Thank you for your submission to Biogeosciences. Your revised MS has received reviews from two expert reviewers who are highly qualified in this field. They felt that this study is interesting and potentially relevant to pika conservation. However, both reviewers had numerous substantive criticisms regarding the clarity and organization of the methods and results presentation and discussion.

Based on the authors' responses to the reviews in the MS discussion, it sounds as if the proposed revisions have good potential to address the concerns raised. Thus, I will be happy to consider a revised submission that substantively addresses the reviewer comments as described in the Authors’ response to reviews.

Please be sure that the clarifications provided in the response to reviewers are also incorporated into the manuscript text. Make sure you clearly describe how the text was revised according to the reviewer comments when submitting your revised manuscript. Thank you for your efforts, and for your support of Biogeosciences.

Sincerely,

Mike Weintraub
Associate Editor
Biogeosciences

Thank you for your submission to Biogeosciences. Your revised MS has received reviews from two expert reviewers who are highly qualified in this field, including one of the original reviewers. Both reviewers had suggestions for improving the manuscript prior to publication, and the new reviewer (Referee 3) offered numerous substantive criticisms.

I will be happy to consider a revised submission that substantively addresses the reviewers' comments. In revising the manuscript, please be sure to address Referee 3's concern that pika patch cause and effect are confounded (see below). In preparing your responses to the reviewers, please be sure that the clarifications provided to reviewers are also incorporated into the manuscript text.

Make sure you clearly describe how the text was revised according to the reviewer comments when submitting your revised manuscript (including those listed below). Thank you for your efforts, and for your support of Biogeosciences.

Sincerely,

Mike Weintraub
Associate Editor
Biogeosciences

I am not certain if the below Referee 3 comments were visible to you, as it appears they were entered as comments to the editor. Please be sure to carefully address them along with the other comments:

Firstly, patchiness in alpine meadow are always induced by multiple factors, such as, grazing, plateau pika disturbance, zokor disturbance, marmot disturbance, permafrost degradation, etc, that is, there is relationship between plateau pika disturbance and patchiness. Plateau pika disturbance also can contribute to the large, medium and small bald patches in your manuscript, because plateau pika dose not has the digging activities, but also has burying activities. However, in your manuscript, it seems that plateau pikas disturbance and patchiness were two different factors. it is confusing. How did authors distinguish the effects of these two factors? As a result the treatment is potentially confounded with other conditions (permafrost, grazing, other small mammals). This is a fatal problem that authors confuse the plateau pika disturbance and patchiness.

Secondly, the size of plot in the manuscript is 10000 m2 (100 m * 100 m). however, pikas are social mammals that live in family group, and the average home range is about 1,262.5 m2 to 2,308 m2, so, any other mammals in the plots? This is, pile could be contributed by other mammals, such as marmot, zokor…

As for statistics
1. One-way analysis of variance (ANOVA) and a multi-comparison of a least significant difference (LSD) test were used to determine differences at the p=0.05 level, however, from the manuscript, pika disturbance and patchiness are two independent factors, if so, authors should use two-way anova. 

Results: the results are rambling, a summary in each section was lacked. 
line 232, “Both pikas disturbance and patchiness significantly affected soil compactness, SOC density, TN density and vegetation biomass”, both? They are independent? it is difficult to find “both” are significant in the table 2.

Discussion:
The discussion is very detailed and specific and repeats the results. Patchiness can be caused by several factors (other small mammals, large herbivore, permafrost degradation…etc), however, the authors consider pika disturbance as single factor. In fact, plateau pika disturbance can contribute to cause any patchiness, such as large patchiness, medium patchiness, small patchiness.

Details:
table 1 and table 2 “ANOVA results of the effect of patches fragmentation and small mammal activities…..” Small mammal, just plateau pika, or any other small mammals? 

Fig. 2. a multi-comparison has been done, so what’s the difference among the different surface types, different letters showing the differences among the different surface types were lacked.

Thank you for your revised submission to Biogeosciences. Potential reviewers were highly interested in your MS, and I received another three reviews, all from highly qualified researchers in this field. The referees in the most recent round of review agree that this MS is much improved, but substantive concerns were raised by Referee 3 about the presentation of the statistical analyses. I agree with this reviewer that the expressed aims of the study suggest a one-way, rather than two-way ANOVA, and that interaction terms from multi-way ANOVAs must be included and properly addressed in the data presentation. Additionally, Referee 1 offered some additional minor edits for the authors to address prior to publication. Thus, I will be happy to consider a revised submission that substantively addresses these reviewer comments as described in the Authors’ response to reviews. Please pay particular attention to addressing the reviewers' comments, and please be sure that the clarifications provided in the response to reviewers are also incorporated into the manuscript text.

Please clearly describe how the text was revised according to the reviewer comments when submitting your revised manuscript. Thank you for these additional edits, and for your support of Biogeosciences.

Sincerely,

Michael N. Weintraub
Associate Editor
Biogeosciences

Thank you for these last minor edits. Your manuscript has now been accepted for publication. We appreciate your support of Biogeosciences.

Sincerely,
Mike Weintraub
Associate Editor
Biogeosciences