Dear Prof. Pan
Two external experts evaluated your reviewed your manuscript. Both reviewers place high rates of scientific significance (good, excellent). Both reviewers indicate that this work fits well with the scope of Biogeosciences. However, the quality of presentation is poor and Both reviewers indicate that comprehensive revisions are needed and it might be time-consuming.
Both reviewers argue that a conceptual framework should be provided to develop testable research questions and to guide the discussion, and the writings are repetitive. Both reviewers particularly argue that there are plenty of vague concept which are unfounded. For example, the term of physically protected organic carbon. It appears to me there is no solid criteria to define “physically protected organic carbon”. In addition, some of conclusions as pointed out by reviewers are self-contrasting. For example, the authors state that “This study further supported our previous finding for bulk soils that long term rice cultivation led to accumulation of SOC and promoted soil biological activities through physical protection of labile carbon in line with enhanced soil aggregation. And labile organic carbons accumulated in macro-aggregates helped enhancing microbial C use efficiency and improving potentially ecosystem functioning”. Labile carbon is often favored by microorganisms when compared to recalcitrant carbon. Therefore, it seems plausible that less labile carbon will lead to lower soil biological activities. Had the labile carbon been physically protected, microbial activities would have been lower than expected?
The reviews also suggest the interested Biogeosciences reader would benefit from a streamlined presentation.
I feel that these criticisms are sufficiently important as to preclude publication of your work at its present form in Biogeosciences. However, both reviewers indeed suggest a re-submission after major revisions as you can see in the comments provided.
Thus, I am not able to accept the current submission for publication. The reviewers make excellent suggestions and I encourage you to consider their comments for improving your work and the manuscript.
If you elect to submit a new manuscript, please include a letter that states the original manuscript number and your disposition to each of the comments of the reviewers and editor. Please note that simple revisions will not remedy the issues raised and substantial improvements are required. In addition, I would like to have your attention that the new manuscript would require a new review (i.e., the editor would not be able to assess the resubmission without engaging reviewers).
I am sorry your manuscript was not acceptable for publication. Your interest to publish in Biogeosciences is very much appreciated, and I hope that you will consider submitting additional manuscripts to the journal in the future.
Yours Sincerely
Zhongjun Jia

Dear Prof. Pan

Thank you for submitting your manuscript to BG for publication

As you can see from the reviewers' comments, the justification of methods used and interpretations still hold significant loopholes and inconsistencies. Please check carefully the first round of review, particularly for those highlighted by the reviewer#1. if a hypothetical concept is not considered essential by the authors, please clearly explain it.

In the meantime, please clearly state the meaning of the terms at the first place where it appears. For example, what does the physically protected carbon means?

Yours Sincerely

Zhongjun

Dear Prof. Pan,
Thank you for submitting your revised manuscript to BG.
Most comments of both reviewers have been adequately addressed, and I also side with reviewers that the data is of excellent quality, novel and, as such, provide important insights on soil organic matter turnover in paddy soil under different rice cultivation regime. The unique point is that conversion of tidal marsh to rice cultivation at different historical stage resulted in a series of soil chronosequence. The soil chronosequence thus serves as a valuable source to document the dynamic changes of organic carbon in differentially-sized fractions.
However, I do concur with one major concern raised by both reviewer, i.e., the coexistence of an increase in microbial activity and contribution of physically protected labile organic matter to C accumulation in paddy soils. For example, provided that microbes had little access to “the physically protected labile carbon”, the accumulation of the physically protected labile carbon could would have made microorganisms starved, leading to lower microbial activity. I also agree with your reasoning of C allocation in different aggregate size fractions.
However, the ms might be revised to facilitate the understandings of general readers without reading the text in detail.
(1) The term of “physically protected organic carbon” can be removed from the title by using more general term. By the way, rice appears twice in the current “rice soils under long term rice cultivation”, pls remove one.
(2) In the abstract please indicate the age of soil chronosequence soil, i.e., rice cultivation for 0, 50, 100, 300 and 700 years

The language usage could be improved further by a professional company before publication
Kind regards
Zhongjun Jia

Dear Prof. Pan

Thank you for submitting the revised ms to BG.
The major criticisms have been addressed, and I would like to have your attention for the following minor concern

(1) L23. Please check the abbreviation OC throughout the manuscript, and revise it where appropriate. For example, what does OC really mean, total organic carbon, soil organic carbon, and what is the difference between soil organic carbon and total organic carbon, between total OC and soil organic carbon. In addition, please use the term as specific as possible, and make sure all terms are used consistently THROUGHOUT the manuscript. For example, the terms such as soil organic carbon, total organic carbon, total OC, labile OC and OC are confusing. One could not understand whether OC refers to total organic carbon or soil organic carbon. More specifically, if LOC and TOC are used, the readers may get confused about the OC and soil organic carbon.
(2) L35.please rephrase the term of coarse sand, or please us it consistently throughout the manuscript. For example, in L34. It is sand (2000-200 μm), the general reader will get a bit confused what is the difference between coarse sand and sand. It is also hard for general reader to understand that the coarse sand and sand actually is opposite to fine sand.
(3) L27-32. It can be rephrased as following: Soil aggregates were fractioned into different sizes of clay (<2μm), silt (2-20 μm), fine sand (20-200 μm) and coarse sand (200-2000 μm). Soil properties were determined to investigate niche specialization of different soil particle fractions in response to long-term rice cultivation, including recalcitrant and labile organic carbon (ROC and LOC), microbial diversity of bacterial, archaeal and fungal communities, soil respiration and enzyme activity.
(4) L33-35. It can be rephrased as follow: The results showed that the mass proportion of both sand and clay fraction increased with prolonged rice cultivation, whereas the aggregate size fractions were dominated by fine sand and silt fractions. Total organic carbon was enriched to the greatest extent in coarse sand fractions, but depleted in silt fractions. Similar trend was observed for ROC content, and the ratio of LOC to TOC showed a slightly decreasing trend with decreasing size of aggregate fractions.
(5) L41. Replace gene abundance with 16S rRNA gene abundance?
(6) L42. Both coarse sand and clay. Please use the term sand or coarse sand consistently
(7) L42, rephrase it as follows: despite of the largely similarly diversity between the fractions.
(8) L43. Can be rephrased as follows: The 18S rRNA gene abundance of fungi decreased sharply with decreasing size of the aggregate fractions, whereas slight change of fungal diversity was observed.
(9) L48. Delete the phrase of “scaled by total DNA concentration”. It can be explained in the materials and methods, and it is also reasonable that soil total DNA is considered as microbial biomass.
(10) L50-53. It can be rephrased as follows: For all particles other than clay fraction, enzyme activity was increased with prolonged rice cultivation, whereas soil respiration appeared to have a decreasing trend.
(11) L53. Delete normalized. The normalization can be explained in the text, or it is a bit abrupt.
(12) L58. It can be rephrased as follows. These results provide a mechanistic understanding of soil organic carbon turnover and microbial community succession at fine scale of soil aggregates that have evolved along with anthropogenic activity of rice cultivation in the field.

Supplemental Table S1 and S2 and S3 (please check Table 2 to 6 in the text too)
(1) Please add a horizontal line under P700. Thus the effect of soil size fraction can be clearly separated and visualized.
(2) Please add a note at the end of the Table showing the actual size for each fraction. For example: These soil fractions have different sizes with 200-2000 µm (coarse sand), 200-20 µm (fine sand), 20-2 µm (silt) and <2 µm (clay). Or the size can be placed under the term in bracket, and rephrased as silt (20-2 µm) in the first column. NOTE: this concern also applies to Table 2 (the name of coarse sand, fine sand and silt need to be specified. The full name of MWD needs to be provided); Table 3

Yours Sincerely

Zhongjun Jia