the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 06 Jul 2026
Permafrost thaw reshapes methane cycling across an interior Alaska peatland
Abstract. Permafrost thaw is expected to increase methane (CH4) emissions from northern peatlands, but it remains uncertain how thaw affects the microbial pathways driving CH4 production and oxidation. We measured CH4 and carbon dioxide (CO2) fluxes during July 2022 using static chambers and combined these measurements with δ13C-CH4 measurements, 16S rRNA and mcrA gene sequencing, as well as environmental data across a fine-scale thaw gradient in an interior Alaska peatland. Mean CH4 fluxes increased from near neutral (-0.1 ± 0.02 μmol m-2 s-1) in stable thaw stages to 40.2 ± 12.0 μmol m-2 s-1 in advanced thaw stages, while CO2 fluxes did not change. Thaw progression was associated with higher water tables and deeper seasonal thaw depths with an increase in methanogen relative abundance and shift in methanogen community composition. Hydrogenotrophic taxa increased in relative abundance with advanced thaw along the gradient, particularly Methanoregula, which explained 36 % of the variability in CH4 fluxes. Despite this shift, emitted δ13C-CH4 values fell within ranges commonly attributed to acetoclastic methanogenesis. Rayleigh fractionation modeling suggests that ~ 40 % of CH4 produced at depth was oxidized before reaching the atmosphere, enriching residual CH4 in 13C and altering the isotopic signature of emitted fluxes. These results highlight the need to integrate fluxes, isotopes, and microbial community data to fully resolve CH4 cycling processes in thawing permafrost peatlands.
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Status: open (until 19 Sep 2026)
- RC1: 'Comment on egusphere-2026-2809', Anonymous Referee #1, 31 Aug 2026 reply
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The authors investigated the effect of the thaw gradient of permafrost in a peatland in Alaska on the CO2 and CH4 fluxes, combining environmental variables like water table depth, seasonal thaw depth, soil temperature and soil moisture with changes in microbial community composition based on the 16S rRNA gene sequencing and analysis of methanogenic communities based on the mcrA gene and measures 𝛿13C-CH4 signatures released from thaw and from deeper porewater. This study addresses relevant scientific questions within the scope of BG, integrating “biological, chemical, and physical processes in terrestrial life with the geosphere, hydrosphere, and atmosphere”. The experiment is well-designed. The authors concluded that combining 𝛿13C-CH4 signatures with characterisation of the changes in methanogenic communities in response to thawing allowed a more reliable interpretation of methane cycling processes.
A taxonomic shift in methanogenic communities indicated an increasing contribution of hydrogenotrophic methanogen taxa, which may reveal a change towards hydrogenotrophic methanogens observed at sites in the advanced stages of thawing. In contrast, based solely on the isotope results, the false conclusion might be drawn that acetoclastic methanogenesis is dominant. Their study indicates that, based on the model used, approximately 40% of the methane produced is oxidised before leaving the soil profile, altering the interpretation of isotopic results and possibly explaining the discrepancy between the results obtained.
Overall, the results described are interesting; however, there is a lack of a more critical discussion of the methods used. (1) The estimated percentage of oxidised CH₄ is valid only for the variables assumed in the model. (2) The mcrA analysis was carried out using forward reads, and (3) the presence of a given physiological group, as determined by DNA, should be interpreted with greater caution as evidence of actual functional activity. (4) It is also necessary to describe in detail the potential impact of the spatial separation of the Permafrost Plateau, with stable and early thaw stages, from the Active Thaw Margin (intermediate, advanced) on the results obtained. It is understandable that in the field it is not possible to plan everything as one would in a laboratory, and that data collection is fraught with methodological problems, but these concerns should be discussed. (5) Raw NGS data should be deposited in an appropriate scientific repository, and the data access number should be included with the article before final acceptance of the manuscript. The journal Biogeosciences favours reliable, public repositories that comply with the FAIR principles and use persistent identifiers
In its current form, the manuscript requires a major revision.
Other comments:
Gene names, such as mcrA, should be written in italics throughout the text, whilst protein names should remain in normal typeface.
L.225: Check the sequence for 926R primer. It looks like you pasted the sequence for a different primer (806R). Additionally, in the supplementary materials, you used another primer 896R. Is it correct? The accuracy of the data in the supplementary materials should be checked.
L. 293 vs L. 375: what was the final number of 16S rRNA samples: 71 or 62? Methodological data referring to the initial number of samples and the numbers remaining after each stage of data preparation should be presented in a single place
The interpretation of Figures 6 and 8 could be enhanced by a brief description of the direction of the environmental-factor gradient at each melting stage. In particular, it is worth noting that the distinction between stable/early and intermediate/advanced communities essentially corresponds to changes in thaw depth, groundwater level, temperature, and CH₄ flux. Moreover, the figure caption should define all the environmental vectors shown in the graph.
L. 397-400: The authors list five types whose relative abundances change significantly. However, in the discussion, they refer to only one of them (Bacteroidota). Besides, in microbiology, classification at the phylum level is useful for the general characterisation of communities and for comparing communities of microorganisms in different environments. Therefore, it is good that fig. 7 is presented. However, such classifications are usually too general to allow for detailed functional interpretation, as presented in Discussion (L. 467-469), because individual phyla include taxa with highly diverse metabolic characteristics. To identify the groups of microorganisms most likely responsible for the observed changes in community composition, the authors should analyse changes at lower taxonomic levels, such as the family or genus level. It is also possible that a significant trend at the phylum level is largely due to a strong response from one or more dominant taxa at lower taxonomic levels.
L. 418-419 The non-linear trend in methanogen alpha diversity is potentially interesting, but has not been discussed. Both Shannon diversity and ASV richness decline from stable to intermediate thaw, then increase markedly during the advanced thaw phase. The authors should discuss potential ecological explanations for this phenomenon.