This is a very interesting study. A combined suite of techniques was indeed employed to address the key relationship between soil structure and function, i.e. flux dynamics of N2O and (N2O+N2) in relation to X-ray CT-based structure analysis. The authors conclude that oxygen supply may be estimated by abiotic proxies like the extent of anaerobic soil volumes or diffusivity, and oxygen demand for respiration can be best predicted by CO2 production or SOM. The interplay of oxygen supply and demand determines the (N2O+N2) fluxes.

All reviewers are very positive about this study and have made useful comments which are satisfactorily addressed.

The editor has some minor concerns

(1) Pls briefly why upland soil is selected because grassland and arable soils are often exposed to the atmosphere containing approximately 20% oxygen. Therefore, it seems that denitrifiers may be favored only in the microanaerobic site. This kind of upland soil may be dominated by aerobic process, particularly for the surface soil.
(2) Pls add few sentences for future study about microbial communities. The implicit assumption of this study is that similar community structure of microbiomes exist in physiochemically distinct soils, leading to similar responsive patterns under oxygen and substrate supply. This is also somehow astonishing. At least the flux pattern are largely similar, which may represent similar communities?
(3) Why not use destructive sampling for microstructure analysis. Yes, one time point result cannot represent the entire incubation period, and why destructive sampling could be conducted to have a time-series analysis of microstructure and ansvf? For example, microbial activity could likely reach a high level after incubation for 24 hours, and stayed largely at a plateau level after incubation for 192 hours. In addition, strong respiration may lead to the growth of microorganisms which in turn generate extracellular enzymes or extracellular polymer substance EPS, which could likely significantly distort the soil microstructure and ansvf?
(4) Can the authors specify the relationship between the volume of a single cell (or population) and the aggregate size. Or in other words, what is the population size of cell that can colonize different aggregates

Kind regards

Zhongjun

Dear Dr. Lena Rohe

Thank you for your submission to BGD.

The reviewers' comments have been satisfactorily addressed. My only concern is that the title may be rephrased as Denitrification in soil as a function of oxygen availability at the microscale
or Denitrification in soil as a function of oxygen supply at the microscale

In addition, please check the tables and figures. It is expected that your figure legends will be quite detailed and very precise. In fact, from the figure title and the axis labels of a graph/table the reader should be able to determine the question being asked, get a good idea of how the study was done, and be able to interpret the figure without reference to the text

Kind regards

Zhongjun

Dear Dr. Bussmann,

Your manuscript has been reviewed by an external expert and myself. The criticism raised during the first round of reviews has been addressed, but still the justification of methane oxidation rate needs to be strengthened and discussed in greater details.

Meanwhile, the figure quality can be significantly improved, particularly for Figure 1. Please also remember that it is expected that your figure legends will be quite detailed and very precise. In fact, from the figure title and the axis labels of a graph/table the reader should be able to determine the question being asked, get a good idea of how the study was done, and be able to interpret the figure without reference to the text

Yours scincerely

Zhongjun Jia

Dear Dr. Rohe,

Thank you for submitting your manuscript to BG

The concerns have been adequately addressed, and I am happy with the revision. I still have two minor concerns for your reference:

(1) Effect of aggregate sizes on denitrification and CO2 release is not significant. The authors argued about the smaller aggregate radii than the thresholds of distance connecting air aeration. Please add few sentences about the oxygen availability. Maybe the oxygen is completely depleted, or maybe oxygen is below threshold value that facilitates denitrification and soil respiration.
(2) Denitrification in upland soil. Please add few sentence about the flux of N2O emission in the field to justify the choice of soil samples.

Meanwhile, I guess in future metatranscriptomic analysis could be of great help for such kind of study, in addition to destructive sampling of the paralleled microcosms.

Kind regards

Zhongjun Jia