Main Points

The manuscript presents a study investigating monthly CO2 and CH4 fluxes from mangrove soils in the Amazon across contrasting seasons (wet and dry) and topographies (high and low). This study is suitable for publication in Biogeosciences and is relevant to the community, especially with the focus on spatial and seasonal fluxes. The methods used are robust and the data presented support the conclusions. However, the paper structure and the presentation of the data could be improved.

The manuscript suffers from lack of structure, presentation of results in the discussion but not the results section (e.g. correlations), repetition of results in the discussion, and a lack of synthesis of previous literature findings with current study findings. This makes the discussion hard to follow and understand. Please rewrite the discussion particularly addressing the issue of stating facts from the literature without giving context on how they are relevant or improve understanding of your findings, removing results into the results section, deleting those sections which are repetitive of the results, and rearranging to include all GHG discussion first before moving onto the C stored in biomass. Additionally, the discussion would really benefit from discussing results in context of explaining observations, drivers through correlations and comparisons to other studies in terms of magnitude of fluxes but also patterns or drivers found.

Additionally, the authors should go through the manuscript and ensure there are no grammatical issues or places where too many words are used that make the sentences difficult to understand. With this, the manuscript would be much easier to understand for the reader.

Scientific Points

A lot of space is given to the aboveground biomass and carbon stored there, however, this is not the main point of the paper and provides minimal impact. It would be better to tie this into the offset from the GHG emissions in the discussion to justify the value in the paper. For example, calculating how much carbon is stored and how much is emitted through soil emissions, however, to do this the best way you need belowground C stocks too and I don’t think you measured these?

It is not clear how the statistical analysis was performed as it is not clear how the data was averaged. For the seasonal data is it average monthly fluxes in the wet compared with average monthly fluxes in the dry season? For the spatial comparison it is stated in Line 182 ‘between the different sites’ but is this the sampling sites or between high and low topographies? It is also not clear when a t-test and when an ANOVA was used, the caption for Table 1 only mentions Kruskal-Wallis. If a t-test was used then this should be paired when comparing seasons because it is the same sampling sites being investigated. A Pearson correlation was used to determine relationships between gas fluxes and soil properties, however, gas fluxes were taken monthly and soil properties only once per season. Were the correlations performed on seasonally averaged gas flux data?

Data from Table 1 would be better presented in a graph instead. I think this is Figure 4 but why is that so far through the paper? The point of the paper is looking at CO2 and CH4 fluxes and I cannot see them clearly presented until the discussion. I think it is really great to provide actual flux values as lots of studies do not, but these could be presented in the SI.

I suggest presenting CH4 fluxes as mg m-2 d-1 as the values are very small as g m-2 d-1

Technical Points

Line 16 – contrasting topographical gradient should be replaced with contrasting topographies

Line 18-20 – this sentence is confusing and has some grammar issues, please rewrite. This is often true through the manuscript so please read through and improve sentence structure throughout to aid understanding.

The abstract does not include the fluxes of CO2 and CH4, instead the variation between topographies and season is first discussed. Please include the values first and then state the variation.

Line 21-22 – These mention CH4 fluxes between high and low topography but are contradictory. Please rewrite with the correct observations.

Line 24-26 – This sentence is confusing and needs rewriting with more context, you are stating the GWP of the mangroves through CO2-equivalents but it is not clear.

Line 29 – replace macro tide with macrotidal

Line 38-40 – This does not fit with the previous sentence and perhaps needs moving earlier in the paragraph

Line 51 – The flux unit needs spaces between g, C and yr

Line 52-66 – This could be restructured so that the estimates of CO2 and CH4 emissions from tropical mangroves are presented together and then the effects of flooding as a control on CO2 and CH4 fluxes discussed.

Related to the point above, there are some issues with the structure of the introduction making it difficult to follow and preventing the knowledge gaps and importance etc being clearly presented.

Line 60-61 – Sulphate reduction generally inhibits methanogenesis, as you discuss in the discussion, but here you say sulphate reduction increases CH4 formation.

Line 67-71 – I think the objectives of the study could be clearer. Spatial variation is being investigated but it is specifically high versus low topography, I would add an extra sentence stating this and that the seasonal variation captures wet and dry seasons. This can then lead to flooding and salinity being key controls you are looking at. Also mention the controls of soil properties on these fluxes are being investigated.

Line 68 – pristine may be a better description than non-anthropized

Line 77 – coastal strip, should this be a coastal strip/area of mangroves?

Line 78 – Am type, best to say tropical monsoon

Line 90-91 – Average mean salinity – is that in the river water or in the mangrove sites?

Line 106 – Four sampling sites - are these what you later call stations? It was not clear to me in the paper if the sampling sites were later referred to as stations or if you are referring to something else? When you state in the results there was no difference between station are you comparing low and high topography or sampling sites at the same topography?

Line 110 – flux for each chamber was measured – at this point it is not clear if a chamber is equivalent to a sampling site, or if there are multiple chambers at each sampling site. I think you can just say gas fluxes were measured during periods…

Line 111 – states when the low topography was measured, was the high topography measured at the same time or when was this measured?

Line 114 – replace ‘by a macro tide dynamics’ with ‘by macrotidal dynamics’

Line 119 – Describe the sampling locations before this section, and then have these subsections talking about what was measured and how. You reference here being the same as the gas flux sites, but we haven’t had details of those yet so I think presenting the sampling locations/plots first will make everything clearer

Line 129 – Soil sampling and environmental characterisation was measured once during wet and dry season, so when the Pearson correlations were calculated, was this done with seasonal flux data? I don’t think this was very clear so please state this in the statistical analysis section.

Line 133 – soil samples were properly stored – please give details instead of writing this.

Line 152 – You switched from gas flux measurement to flow measurement, be consistent throughout and use gas flux measurement.

Line 152 and 155 – Suggest using T_air with air as subscript, same for T_s for soil temp

Line 156 – Remove sequentially

Line 159 – Should be flux measurements

Line 161 – how were plots randomly selected?

Line 169 – Please give details of the standard gas used for calibration

Line 177-178 – So the 6% of data with weak regression were considered as zero?

Line 182 – different sites, is this between the high and low topography?

Line 186 – Remove ‘and’ after with.

Line 188 – Please add the details of the relationships between gas fluxes and soil properties to the results section.

Figure 2 – Axis label Dez should be Dec

Line 200 – Rearrange the gas flux data to first present the mean and range of the fluxes and then discuss the stats and differences spatially and seasonally.

Line 203 – Should this say only differed significantly?

Line 203 – Replace among with between

Table 1 – The presentation of the stats in this table is very confusing. Do lowercase letters compare monthly fluxes between high and low topography, and uppercase letters compare dry versus wet seasonal data for each topography? As stated above I do not know what the stations refer to and so I don’t understand some of the comparisons – maybe the uppercase letters are not comparing dry versus wet but something to do with the stations?

Line 213 – Add here that this is seasonal data comparison now

Paragraph on line 222 – This would be clearer if it was rearranged to start saying greenhouse gas fluxes were only sig different between topograpohies in the dry season where co2 fluxes were higher at the high topography and ch4 fluxes were higher at the low topography.

Line 225 – I am not sure what you refer to here with ‘with this’ and so I am not sure if you are presenting here the fluxes over the dry season or across all topographies?

Line 229-242 – Here you sometimes say high versus low topography and sometimes between stations. As mentioned earlier I am not clear on what the stations are referring to, in any case it would be best to stick with the same naming e.g. always talking about high versus low topography.

Line 234 – remove variable

Line 249 – Replace CT with TC, here and elsewhere

Line 258 – Replace MO with OM, here and elsewhere

Line 266 – Tar should be Tair?

Line 271 – Vv is not defined, please define here

Line 292 – Replace e with and

Line 293-294 – I think you mean to say rainier than long-term average in the dry and less rainy in the wet season than the long-term average, because on figure 2 ppt is higher in the wet and lower in the dry.

Line 298 – Here you present the total carbon rate – do you mean the total carbon fluxes? The units are in CO2 not C so I am not sure how this is carbon flux. How was this total emission calculated? Through converting CH4 emissions to CO2-equivalent emissions using sustained global warming potentials?

If figure 4 is the data from table 1 plotted onto graphs, then why are there no statistical differences presented on here?

Figure 4 – I suggest a different naming scheme for topography, using T_high and T_low I am automatically thinking of temperature and then I was trying to work out what the temperature differences were.

Line 315-316 – Why not compare the annual CH4 flux, like you did for CO2?

Line 314-323 – Here it is stated that CO2 is higher than literature values and CH4 is lower but this is just stated with no discussion of why this may be true, for example, do you have less flooding due to combining the low and high topographies in this analysis? Is it due to soil properties here being less favourable for methanogenesis and more favourable for aerobic respiration?

Line 324 – Here the discussion on biomass is in the middle of all the gas flux discussion, move this to after the gas flux has been discussed.

Line 333-334 – I’m not sure how your results show the mangroves are more productive than previously known. You have C storage at lower capacity than estimated for brazilian mangroves, then state a primary production for tropical mangrove forests with no relation to your measurements here (unless I missed it) and then say the mangroves are more productive than previously known.

Line 372-374 - This sentence is very hard to follow. This is an example of where the whole manuscript could benefit from another proofread to check for clarity. Additionally, to reduce sentence length where unnecessary text is used that makes the point of the sentence harder to understand as the reader.

Line 379 – High tide or rainy season? Because all fluxes are measured at low tide I think. If this is not correct please make this clear.

Line 388 – replace generates with favours

Line 389-392 – Please also rewrite this sentence

Line 409-410 – Better correlate dto which characteristics?

Line 410 – Positive or negative correlations?

Line 415 - Here this is an interesting point but it seems you are saying that higher soil moisture should give a lower ch4 efflux, but you also show and state earlier that lower topography with more flooding has higher ch4 due to anoxic conditions. I think it would be good to really refine these points and discuss them together. This is another example of where there is lots of comparison and citations of other literature but it is not always pulled together in a coherent way.

Line 424-425 – Here you say increasing soil moisture increases gas diffusion rates but earlier you said high soil moisture decreases gas diffusion rates

Line 430 – DO you mean here that during the dry season the high tides cause anoxic soil conditions, or are you comparing dry and wet seasons?

Line 430-432 – I am not sure what this is relevant to.

Line 433 – I am not sure why this is relevant, you are not discussing sulphate reduction but CO2 and CH4 fluxes, and this sentence does not seem to link to your next points clearly.

Line 441-444 – Is there a reason that this same mechanism would not be occurring in the mangroves you are comparing your results with?

Table 5 gives correlation coefficients with annual data, so it would be good to plot the annual fluxes onto figure 4.

Line 451 – This was not clear to me. Are you saying that tidal movement is more important for flooding in the dry season, therefore, there is also higher salinity?

Line 462-463 - Here you say salinity is negatively correlated with CO2 but this paragraph earlier states that high sulphate leads to increased CO2. There are lots of these instances and I think the discussion could really benefit from more structure and focus into the synthesis of previous work on drivers and patterns related to this study, rather than stating lots of observations from the literature and then saying in this study we found X.

Line 498-500 – Consider using the sustained global warming potential instead – moving beyond global warming potentials to quantify the climatic role of ecosystems. Scott Neubauer and J. Patrick Megonigal, Ecosystems. 2015

General comment

The manuscript “Greenhouse gas fluxes in mangrove forest soil in the Amazon estuary” examines CO2 and CH4 fluxes from mangrove soils and evaluates topographic and seasonal variations. Moreover, environmental drivers such as vegetation structure and soil characteristics are studied. I highly agree with the comments made by RC1. The topic of the paper is timely and fits the scope of Biogeosciences. The study design is appropriate, and the data set sufficient to answer the stated research questions. However, the manuscript is hard to follow and should be streamlined. It would be helpful to put some of the results (e.g., detailed statistical analysis of all parameters) into a supporting information and report only relevant findings. The general structure and story line should be more focused.

Specific comments

Abstract

L 13 – 14 First time reading “especially in a scenario of global climate change” I thought you would test the impact of climate change on GHG in mangroves. Maybe rephrase as “to asses their impact on climate change”.

L 17 – 18 Delete this part of the sentence and use the extra words to give more quantitative results, such as gas fluxes.

L19 – 22 Write how much higher (x-times higher) fluxes were between sites/seasons. Do never start a sentence with “only”. Chance this throughout the manuscript.

Introduction

L28 – 30 Move this sentence to the study site description or the aim paragraph of the introduction. Then start with (tropical) mangroves in general. Consider restructuring the first paragraph by starting with carbon storage in mangroves and benefits for climate change. Then state that it is important to consider GHG outgassing as offset of the carbon storage.

L41 Change “attributable” to “driven by”.

L50 Write “CO2 outgassing” instead of “CO2 production to the atmosphere”. Make clear which statements in this and the next paragraph are specific to mangrove and which to estuaries/coasts/vegetated coastal wetlands. Preferably use only mangrove publications, there are enough publications to underline each of your statements.

L55 Confusing statement. Consider rephrasing.

L61 How does reduction of sulfate produce CH4?

L67 Be more specific what you mean by spatial and seasonal variation.

L70 Remove years but describe in more detail which drivers you were testing.

Methods

Please add GPS coordinates of your stations in the text.

L77 “exclusively untouched mangrove forests” use “pristine mangroves”. Consider splitting this sentence.

L86 Use tidal “amplitude” instead of “height”.

L109 – 111 This sentence is not a part of the study site. Put it into “Flux measurements”. Is suggest putting “Greenhouse gas flux measurements” as 2.2, since this is your focus.

L120 When did you conduct the floristic survey? Report dates.

L130 Why did you take only very shallow soil cores? It sounds like you measured pH and redox at the same spot where you took the soil sample. I hope it was just next to it. Please clarify.

L137 I personally would not capitalize all parameters, but wright “Organic matter…”.

I agree with RC1 that the abbreviations should be changed.

L150 When did you conduct the soil sampling? Report dates.

L160 Also add dates of chamber sampling.

L164 I personally would have measured above the mangrove roots since these are important parts of the mangrove ecosystem. At healthy mangroves, spots without roots are rare, thus including them yields more representative flux rates for mangrove soils. Something to consider in your next study.

You need to add more info about the flux measurements. How often did you measure per month? One or more rings? Did these rings stay at the same spots?

Consider matching headings with the results headings. The wording and also the order.

Results

The results section is very hard to read. I would only report values of each parameter and describe general trends without using any statistics. Then add a section where you look at the statistics, but only in regard to the GHG not of the statistics between the drivers.

3.1 Carbon dioxide and methane fluxes

• Fig 4 (put table 1 in SI)
• Describe values and trends for CO2 and CH4 in sperate paragraphs

3.2 Weather data

• Fig 2 + Fig 3

3.3 Soil characteristics

• Table 2 + Table 3

3.4 Vegetation structure and biomass

• Table 4

3.5 Drivers of greenhouse gas fluxes

• Table 5 (also add correlation of all other parameters, to shorten the table you could only keep significant correlations and mention in the text which parameters were not significantly correlated to the GHG)
• I would not distinguish between single months for the correlations, but focus only on wet and dry seasons

Alternatively, you could only use subsections 3.1 – 3.4 from above. Start each subsection with describing values and trends of each parameter. The second part of each subsection should briefly report the stats between the GHG and the parameters (not amongst parameters!).

In all tables use mean ± standard error instead of mean(standard error).

Discussion

Generally, try to link your results with the literature more closely. Often you have one sentence about one study and then and an vaguely related sentence about your study. You need to link those “bigger/smaller than, similar to, supported by/contradicting to…”

Possibly use the following structure:

4.1 Carbon dioxide and methane fluxes

• Compare fluxes to literature and discuss differences
• Separate CO2 and CH4 in paragraphs

4.2 Drivers of greenhouse gas fluxes

• Possibly get subheadings for parameters similar to results section
• Discuss drivers and find literature backing up your statements, only focus on significant differences but do not repeat statistics

L 309 Add a, b, c, and d to the figure. Reduce scale for c and d.

L294 – 295 To speculative – delete.

L 295 – 299 Also needed in results section, here only short repetition. What do you mean by total carbon rate? Separate CO2 and CH4.

L 301 Slufate reduction? Explain.

Make sure that all studies you compare your results to used similar methods and did note examine water – air fluxes instead of soil – air fluxes.

Calculate all GHG fluxes in the discussion in the same unit to make comparisons easier.

L318 What was expected?

4.2 Mangrove biomass: would only focus on the impact on GHG. This section interrupts the flow of the manuscript.

L336 Larger flood volume during ebb tides? Explain.

L433 – 435 I do not understand your general focus on sulfate reduction. This is an alternative process to methanogenesis. Always focus on CO2 and CH4 production.

The difference between different topographies can probably be explained by differences in chemical soil characteristics.

L493 Which authors?

Conclusion

495 – 498 Be more specific. What seasonal trends? Rainfall compared to climatology?

Add a sentence about the general relevance of the study.