General: This manuscript describes an interesting case study on the effects of top soil removal, rewetting and the use of different wetland plant species on greenhouse gas emissions. The emissions fluxes were compared between these different plant species, but also with a reference grassland site.  It would be nice to mention the total greenhouse gas balance in the abstract also, in CO2 equivalents, so that the reader can directly see the effect of the treatments on the greenhouse gas balance.

Introduction:

L75. This is the first time that I hear that vegetated conditions may have higher CH4 emissions than non-vegetated conditions. Moreover, in the paper of Antonijevic it is stated that the period with elevated CH4 emissions ended with the occurence of cattail. So please correct that reference. And why are there no measurements of non-vegetated conditions in this experiment?L

L95. No CH4 measurements at the reference site?

Methods: are the two Typha compartments 430 m2 in total, or are they each 430 m2? 

Figure 1C: indicate the inlet ditch and the water flow.

L135. Is it realistic to provide only inorganic fertilizer to the reference site? Does this give an underestimation of carbon fluxes to the atmosphere?

L180. It is a weak point that CH4 fluxes have appartently not been measured in the reference site. This flux could be zero of course, but then the authors should mention this. Also no N2O emissions were measured, which could have a major effect on GHG emissions, especially on the reference site. Please discuss the importance of N2O emissions somewhere in the introduction or discussion.

Results: it would be good to provide the actual biomass harvest values (per m2 or per ha). Now this is only mentioned in the discussion.

Fig.7 typo (And).

L370. Table 3. Figure 9. Why is all harvested biomass (C-export) considered as CO2 loss and thus as GHG flux? This totally depends on the biomass use. The grass from the reference site will partly be converted in CH4 by cows and the Typha biomass will for example only be converted to CO2 after a long time if it used as building or insulation material. This seems to be an important disclaimer here. The authors mention this in the discussion, but the disclaimer can also be mentioned here already.

Discussion: how do Typha roots supply easily degradable carbon to the sediment? And is this in a significant order of magnitude to have effects on CH4 production?

L408-410: several typos.

L410: I think that the damage to the T. latifolia plants is een important thing to mention, also in the abstract and conclusions, as it seems to be the reason for the very high methane emissions.

L451-453: the authors mention the CO2 emissions for cultivating and processing Typha here, but do not mention the CO2 (and CH4) emissions for the reference site, i.e. the cultivating and processing of grass, milk, etc. This probably also (more than) compensates for the grass biomass harvest. So please make a fair comparison, or leave the statement about CO2 emissions for cultivating and processing Typha out of the text.

L456: if the topsoil would have been stored under anoxic conditions, much more CH4 would have been emitted in CO2-equivalents than the 557 t CO2 per ha under oxic conditions, based on the papers of Harpenslager et al., (2015) and Quadra et al. (2023). The authors also mention this in line 468. So in that sense, the authors could be more positive, or less negative, about topsoil removal here.

L468: typo

L475-478: the highest chloride concentrations measured in the surface water were 62 mmol/l, which is equivalent to 2.2 g/l. This is in the range of the upper limit for T. latifolia and far under the upper limit of T. angustifolia. So the statements made here are not true.

L482: typos.

Conclusions: please rephrase based on the feedback given above.

General comments:

This is a comprehensive and well written paper which constitutes an important contribution about species-specific GHG balances from species relevant for paludiculture. The measurements have been conducted over a single year with limited frequency, which is common practice with this type of studies, but remains an important limitation. The study is ambitious as it aims to capture the fluxes of both CO2, CH4 (both diffusive and ebullitive fluxes) as well as important soil and water chemistry. There were also mentions of DOC, but these fluxes have not been reported. Inclusion of N₂O would have strengthened the study further.

The paper concludes that rewetting (flooding) with paludiculture reduces GHG emissions compared to an intensively used drained fen grassland, and that the choice of species is relevant for the success. Moreover, the paper discusses the pros and cons of topsoil removal at this site, and seem to suggest that topsoil removal may not have been positive here due to the removal of soil C, high CH4 fluxes, and possibly P-limitation for the plants. This is an important consideration for future studies as topsoil removal has been suggested to decrease CH4 emissions and limit P-leakage, without much consideration of where this soil should be stored to avoid continued soil C-oxidation off-site.

However, the study cannot determine the role of topsoil removal itself on post-rewetting GHG emissions as they have no reference site for this particular question.

The study is also unable to answer questions about how GHG emissions from rewetting may be managed by the choice of water table depth, which asserts strong control on CH4 emissions in particular. This was briefly mentioned in the discussion but deserve further consideration due to its importance.

All in all, the study clearly answers the questions they set out to investigate, which is well-described by the title.

Scientific comments:

Material and methods:

There is a mention in the methods that Azolla died off and was replaced by Lemna spp. This is not discussed further anywhere. How fast did the Azolla deteriorate, was there x% left in September/October when the data in figure 6 suggest high concentrations of ammonium and total phosphorus in the pore water? And isn’t that ‘weakness’ something worth mentioning when suggesting Azolla as a paludiculture species?

The reference site is presented in this section, and I wonder to what extent this site is representative of the conditions before topsoil removal and rewetting. The text does not discuss why this site was chosen, and the choice is not defended anywhere. Primarily the site is described to be different (intensively used, grazed, fertilized), hence my worry.  

The study mention that diurnal fluxes were captured, but this data is not presented anywhere, which is unfortunate. There are several studies showing diurnal patterns of CH4 emissions from plants, but more data is needed to confirm which species this is relevant for. It would have been a nice addition to the supplementary material to visualize diurnal patterns, both if there are clear patterns or not. There is also no further mention if these diurnal patterns were included to interpolate data or to correct it.

I am somewhat unfamiliar with bubble traps and would have liked a reference to the method to indicate if this is standard measurement practice.

There seems to be no measurements of CH4 from the reference site, although emissions may have been negligible from the soil, they could have been rather large from ditches (if present). This is not discussed fully anywhere.

The authors use the term soil T when measurements are done in the ‘soil’ beneath a water column. It may be clearer to use the term sediment T when the site is flooded as in this case. I leave this to the authors’ discretion, however.

The interpolation of CH4 based on soil T (or water T in case of Azolla) seems rather risky (which figure 7 clearly shows). The R-square is not high. Could it be possible to reach a higher R-square if more environmental parameters are included? This methodology is also not discussed, and no references to other studies applying this method are made. Is there a risk of an overestimation or underestimation of annual emissions?

Results:

It would have been interesting if the authors had supplied a simple RF-modeling to describe the GHG balances for the different species and the reference site (see Günter et al. 2020 – code freely available). This could also have included the C losses from the topsoil removal.

I personally think that better visualizes and describes the net GHG impact from rewetting, where CH4 release is mitigated by CO2 uptake. However, I concede that in this particular instance, where measurements have only been made over a single year, with insect infestations etc. it may not be prudent to extrapolate emissions over several years (which is done in RF-modeling). This is perhaps something the authors could discuss though. Also, for future studies.

Discussion:

The discussion is overall very good with much to consider and some helpful guidance to understand the results. I have mentioned some parts which are not discussed, which the authors may want to consider including for a strengthened paper.

I am very pleased to see that the authors mention that high DOC inputs may have influenced the CH4 emissions, but would also have liked to hear more about the authors’ thoughts on its influence on CO2. Is it possible that NEE measurements were contaminated by allochthonous C? If the inflow had high concentrations of DOC, some of it may have been oxidized to CO2. Would the contamination be negligible or not?

The authors make a good point when they question to what extent (typo in text) the carbon storage in Typha will continue in the future. These studies should ideally cover more years than they frequently do…

I am very glad to see that the authors have included numbers on the potential C oxidation from the topsoil removal and how many years it would take to reach the same numbers from the reference site. This is often overlooked.

Technical issues

Abstract:

Please note that the species-specific CH4 fluxes do not match those in table 2.

L30 “Azolla and T. angustifolia seem to have the highest potential in reducing…” (of these three species)

L30 “complete rewetting” please consider using the term flooding.

Introduction:

L43 The increase of CH4 emissions after rewetting depends primarily on the water table depth. This should be introduced here.

L43 “this gives an extra impulse” please reword to incentive.

L44 “Rewetting 60%” This sentence does not describe what the reference presents. Clarify this statement. I.e. Rewetting 60% of the drained organic soils would turn the global land system into a net C sink by 2100, as opposed to a net C source as projected.

L51. It is quite possible that the degree of degradation (increased bulk density and thus higher SOC content per cm3) of the topsoil is important along with the nutrient status when it comes to the CH4 emissions. https://doi.org/10.1016/j.agee.2016.01.008

Material and methods:

Figure 1B is very hazy. Is it possible to produce a map with higher dpi?

Equation 1, the minus sign within the brackets is difficult to see.

Discussion:

L410 Please capitalize the two Wainscot bugs.

L452-453 Typha as insulation material, emissions…? I do not understand this sentence. Is it possible to clarify?