Summary:

This manuscript details the experimental design, configuration/modifications, and utility of a dual system of commercial dynamic chambers for simultaneously quantifying emissions fluxes of reactive nitrogen species and greenhouse gases. This work carefully outlines the system details as well as the many considerations that go into the flux calculations, which are further described in the context of a proof-of-concept experiment aimed at quantifying emissions fluxes of nitrogen species and greenhouse gases from agricultural soils. This manuscript is a highly valuable addition to the literature because it provides: 1) a description of the dual-chamber system detailed enough for others to reproduce, 2) a comprehensive account of the considerations and calculations needed for dual-dynamic chamber flux calculations, and 3) initial proof-of-concept results from controlled laboratory and field experiments. The latter shows great promise in being able to set a foundation for charactering changes in emissions fluxes of nitrogenous species and greenhouse gases from agricultural soils as a function of relative humidity, temperature, soil moisture, fertilizer applications, and more, which are critical for understanding emissions from food systems that impact air pollution and climate. This manuscript is well written, and it fits well into AMT. I recommend this manuscript for publication. Please find a few minor comments and suggestions below.

General comments:

While this paper is very comprehensive, a missing component of this work seems to be a brief, clear, and upfront discussion of the advantages of this dual-dynamic chamber system compared to the system described in Pape et al., 2009, who also implemented a blank chamber in reference to up to as many as 6 sampling chambers and measured Nr species. It would strengthen this work to be more explicit about the novel aspects of this dual-dynamic chamber system and proof-of-concept experiments in comparison to the dynamic chamber system and field measurements described in Pape. This could be integrated into the last 1-2 paragraphs of the introduction.

At first look, the 30-minute sampling cycle for the MC and RC chambers seems a bit short. On the other hand, a longer sampling time probably allows for more dilution, reactivity, etc. It seems like there is a delicate balance of the time to observe enhancements in the chamber, trace gas analyzer response times, chamber flush times/flow rates, dilution times from the replacement make-up gas, and the time associated with wall loss in the chamber, etc. Is it possible to combine all of these timescales into a single schematic to demonstrate this balance? Is there a sweet spot in the schematic that clearly stands out for this set up? At a minimum it might help to add some more detailed explanation about why the chamber time to reach a reasonable detection limit for HONO (e.g., Section 2, L250) is used compared to the longer chamber fill/empty time for sticky NH3 (e.g., Figure 2 and Table 1). How would using a different chamber sampling time impact your flux results? It seems like a good bit of the chamber timing characterization was also discussed in Pape et al., 2009 (e.g., their figures 6 and 7). Briefly summarizing the timing simulations in Pape with respect to your timing scheme could help clarify and strengthen this work.

This paper is well-written and comprehensive. However, it is a bit cumbersome in places. A suggestion for improved readability could be to reconsider what goes in the main paper vs. the SI. For example, Section 2.1.2 seems better suited for the SI, while important analyzer calibrations and gas handling considerations are handy to have in the main paper. Similarly, important equations and calculations, such as those in Section S7, while cumbersome for the main paper, could go into an appendix of the main paper for increased visibility.

Specific comments:

L183: Suggest changing “manipulated” to “performing controlled experiments”

L250: Is there a reason that HONO is used to determine the sampling time interval, compared to say NH3? Section 2.6 did not seem to provide further explanation for this selection. Is this somewhere else? At a minimum, this section seems like a good place to summarize some of the chamber timing simulations in Pape et al., 2009. It would also be a good place to discuss similarities and differences in timing between your experiments and their studies (e.g., differences in timing with respect to differences in flow rates).

L279: This should be Section 2.1.3, right?

L281: Section 2.1.2 seems like it could go in the SI, and then the instrument descriptions can naturally follow on Section 2.1.1.

L305-317: Can you determine an analyzer detection limit for HONO?

Section 2.1.3 and L309: Did you actually measure interferences from other oxidized nitrogen species in the NO2 measurement?

L329: The Picarro analyzer response times are given as 8 s for non-sticky species, which are assumed to be 1/e times of a single exponential function. While this seems sufficient compared to the chamber empty/fill times for non-stick species, the longer analyzer response time for sticky NH3 (reported as <2 min) may rival the chamber fill/empty times (e.g., Table 1) when a double exponential fit and a longer, more appropriate, signal recovery time (e.g., t90, the time for 90% signal recovery) for sticky molecules are considered. Can you comment on this?

While the chamber response times are well-addressed in Section S3, it was not obvious how the analyzer’s response times are characterized for stick molecules (NH3 and HONO). What is the modified NOx analyzer’s response time for the HONO measurement and how is it defined?

Another consideration is whether the time responses of these analyzers and the chambers were characterized multiple times throughout the study period to ensure that they did not change. The time response of instrument systems measuring sticky molecules are well known to degrade over time and usage as sampling surfaces get dirty or saturated with moisture (e.g., Ellis et al., 2010; Moravek et al., 2019; Roscioli et al., 2016, https://pubs.acs.org/doi/10.1021/acs.jpca.5b04395, etc.). How might changes throughout the study period in analyzer and chamber response times for sticky molecules impact your results? Some additional discussion could help clarify. (See also additional related comments below with respect to lambda.)

L337: I agree that full span checks for greenhouse gases are not regularly needed for the Picarro, but I’m not sure that holds true for sticky NH3. You mention performing regular calibration checks anyway, which is good. How often were those performed? Did you observe changes, or more variability, in the NH3 channel? How about checks of the instrument time response, especially to NH3? Did that time response change over the duration of your study?

Related details about analyzer calibrations (in the SI) could also be clarified. Specifically, how was the modified NOx analyzer calibrated for HONO and how was the Picarro analyzer calibrated for NH3. This should be added to Section S2 if different from the methods used to characterize the chamber time response measurements in Section S3. If they are the same, it might be clearer to add the calibration procedure to section S2 and then refer to it in section S3.

L354 and Section 2.2: It would help to see a photo of the chambers in the lab or in the field in the main paper in this section. Maybe a photo of the chamber set up in the lab or field (like in Figure S2 - very cool!) could be added to Figure 1 as a part C in the main paper?

The PFA film over the lid is a smart addition to reduce surface interactions. Is the air sample completely isolated from the polyacrylate cover (aka. is there a leak-free seal between the PFA film and the cover)? If not leak-free, does the adhesive on the double-sided sticky tape create any chemical interference? How are the chamber fill/empty times impacted by sample air getting between the PFA film and the lid? Could these factors impact lambda?

Section 3.1.2: It would help to add callouts in this section, like where D and NO2 reactivity are discussed, to their respective details in the SI (S3 and S7).

L630: Can you determine an uncertainty for Lambda?

Table 1 shows substantial differences in %D for the chamber empty vs. chamber fill times for NH3. Does %D change over the duration of the study period as the chamber gets dirty with usage? By the same reasoning, can or does lambda change over the duration of the study period (e.g., can or does Figure S11 change over time throughout the study period as the chambers are used and get dirty)?

Figure 4: This is a nice figure. It’s a bummer that there are no N2O or NH3 measurements for the samples with “none” and “AN” fertilizer applications, as N2O and NH3 fluxes are predominant from the other treatments. Will a comparison of soils and treatments using this system be included in your forthcoming paper about the field study? That would also be an exciting addition to the literature. :)

Figure 5: The timescales in this figure could use some clarification, and this might be easily solved by simply adding some labels to each panel. These labels could simply say “after fertilization” for the NH3 time series and “before fertilization” for the NO and N2O timeseries. It is also unclear why the dates and times are not the same (e.g., 2 pm versus 5 am on 9/5/2022) for simultaneously measurements of NO and N2O during the “before fertilization” sampling. Is this because of differences in peak emission times as shown in Figure 3? 

Section 3.3.3: How would propagating an uncertainty in lambda impact the total uncertainties in the fluxes, especially for NH3? Since lambda is time dependent (e.g., Figure S11), can you comment on how a longer chamber sampling interval might impact the fluxes, again especially for NH3.

Sections S2 and S3: It seems that the instrument calibration methods for NH3 and HONO are missing from Section S2. It could be the case that the HONO and NH3 calibration sources used in Section S3 are also used to calibrate the analyzers and characterize instrument time responses. If that is the case, then I suggest reorganizing these sections to clarify. Along the same lines, section S2 should also describe how the analyzer response times are characterized. (Sorry if this is a repeat comment from above.)

Section S7: It is helpful for readability if you can redefine parameters in the equations (like A, Q, F, c, R, X, t1, and t2, etc.) for the equations in the SI.

Figure S9: Suggest adding the absorption cross section spectrum for NO2 to this figure for comparison. Can you estimate how modifying the chamber with the PFA film attached to the lid might impact loss by photolysis? Is there a transmission curve somewhere for this commercial material?

Summary:



This manuscript presents the development and validation of a dual-dynamic chamber system enabling simultaneous flux measurements of multiple reactive nitrogen species alongside conventional greenhouse gases. The topic is interesting, given the increasing interest in quantifying Nr exchange processes and addressing their cascading environmental impacts. The study is ambitious and relevant: the integration of destructive analyzers, surface passivation strategies, and a dual-chamber configuration represents a potentially valuable contribution to the scientific community that deal with gas exchanges. The proof-of-concept laboratory and field applications, along with error characterization, support the method’s applicability. Overall, the manuscript addresses a recognized gap in the simultaneous quantification of Nr species and GHG fluxes, and the results appear encouraging. The manuscript is well written and suitable for publication in AMT, and I recommend its acceptance. Nevertheless, I have a few minor suggestions regarding structure and clarity in specific sections, as well as some questions that may lead to further elaboration in the text.

General Comments

The manuscript is rich in technical details and provides valuable information that can support reproducibility by other research groups, which is a key strength of the study. Nevertheless, I have several general observations related to structure and readability, some of which are expanded in the specific comments in the next section. For now, the general suggestions is the following:

In its current form, the abstract appears excessively long. Even for a complex methodological study, an abstract should provide a concise synthesis focused on essential elements: state of the art, research gap, objectives or hypotheses, methodological approach, key results, and main conclusions. Many of the finer details presented there would be better placed only in the main text.

A similar issue arises with the introduction, which is pretty long and demanding to read. Condensing this section could enhance accessibility, particularly for readers primarily interested in process-oriented assessments rather than methodological development. Given that such readers may represent a substantial portion of the intended audience, a more streamlined introduction could improve engagement without sacrificing scientific relevance.



Additionally, where feasible, I encourage updating some of the citations, as many references are 15–20 years old and more recent literature could strengthen the framing.

The results section is also extensive. While this reflects the dense amount of findings, a more concise presentation focused on the key messages would improve clarity. The scientific content is strong and insightful, but at times becomes redundant or overly verbose. A tighter structure could help highlight the main contributions more effectively.

In contrast, the conclusions appear relatively short compared to the rest of the manuscript. Expanding this section to further emphasize applicability, remaining uncertainties, and open research questions would reinforce the overall impact of the work and guide future studies more clearly.

 Specific comments:



L122: Suggesting to add a couple more up to date references: 



Chiaravalloti et al., 2023: https://doi.org/10.3389/fclim.2023.1203043

Anthony & Silver, 2024: https://doi.org/10.1007/s10533-023-01095-y

Manco et al., 2025: https://doi.org/10.3390/horticulturae11060708



L131-144:  I would suggest reorganizing the presentation of reaction schemes. Similar to the equations used later in the manuscript, each reaction could be introduced within the relevant section of the text, framed in a small boxed or separated layout, and assigned a numbered identifier in parentheses for subsequent citation. For example:

“…at night, if sufficient O₃ is present to fully titrate NO”

NO + O₃ → NO₂ + O₂ (R1)

NO₂ +O₃ → NO₃ + O₂ (R2)



This approach is preferable to listing all reactions together only once in the early part of the Materials and Methods, as it improves readability and allows the reader to refer to each reaction when it is conceptually needed.

L158-159: Also for this part I suggest more up to date references, like: Pugliese et al., 2023 https://doi.org/10.1038/s41467-023-40661-8



L177-179: As suggested before, there are a plenty of more up date publications to refer to, about meaurements of GHG and Nr with soil chambers in relation to fertilization. Regardin GHG, I have listed some of them before.



L275-279: I suggest to explain in details the gas analyzer equipments only in the Section 2.1.3. There is no utility to list them at the end of this alrealyd long section.



Section 2.7: I am referring with this larger comment to this section, but these aspects appear also in other sections of the manuscript. Indeed, like in the general comment, I suggest the author to try to optimize and gather all the discussion about this in one section into the discussion.

Dealing with the specific observation...

A further point that may require clarification concerns the attenuation factor used to account for surface interactions, particularly for highly reactive species such as NH₃. The manuscript discusses chamber wall effects, but it is not clear whether the authors considered potential losses along the sampling lines. Reactive gases like NH₃ may interact significantly not only with chamber surfaces but also with tubing, connectors, internal multiplexer components, and the analyzer inlet, and these losses typically scale with tubing length and residence time.

For example, field chamber systems—such as those deployed for multi-site measurements or spatially distributed installations—may involve sampling lines up to 30–35 m in length. In such configurations, tube material, conditioning, and line heating are commonly used mitigation strategies (as applied also in VOC measurements) to reduce wall adsorption under low flow rates.

It would therefore be useful to know:

• What tubing materials were used in this system?

• What were the actual sampling line lengths, and were they varied and characterized?

• Were line losses quantified in relation to the tube length, and if so, how were they incorporated in the attenuation correction?

• Did the authors consider or test heating of the sampling lines to minimize adsorption effects, particularly for NH₃?

Providing this information would strengthen confidence in the attenuation treatment and in the transferability of the system to field deployments where sampling geometries differ from the laboratory setup.

L131-136: A clarification may be needed regarding the derivation and implementation of the attenuation factor (λ). The current definition — “the ratio of the theoretical concentration signal to the measured signal over the chamber closure period” — raises several questions. Specifically, it is not clear what is meant by “theoretical concentration”:

• Is this inferred from a mass-balance model, expected accumulation kinetics, or an external reference concentration?

• Does it rely on empirical baseline values, tabulated concentrations, or ambient background levels?

• How sensitive is λ to assumptions about these theoretical inputs?

Because λ is a key component in correcting surface interaction artefacts for reactive gases, the conceptual basis and calculation procedure would benefit from clearer explanation. I would recommend introducing a concise but explicit description of how λ is computed in the Materials and Methods section rather than within the Results. Additional procedural detail — including underlying assumptions, modelling basis, and any validation performed — could be provided in the Supplementary Information to ensure transparency and reproducibility.



L1044-1046, Figure 6: "Error bars are calculated using the mean value of the corresponding terms from three reference chambers plus their standard deviation".

I did not understand properly why the error bars were calculated using mean and SD of the reference chambers.

Maybe it is very simple, but it is not clear to me at this point.



L1066-1070: I believe it would be useful to cite Manco et al. (2025; https://doi.org/10.3390/horticulturae11060708) to provide a more complete context. Under granular urea fertilization, that study reported hot-moment emissions approaching ~3 nmol m⁻² s⁻¹, which appears relevant for comparison with the flux magnitudes discussed here.