Here we post the answers (in italics) to the comments that Reviewer 1 did about our manuscript. Besides, all these answers to the general comments together with those of specific comments are included (in blue) in the attached document. We would like to thank the feedback and all the suggestions given. 

Comments R1:

This is a promising study of carbon emissions and soil mineralization potential from non-tidal salt marshes which offers unique data with which to improve understanding of relationships between gas fluxes, plant physiology, and salinity. Marshes in the region are relatively understudied and the non-tidal system is also poorly known in terms of methane dynamics. The measurement of CO2 exchange from woody plant tissues reveals new insights about the capacity for carbon uptake throughout the plant body in the salt marsh species studied here.

Thank you very much for the feedback on the value of the study.

One major finding is that the salt meadow and halophilous scrub had lower soil mineralization potential but higher soil CO2 emissions than the glasswort sward. This result seems counter-intuitive and I would like to see more discussion to potentially explain how longer term carbon could be sequestered despite the shorter term CO2 fluxes from soils.

We agree that, at first glance, this result may seem counter-intuitive, but it is important to remember that the mineralization quotient is calculated as the ratio between carbon emitted and carbon stored as soil organic carbon (SOC) (Pinzari et al., 1999). In a parallel study, we found significantly higher amounts of carbon in the soils of the halophilous scrub and the salt meadow than in the glassword sward, in accordance with a much higher aboveground, belowground and litter biomass in the former two habitats (Carrasco-Barea et al. 2023). Therefore, despite the higher soil CO2 emissions in the halophilous scrub and the salt meadow, they showed lower mineralization quotients due to their much greater amount of SOC. We have clarified this in the discussion in lines 404-409(“Despite the halophilous scrub and the salt meadow had higher soil CO2 emissions than the glasswort sward, they showed lower mineralization quotients due to a much greater amount of SOC (Table S3), which was in accordance with a much higher aboveground, belowground and litter biomass (Carrasco-Barea et al., 2023). Hence, our results would indicate that soils of the halophilous scrub and the salt meadow would have a higher carbon sequestration potential, despite their higher soil carbon emissions”.).

Authors meanwhile found higher CO2 uptake from woody tissues of the plants in the former two habitats. I wonder whether this might contribute to or be related to the higher carbon sequestration rates in those soils?

As commented above, soil carbon sequestration capacity is related to soil CO2 emissions and soil organic carbon content, which is directly linked to the amount of organic matter that arrives to the soil surface, ready to be decomposed and integrated into the soil. The CO2 fluxes from woody stems measure the net CO2 exchange between the woody living surface of plants and the atmosphere, and thus are not directly related to what happens at the soil compartment. Nevertheless, we could speculate that higher CO2 uptake by woody tissues might lead to increased woody tissue biomass, potentially resulting in greater incorporation of more recalcitrant organic matter into the soil. However, this remains speculative, and we have decided not to include it in the discussion.

Another highlight from the study is that relatively large methane emissions were observed despite the salinity of the marshes. Authors partially attribute these high methane fluxes to the influence of low salinity groundwater, which is logical. However, I am concerned that the value of the methane emissions may be over-estimated due to the long duration of chamber closure (24h). Taking only 2 samples (initial and final) over this 24 period limits the precision of the methane fluxes as well. Authors should take care to interpret their emissions in relative terms (comparison between habitats) rather than drawing comparisons with literature, unless they find studies that have employed similarly long chamber deployments.

We agree that using different methodologies is a handicap when comparing results from various studies. Thus, we have included a sentence indicating which of the mentioned studies collected samples after 24h of chamber closure as we did, in lines 453-455 (“although it is worth mentioning that only Hirota et al. (2007) took samples after 24h of chamber closure, as it was performed in the present study”).

The data presentation does need to be improved. Please use different symbols or colors to distinguish the marsh habitats or plant species in all data figures. With the current version (all gray), one cannot discern these groups.

Following your suggestion, we have improved data presentation using different types of lines to distinguish the different habitats and species in all the figures.

Here we post the answers (in italics) to the comments that Reviewer 2 did about our manuscript. Besides, all these answers to the general comments together with those of specific comments are included (in blue) in the attached document. We would like to thank the feedback and all the suggestions given. 

Comments R2:

General comments: 

In a world dealing with climate change, there is a need to better understand all ecosystems. Studies like this one, investigating GHG exchange in understudied ecosystems like non-tidal salt marches are relevant and important. The combination of in-situ CO2 – CH4 soil fluxes with CO2 vegetation fluxes in the different habitats results in interesting insights and a valuable addition to the laboratory studies with controlled conditions previously carried out. The study highlights the seasonal variability and the differences between species well.

Thank you for your positive feedback on the value of the study.

The Materials and Methods sections could be more detailed. Many elements are not mentioned here such as soil information, salinity, more specific climate data, the amount of data points taken and details about calculations are also left out. Possible additions and suggestions are mentioned in the attached file.

We have included information about salinity and climatic data in section 2.1. We have also added more specific climate data (Figure S2), and a table showing mean soil SOC, TN and bulk density parameters obtained for the three studied habitats (Table S3). Detailed information about the samplings performed are shown in the Supplementary Material tables, while further explanation about the mineralization quotient calculations has also been added. Lines where this information has been included are specified in the responses to the specific comments (see the attached document).

The Carbon mineralization quotient is not entirely clearly explained for me in the method section and not much explanation is given in the result and conclusion section. I think more explanation is needed around the mineralization quotient calculation and some discussion is needed around the carbon sequestration potential of the habitats as this result is interesting but not well supported.

The mineralization quotient has been more thoroughly explained in the Material and Methods section and commented in detail in the Discussion section. The lines where this information has been included are specified in the responses to the corresponding specific comments (see the attached document).

The authors mention large discrepancies between measurement methods (GC, soda lime) and between in situ and laboratory experiments, therefore this information should be added when comparing to literature. Especially for the soil fluxes it should be mentioned which method and closure time is used in the literature you compare to. In this study, the closure time of the chamber for the GC method is very long, with only 2 data points (before and at the end of the closure time), so this will seriously influence the fluxes.

We have always compared our results with previous studies of soil carbon fluxes conducted under field conditions. This has been clarified in the caption of Table 1. We have also added information about the methodology used in these previous studies (Table 1), emphasizing the limitations of comparing data obtained by means of different methodologies (lines 420-423 and 427-428). Moreover, we have specified which previous studies used the same chamber closure time (lines 453-455) and we have highlighted the reliability of the soda lime method to estimate integrated soil CO2 fluxes over long time periods, such as the one used in the present study (lines 128-129 and 151-154).

Data presentation can be improved by the inclusion of a table with soil parameters, a table with the main results, a map of the study region and graph of climate data (either in supplementary or in the main text).

We have included all this information as Supplementary Material.