion, lines 1084-1136.

Comments 11: The paper is crowded by too many language / syntactical errors / mistakes. Next, I´m showing several examples, but this is far from exhaustive. Please, revise all the paragraphs and sentences to improve de English.

Lines 28 and 30. “C” should be “ºC”.

Lines 29 and 31. Please change “ha-1”. It should be “ha-1”

Line 37. Units of the metabolic quotient?

Line 119. Is semicolon correct?

Etc., etc.

Response 11: Agree. The comments have been corrected.

4. Response to Comments on the Quality of English Language

Point 1:

Response 1: The quality of the English language has been improved. The translation was done by highly specialized and professional translators with the text being proofread by a native English speaker.

5. Additional clarifications

The manuscript was revised taking into account all comments and three reviewers.

Abstract

Comments 1: The abstract presents serious issues in terms of writing quality, clarity, and structural coherence. It contains overly long sentences that hinder readability and comprehension. Terms like "carbon productivity" are overused without providing an operational definition.

Response 1: Agree. Added relevance, specified the obtained results. Lines 18-42.

Comments 2: There is no clear separation between background, objectives, methodology, results, and conclusions. This lack of structure makes it difficult to identify the study's key contributions.

Response 2: Agree. We tried to separate the background, goals, and clarified the methodology.

Comments 3: Quantitative data is presented in a disorganised way, without comparative context. Numerical values are listed, but there is no interpretation or discussion of their relevance or consistency with previous literature.

Response 3: It is impossible to display everything in the limited space of the abstract, and comparisons are usually not provided in the abstract. The comparative context is provided in the Discussion section.

Comments 4: The novelty of the work is unclear. The research gap being addressed is not explicitly stated.

Response 4: Agree. Novelty, goals and objectives of the research have been added. Lines 114-130.

Comments 5: A full reorganisation of the abstract is recommended: eliminate repetition, improve scientific writing, and clearly state the study’s innovative contribution

Response 5: We tried to improve the quality of presentation, reorganized the text, there are no repetitions. Lines 18-42.

Introduction

Comments 1: The introduction lacks a clear logical flow to support the justification of the study. Multiple concepts (e.g., cryogenic processes, microbial activity, vegetation composition) are introduced without a solid theoretical framework or integration.

Response 1: Agree. Justified, unnecessary removed. Section reworked, lines 47-130.

Comments 2: The literature review is shallow and outdated. Key recent studies in tundra ecology, carbon dynamics in permafrost, and ecosystem responses to climate change are not cited.

Response 2: Added a literature review, including new publications. The purpose of our article is not to review all world literature. Ours is not a theoretical article, but an applied one. And here we tried to cite those articles that provide research data on our region and our objects.

Comments 3: There is an abrupt mixture of global context and local descriptions without smooth transitions or coherent argumentation.

Response 3: We tried to exclude unnecessary global context.

Comments 4: Explicit hypotheses are missing. There are no research questions to guide the methodological design.

Response 4: Ours is not a theoretical article, but an applied, evaluative one, and here we can do without setting major hypotheses. The article consistently highlights the specific results of our research, and this coincides with our understanding of the style of presentation and content. We will be ready to set hypotheses and answers to them in subsequent final articles.

Comments 5: Recommendations: Restructure the introduction logically as follows: general framework: the importance of carbon in cold-region ecosystems, state of the art: what is known about plant and soil productivity in tundra? knowledge gaps: what remains unexplored? regional relevance: why is the Yana-Indigirka Lowland significant? problem statement: what research questions are addressed? What hypotheses are being tested? Include at least five recent review references (post-2015). Clearly highlight specific gaps in current knowledge.

Response 5: The importance of the Yana-Indigirka Lowland as a large, poorly studied territory is mentioned.

Materials and Methods

Comments 1: This section is vague, incomplete, and lacks replicability. Sample size, sampling depth, and parcel selection criteria are not reported.

Response 1: We took into account all the comments and made them more specific. Section corrected, lines 132-479.

Comments 2: The sampling protocol per vegetation community is not explained, nor is the rationale behind the selection of these communities.

Response 2: The article's size does not allow us to provide the entire protocol, but we have tried to include a lot and to be more specific. And for detailed review, references to methodological literature are provided.

Comments 3: Critical methodological details are missing: biomass productivity estimation (cutting frequency, growth duration, drying process), type of balance used, laboratory parameters, microbial activity measurement methods, etc.

Response 3: We took into account all the comments and made them more specific.

Comments 4: Statistical analyses are not described, nor are the techniques used to evaluate differences between communities or variables.

Response 4: We took it into account. We added correlation analysis.

Comments 5: Carbon content calculation methods and the units reported (e.g., dry mass, total carbon) are not clarified.

Response 5: The comments were taken into account and described in detail.

Comments 6: Recommendations: Include a methodological summary table detailing all variables measured, analytical techniques, equipment used, measurement units, and number of replicates per community. Add a specific section on statistical analysis, even if it includes only descriptive statistics or mean comparisons.

Response 6: We were unable to include a methodological summary table describing in detail all the measured variables: the size of the article does not allow it and we do not see a great need for it, since we included specifics in the text.

Results

Comments 1: The results section is confusing, poorly structured, and full of descriptive redundancies.

Response 1: We tried to structure it, introduced subsections. It is not always possible to avoid redundancy of description in such practical studies, since the main results still need to be shown. Section corrected, lines 481-792.

Comments 2: No statistical tests are provided to support comparisons between communities. Means are presented without standard errors or significance testing.

Response 2: Average deviations are given where appropriate.

Comments 3: Figures are unclear, with missing axis labels, absent or inconsistent units, and incoherent scales across comparable graphs.

Response 3: The drawings were redone, and we tried to take into account the comments as much as possible.

Comments 4: Some results lack contextualisation or interpretation. Trends are mentioned without the corresponding numerical support.

Response 4: The trends of complex and unpredictable natural phenomena cannot always be clearly defined by numbers; they can be discussed as assumptions and forecasts.

Comments 5: Recommendations: Completely restructure the section with clear thematic subsections: above- and below-ground productivity, plant community composition and its relationship with soil carbon, microbial activity and cryogenic processes. Create clear and well-organised comparative figures with: fully labelled axes, units and explanatory legends, inclusion of significance values, means with ±SD or 95% CI. Avoid unnecessary repetition and clearly highlight key trends and outlier values.

Response 5: The section has been revised, subsections have been added, and the figures have been corrected.

Discussion

Comments 1: The discussion is superficial, lacks critical depth, and is poorly connected to relevant literature.

Response 1: The comments were taken into account and corrected. Section corrected, lines 794-1082.

Comments 2: Many results are repeated rather than critically analysed. Differences between communities are not explained through ecological mechanisms (e.g., resource use efficiency, functional composition).

Response 2: We agree only partly. We tried to provide ecological reasons and mechanisms as much as possible at this stage of research. The efficiency of resource use by plants and communities is a separate, deep topic, and its solution was not part of our tasks. The functional composition is discussed sufficiently for this stage of research.

Comments 3: There is no comparison with tundra studies from other regions (e.g., Canada, Alaska, Greenland).

Response 3: There is a comparison with studies of tundra from other regions, as far as we think it is sufficient. There is such a point here that natural conditions are often incomparable. That is, the conditions of the Yano-Indigirka tundra are much harsher than in Canada, Alaska and Greenland. Therefore, direct comparisons are incorrect, they are possible only as an approximate correlation.

Comments 4: Study limitations are not acknowledged (e.g., sampling seasonality, root depth variation, unmeasured cryoturbation).

Response 4: Restrictions have been introduced.

Comments 5: Recommendations: Restructure the discussion as follows: interpretation of key findings, comparison with international studies, discussion of ecological mechanisms (e.g., cryoturbation, microbial respiration), study limitations (e.g., spatial scale, lack of statistical replication) and future implications: how can these data inform carbon models or conservation? Incorporate recent key references (e.g., from Nature, Biogeosciences, GCB, Arctic, Antarctic, and Alpine Research). Discuss the potential limitations for extrapolating these findings to other tundra ecosystems.

Response 5: Potential limitations to extrapolation have been identified.

Conclusions

Comments 1: The conclusions are vague and lack impact. They do not adequately summarise the main findings or articulate their scientific or applied relevance.

Response 1: The conclusions are clearly stated and reflect the essence of the research. Section corrected, lines 1084-1136.

Comments 2: Limitations are not addressed, and no critical reflection is offered regarding the generalisability of the results.

Response 2: We think it is not necessary to provide a critical analysis in the conclusion. We have provided where and how the results of the work can be used.

Comments 3: No future research directions or implications for tundra environmental monitoring are suggested.

Response 3: The necessary context is provided.

Comments 4: Recommendations: Include 3–4 concise sentences that: Summarise the main finding. Highlight its regional or global importance. Suggest future research directions. Propose practical or policy applications (e.g., carbon monitoring, tundra management, climate modelling)

Response 4: Regional significance, application and need for future research are highlighted.

4. Response to Comments on the Quality of English Language

Point 1:

Response 1: The quality of the English language has been improved. The translation was done by highly specialized and professional translators with the text being proofread by a native English speaker.

5. Additional clarifications

The manuscript was revised taking into account all comments and three reviewers.