Reply on RC1

This is a topically relevant paper, given how little is known about peatlands in South America, and growing interest in understanding how tropical peatland management worldwide influences regional and global exchanges of greenhouse gases. This paper adds to the growing body of knowledge on the biogeochemistry of South America peatlands, and nicely integrates field-based flux measurements with more process-based laboratory assays. However, while I am broadly supportive of this paper, I think that the paper needs to be revised in order to enhance reader understanding and to acknowledge potential limitations with the experimental methods and design.

Thank you for the supportive comment! We will revise the manuscript accordingly.
First and foremost, given that this study is of limited geographic scope, with data collected over a relatively narrow window of time (i.e. only 6 months of measurements), the authors need to do more to acknowledge that it may be difficult to generalise their findings to larger spatial domains or longer periods of time. For example, I was concerned that the authors were over-reaching when they extrapolated their data over the entire Pastaza-Marañon foreland basin region (see point 10 below).
Agreed. We originally intended the upscaling intended as a general guideline to the reader for context of our numbers, not a central point of the paper. We will remove the upscaling.
Second, the authors need to clarify for non-expert readers if their measurements captured both wet and dry seasons (see point 4 below), given that water table depth and other environmental conditions vary substantially between wet and dry seasons, with a strong wet/dry season signal in CH4 and other trace gas emissions detectable not only from Amazon-basin wide studies of atmospheric chemistry and from smaller scale, site level studies of ecosystem gas exchange (e.g. Wilson et al. 2016). Seasonal affects will have ramifications not only for their field data, but could also influence their incubation results, as water table and other environmental conditions will influence the status of the microbial community at the time of soil collection; e.g. soils collected for incubation during the wet season could have a different activity profile or functional composition from the same soils collected during the dry season.
We are wary to attribute any seasons to our measurement time. The start of our study period in September 2019 is most accurately described as the end of the dry season. However, the ensuing rains only lasted up until late December. The area received hardly any rain from January till March. The water table, however, remained high and stable during the January till March observations, due to the buffering effect of the peat and adjacent Lake Quistococha. We assume the microbial community responded to the immediate environmental conditions, not the multi-annual average pattern of seasons.
Third, the cold storage of soil for incubations is problematic and could lead to significant treatment effects (point 8). Historic studies by Louis Verchot, Marife Corre, Ed Veldkamp and others have demonstrated adverse impacts on N cycling microbes (relevant to this study given it's focus on N2O), and many tropical research teams now transport soils at room temperature or conduct laboratory experiments near their field sites to avoid these treatment effects. While potential treatment effects do not invalidate the incubation studies presented here, the authors need to acknowledge the potential issues caused by cold storage and discuss how this may impact their interpretation of the results.
We will provide information on the transport, storage, and acclimatisation of the intact soil cores in the Material and Methods section. The bottom line is that the incubations showed various denitrification rates unrelated to sampling time but related to their ambient environmental conditions.
Fourth, on a more technical point, the authors need to clarify how they treated non-linear data and chambers that show potential evidence of ebullition. Fitting linear curves to nonlinear data or excluding ebullition data will tend to underestimate flux rates.
We closely examined all our gas concentration trends in each individual chambers. Practically all significant deviations from a linear trend were apparently caused by a faulty chamber sealing. We did not observe any signs of ebullition such as jump rises in concentration not followed by a drop in concentration. An unnoticeable share of ebullition may be a peculiarity of our long chamber closing time of 1 hour.
Specific comments are provided in the section below.

SPECIFIC COMMENTS
Lines 70-72: Since this study only investigated a sub-set of land-uses in the region, it would be clearer and more transparent if the authors indicated here which land-use types they focused on in this paper, with a brief justification for why they have concentrated on these land-uses in particular.

We will clarify the targeted land uses better, both here and the Material and Methods section.
Lines 76-80: For readers unfamiliar with the Roucoux et al. (2013) paper, I recommend expanding the site description for the human-affected sites so it's clearer how human intervention has altered these study sites.
We will specify that we took a 0-sample at the start of every 1 h session.
Lines 95-96: Did these sampling campaigns cover both wet and dry seasons? This is not clear -please clarify this in the narrative. Also indicate in Table 1 what season the campaigns were conducted in so it's clearer if there was even sampling between seasons.

See the comment on seasonality in the General Comments.
Lines 101-102: How was CO2 determined? Did the instrument have a methanizer?
The GC-2014 does not have a methaniser. We will specify that CO2 was also determined with the flame ionisation detector.
Also -N2 flux is mentioned in the Results and Discussion section, but it's not clear how N2 was measured in the field flux measurements -this must be clarified.

The protocol for N2 denitrification potential determination is specified in lines 128-139.
Lines 102-104: How were non-linear data treated or chambers which showed evidence of ebullition (i.e. erratic or very large non-linear changes in concentration)? Were these data discarded or included?
We closely examined all our gas concentration trends in each individual chambers. Practically all significant deviations from a linear trend were apparently caused by a faulty chamber sealing. We did not observe any signs of ebullition such as jump rises in concentration not followed by a drop in concentration. Data that showed a decrease after initial large increase, were excluded. The small share of ebullition may be a peculiarity of our long chamber closing time of 1 hour.
Line 106: Treating non-detectable fluxes as zeroes (rather than as a "n/a" or flux at the limit of detection) is a judgement call, given that there is a line of reasoning which argues that treating these data as zeroes biases your dataset towards zero values, when in fact these data points may be producing/consuming gases below the limit of detection. I recommend that the authors provide some justification for this judgement call, given that this is a non-trivial decision.
This concerns only the N2O measurements, as we did not set any CO2 or CH4 measurements to 0. We set 32 out of the 165 N2O datapoints to 0, mostly among small fluxes or faulty chambers. Excluding them would bias the data towards larger fluxes while low microbial activity under unfavourable environmental conditions is a perfectly reasonable assumption. We will explain this in the Material and Methods section.