Dear Dr. Cassidy,

Thanks you for your responses to the three reviewer comments. I am pleased with your detailed responses and invite you to submit a revised manuscript with the suggested changes implemented. The revised manuscript will be subject to editor review, and I should be able to make a quick decision of its acceptance for publication in Biogesciences.

I am looking forward to receiving your revised manuscript.

With best regards,
Daniel Obrist

I intend to accept your manuscript for publication in Biogeosciences if the following minor corrections can be implemented to the manuscript. In particular, I have three points that need to be addressed:

(1) In the author’s response to reviewer 2 criticism about the heating issues of the open-path IRGA, the authors present detailed evidence that this is not likely a concern. These points of the author response, however, should be published with the manuscript to distribute this information to the readership, e.g., submitting this information in a supplemental information section. In the methods section and/or discussion, the authors should then refer to this supplemental information.

(2) The measurement period are extremely limited, ranging from June 23 to July 3 (early), then to July 20 (middle), then to July 28 (late). These periods really don’t correspond to early/middle/end of growing season, and don’t cover the full growing season (which to my knowledge range from May to September in the High Alaskan arctic (e.g., at Toolik). It needs to be clarified that these measurements don’t represent early, middle, end of growing season, but rather a month with some phenological and physiological differences).

(3) Chamber measurements and partitioning of NEE: It should be emphasized and clarified that chamber measurements were performed only during daytime periods. When comparing EC with chamber-based fluxes, daytime measurements only should be compared for a meaningful comparison. Similarly, flux partitioning is based only on daytime measurements, and of course during daytime a significant respiration term is from plant autotrophic respiration (and respiration at nights can be quite different). Therefore, it needs to be clarified that respiration does not only refer to heterotrophic respiration from soil carbon losses, this is quite important.

Minor comments in regards to these points:
Table 1: add dates to day of the year
Line 36: “Before full leaf out in early July, the undisturbed tundra was a small source of CO2, but shifted to a sink for the remainder of the sampling season (July), whereas the disturbed tundra remained a source of CO2 throughout the season.” Clarify that late July does not necessarily correspond to late growing season, in the high Alaska arctic the growing season generally lasts until September.
Line 39: A static chamber system was also used… - clarify that these are daytime measurements/partitioning, therefore ecosystem respiration is unlikely dominated only by heterotrophic soil C loss (but includes plant respiration).
Line 46: during one month in the growing season.
Line 427: change “during the 2014 growing season” to In June and July of the 2014 growing season….
Line 439: “Based on chamber measurements, we found permafrost disturbance alters carbon dynamics by decreasing GPP and Re”. A problem here is that lower plant respiration also contributes to lower ecosystem respiration, so reductions in respiration can not only be attributed to heterotrophic respiration processes. This needs to be clarified here, and the limitations of measuring respiration during daytime with a dark chamber needs to be clarified.
Line 457: here, it needs to be clarified that the measurement period only covered end of June to end of July, i.e., a small component of the full growing season. This needs to be clarified. This does not allow to fully characterize early, peak, and end of growing season processes.
Line 523: ”nearly continuously over a majority of the 2014 growing season” – this statement is misleading, the one month period is unlikely covering a “majority” of the 2014 growing season.
Line 525: “The disturbance reduced the magnitude of both Re and GPP, although reductions to GPP were greater.” – clarify based on daytime flux partitioning.

Dear Dr. Cassidy.

Thank you for your final edits to the manuscript. I am glad to let you know that I have decided to accept your manuscript for publication in Biogeosciences. Congratulations, and thank you for considering Biogeosciences for your work.

Best regards,
Daniel Obrist