the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 27 Oct 2025
A cross-site comparison of ecosystem- and plot-scale methane fluxes from wetlands and uplands
Abstract. Wetland and upland ecosystems play significant but opposing roles in the global methane (CH4) budget, acting as natural sources and sinks, respectively. Two of the most common approaches for measuring CH4 fluxes (FCH4) are chambers, which capture temporally intermittent, fine-scale spatial heterogeneity (ca. 1 m2), and eddy covariance (EC) towers, which cover a larger area (ca. 100–10000 m2) at a longer term. Although chamber and EC observations have been combined in various syntheses and databases to estimate CH4 budgets, a unified cross-site evaluation of FCH4 estimates at plot and ecosystem scales is lacking. As a first step toward a systematic spatiotemporal scaling of EC tower and chamber footprints, we quantified the differences between site-level aggregate FCH4 (EC vs chamber; ΔFCH4) from ten wetland and upland sites at half-hourly, hourly, daily, weekly, monthly, and annual timescales. We found that ecosystem-scale median FCH4 was consistently higher than plot-scale FCH4 at all temporal scales, with the smallest difference at daily timescale (multi-site median ΔFCH4: 1.36 nmol m-2 s-1; ~ 104 % higher ecosystem-scale than plot-scale FCH4) and largest at annual scales (2.58 nmol m-2 s-1; ~ 87 % higher ecosystem-scale than plot-scale FCH4). In general, the agreement between ecosystem- and plot-scale FCH4 decreased with finer temporal resolution (from Spearman ⍴ = 0.95 at annual scale to ⍴ = 0.65 at half-hourly scale), while ΔFCH4 variation was greatest at daily-to-annual scales. Key environmental predictors of ΔFCH4 included plot-scale spatial heterogeneity, dominant vegetation type, vapor pressure deficit, atmospheric pressure, and friction velocity at the daily and monthly scales. Wind direction was a significant predictor only at the monthly scale, suggesting EC footprint effects. These findings suggest accounting for variation in EC footprint extent, chamber measurement placement and artifacts is key to reconciling multi-scale FCH4 observations in diverse ecosystems and refining CH4 budgets.
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Status: open (until 02 Jan 2026)
- RC1: 'Comment on egusphere-2025-5023', Anonymous Referee #1, 04 Dec 2025 reply
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Cross-site comparison of ecosystem- and plot-scale methane fluxes from wetlands and uplands (Version v1) T. Määttä et al. https://doi.org/10.5281/zenodo.17312404
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- 1
This manuscript presents a valuable cross-site comparison of methane fluxes measured by eddy covariance (EC) and chamber methods across 10 wetland and upland sites. The work addresses an important gap in understanding how these two common measurement approaches compare across multiple sites and temporal scales. The dataset is substantial, the statistical analyses are appropriate, and the findings have significant implications for combining multi-scale flux data in syntheses and modeling studies. The multi-site and temporal scales approach, practical recommendations and transparency about limitations are significant strengths.
However, the manuscript would benefit from major revision to improve clarity, address methodological concerns, and better contextualize the findings.
Key issues to resolve:
Section-specific comments and key issues:
Introduction
Line 90-91: “Thus, chambers provide a greater spatial site-level representation than EC sites and are needed to fill the missing data gaps.” – contradicting your statement about area representation in lines 80-81
Line 99: “Plot and ecosystem-scale FCH4…” : You mention in your line 78 that different ecosystem and hydrological subtypes within the EC footprint are defined as “plots” (see also line 80), but here it seems to me that by “plots” you mean chamber studies and chamber plots? To avoid confusion, consider re-wording/defining.
Line 113: “…than the true, mean ecosystem-scale FCH4”: this insinuates that the EC ecosystem-scale measurement is the “true” FCH4, but in reality, we do not know this for sure, as EC also comes with its own uncertainties.
In the introduction, you could also discuss the different chamber systems used in GHG studies, i.e. manual sampling with gas chromatography analysis, or in-situ measurements with portable gas analyzers. This distinction affects comparability and should also be discussed in the limitations section.
Methods:
Key issue: Inconsistencies in ebullition treatment
Most sites removed ebullition events from chamber data (Text A1). However, ebullition is mentioned repeatedly as potentially explaining EC > chamber fluxes, and the authors suggest EC captures ebullition better than chambers (lines 477-482, 491-494, 497-499, 569-570). This is circular reasoning: chambers are processed to remove ebullition, then the authors express surprise that EC is higher. Recommendation: Clarify whether ebullition removal from chamber data is appropriate for this comparison or acknowledge it as a limitation. Discuss implications: if ebullition is real and important, should it be removed from chambers when comparing to EC?
Table 1: I wonder if Table 1 could be better presented in the final publication? Perhaps landscape orientation would make the column titles and words not be cut off.
Line 215: I’d like more information about seasonality of measurements and when they were conducted. I see this in supplementary material (Figure B1), but I think this is important information for the main text. Perhaps integrate to Table 1?
Results:
Line 310: What do you mean by large CV? Please quantify.
Lines 313-315: I think it is good practice to put units behind all numbers, even if you are repeating them/listing them.
Figure 3:
Figure 4:
Figure B6-B7: without reading the captions, there is no way to understand what these figures are illustrating.
Table 3: Formatting needs improvement - currently difficult to follow. Try to make more compact.
Discussion
Key issue: The title of the manuscript emphasizes "wetlands and uplands" but there is minimal comparison between these ecosystem types in the results and discussion. Lines 592-595 briefly mention this, but given the title's prominence, this deserves substantially more attention. How do the ΔFCH4 patterns differ between the two ecosystem types? Do different processes drive differences in these contrasting systems? If data are insufficient for robust comparison, consider revising the title.
Line 450: Avoid starting immediately with “contrary to our hypothesis.” Start by summarizing key findings, then contrast with hypothesis.
Lines 457-460: long sentence, consider splitting into two.
Lines 463-474: This section could use some citations to back up your claims and relate to previous findings.
Line 475 and onwards: however, you could also discuss here that chamber artifacts can increase chamber fluxes: e.g. disturbance of soil/water surface and thus causing a pulse (especially for manual sampling).
Lines 481-485: long sentence, consider splitting into two.
Lines 485-486: Yes, but Meijide et al found the opposite trend – that chamber fluxes exceeded EC fluxes. Can you make direct comparisons with your results and how would your interpretation change?
Lines 486-489: So what may be the implications of this poor detection of differences at low fluxes? How may it compromise/influence your results?
Lines 489-492: again, consider splitting into two sentences
Line 496: consider if statistics such as p-values are relevant for discussion or if they should be kept only in results.
Lines 495-499: This is a good thought about PA, however, you bring out that your results show decreasing ΔFCH4 with higher PA at the weekly scale, which is not something relevant for ebullition events (very short term). I wonder if you could elaborate on this point.
Lines 501-502: but consider that low u* values are typically removed from EC data if using standard protocols – how would this influence your results’ interpretation?
Line 504: change ‘may be’ to ‘was’. I think overall the word ‘may’ is used excessively in the discussion. Try not to use ‘may’ if you are referring to your own results: your results are certain, not ‘maybe’; the implications of your results and how they relate to previous findings, that is where the word ‘may’ comes in.
Line 511: ‘As expected’ replace with ‘As hypothesized’, or similar
Lines 517-519: You talk about soil CO2 respiration hotspots and hot moments and then bring those same conclusions to explain CH4 hotspots and moments. I think CO2 respiration hotspots do not directly translate to CH4 dynamics. You could try to find studies describing CH4 hotspots/hot moments with chamber measurements; or better integrate the CO2 ideas.
Line 521: By overcome do you mean exceed, i.e. EC FCH4 is higher? Overcome is a strange verb to use here.
Line 530-531: Good point about using representative chamber patches, but discuss the issue of how to best determine these?
Line 535: add ‘the significant effect of uWD…’
Lines 542-544: Rewrite the final sentence of this paragraph; it is confusing. What is ‘significant April’?
Lines 546-548: Why would chambers not capture the release of stored CH4 below the ice and snow cover? Freezing and thawing dynamics also occur inside chambers. I also struggle to see very specific “higher ecosystem-scale FCH4 at CN-Hgu and US-Ho1 in cooler months” in Figure B14. But maybe this is an issue with figure readability.
Lines 550-554: the chamber measurement system issue seems to not belong together in the same paragraph with seasonality issues. Consider re-arranging. Would chamber system issues better be placed in limitations? Perhaps you could also integrate the use of different chamber flux analysis methods (GC vs portable analyzers) and create a new paragraph.
Line 556: I’d suggest removing ‘As we expected’ and just staring the sentence with ‘Diel analyses revealed…’
Line 559: What do you mean by ‘higher diurnal EC FCH4 than chamber FCH4’? Do you mean higher diurnal variation? Or higher daytime flux overall?
Line 573: this sentence needs a citation.
Lines 599-601: This sentence is confusing, consider re-writing.
Limitations:
Could the specific instrument for chamber measurement (e.g. Licor, Picarro etc) also play a role in method discrepancies?
Acknowledge that lack of winter measurements at most sites is a major limitation and may bias annual comparisons.
Supplementary materials
Try to keep figures and figure captions on one page.
Just suggestions: Confusion in Supplementary Material/Appendices naming: Text A1-A3 and figures B1-B19 and Tables C1-C14. They make sense once you make it all the way down to the supplementary material and realize that the letters refer to Appendix A, Appendix B and Appendix C, but when they first pop up in-text, it is confusing. Also, instead of Text A1-A3, you could do Supplementary Methods 1 etc. maybe, as “Text” is ambiguous.
Text A1 regarding QC/QA of chamber measurements on each site: I’d like to see a more uniform description of these. Currently, some sites mention R2 filtering, some not. Some say ebullition was not significant and thus it was removed, some say ebullition was not significant and thus it was *not* removed. Perhaps you could combine Text A1 into a table with different QC/QA criteria for better comparison (i.e. R2 threshold, dark/transparent chamber, GC vs PGA instrumentation, pressure vent and fan, H2O correction, ebullition removal…). Similar to Table C1.