the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 15 Apr 2025
Effects of permafrost thaw on seasonal soil CO2 efflux dynamics in a boreal forest site
Abstract. Permafrost regions in subarctic and arctic areas harbor substantial carbon reserves, which are becoming increasingly vulnerable to microbial decomposition as soils warm. As the seasonally thawed active layer deepens and anthropogenic disturbances escalate, accurately predicting carbon fluxes from thawed permafrost requires a comprehensive understanding of soil respiration dynamics. This study aimed to investigate the impact of disturbance on soil respiration rates and identify the key environmental and geochemical factors influencing these processes in a boreal forest ecosystem near Fairbanks, Alaska. The disturbed site demonstrated an increase in mean annual soil temperatures, recorded at 0.60 ± 0.16 °C, along with a 14.4 % rise in mean annual microbial activity, which peaked at 20 % during the summer, in contrast to the undisturbed site, which had a mean annual temperature of -0.37 ± 0.08 °C. Furthermore, bacterial and fungal community composition differed significantly between the two sites, suggesting a potential mechanism underlying the variation in CO2 efflux. Our research underscores the essential importance of considering the rise in carbon emissions from anthropogenically disturbed soils in permafrost areas, which are frequently neglected in assessments of the carbon cycle. This study contributes to a deeper understanding of the complex interactions governing soil respiration in thawing permafrost, ultimately informing more accurate predictions of carbon fluxes in these ecosystems.
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Status: final response (author comments only)
- RC1: 'Comment on egusphere-2025-1204', Anonymous Referee #1, 02 Jun 2025
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RC2: 'Comment on egusphere-2025-1204', Anonymous Referee #2, 12 Nov 2025
This study reports a comparison of soil respiration and associated edaphic and microbial community data between two boreal forest sites. It is well written in terms of readability and the data are well presented. The primary novelty is that such comparisons are rarely as detailed and comprehensive as this one which includes a plethora of soil physical, chemical and microbiological data.
My main concern with this study is that it is portrayed in a way that does not make sense to me. The sites are different – one has not been disturbed for multiple centuries and seems to be classic interior Alaskan Black Spruce forest with a moss-dominated understory. The other is described as ‘disturbed’ due to trail-building and firewood harvesting a century ago, and now has scattered birch and white spruce with a ground surface of grasses and sedges. The two sites are 10 m apart (line 89 p.3). The hypothesis is that soil respiratory carbon emissions are larger in the disturbed site compared to the undisturbed site in permafrost areas (lines 78-80, p.3). But the title is ‘Effects of Permafrost Thaw on Seasonal CO2 efflux dynamics in a boreal forest site’. But both sites are on permafrost, the comparison is about the effect of disturbance, and there are two sites not one. This title seems like an extraordinary mismatch with the actual data. With respect to the permafrost thaw issue, yes the max active layer thaw is much deeper (~ 1m ) in the disturbed site, but the explanatory variables that best explain the patterns of soil respiration are from relatively shallow depths – all within the ‘normal’ active layer depth range (as indicated by the undisturbed site). In other words, there’s no evidence anywhere in the manuscript that the deeper thaw in the disturbed site is the cause of the differences in seasonal CO2 efflux dynamics. The title is way ‘off the mark’, and this mismatch creates a very bad initial impression that leads to niggling concerns about the ensuing manuscript.
Hence, I have great concerns about the permafrost context in which the Conclusion opens. I do however understand and agree with the final conclusion that the study demonstrates that disturbed areas of the boreal forest such as this one, are fundamentally different in terms of CO2 efflux and therefore warrant specific inclusion in forest C models. I recommend that the authors really step back and review the validity of the many, many references to permafrost. Yes it does provide some overall significance to the study, but only that (as far as I could tell). Hence, I recommend that they review and greatly restrain the linkages because the data simply don’t warrant it.
By contrast, the authors do have a basis for comparing soil respiratory CO2 release between the two sites. The problem for them is that there are significant differences between the two sites in daily rates only in summer (p. 13, line 345) (Fig 6). So in essence, they are left with a whole lot of potentially explanatory variables that they have used to predict the CO2 release rates at the two sites, and to compare which variables are most effective between the sites and soil depths. The second problem is that the relationships between efflux and the explanatory variables do not differ significantly between the two sites – there’s no site effect - line 365-367 page 14). Overall this data set may well contain useful information – I do not know for sure, but would assume there are many similar studies that have also done such comparisons... Therefore the particular novelty of this study that would warrant its publication is not at all clear. Perhaps the novelty is the unusually comprehensive data set of physical, chemical and biological variables.. . - if so the Introduction needs to highlight that. One other novelty aspect that strikes me is the inclusion of winter respiration data.. always difficult – especially in tundra. And therefore comparison of the seasons and in particular the proportion of total annual soil respiration that occurs in the non-growing season may be of interest.
Please find some specific comments and suggestions to the text below that I hope will assist the authors in improving the manuscript
Title: NEEDS complete revision. See comments above.
Abstract:
12-13... this study does not necessarily directly report carbon fluxes from thawed permafrost.... see above.
14 The type of disturbance needs to be described.
- ..suggesting a potential mechanism....But the variation (which needs to be fully explained in the Abstract) in CO2 efflux between sites seems to be minimal (as described above).
23.. in thawing permafrost.. see comment above.
Page 2.
44 why would a decrease in net radiation lead to increased CO2 efflux... would more radiation reach the soil surface in disturbed sites, and therefore raise soil temperature as you found (and consequently stimulate microbial respiration)?
46 .....substrates for soil microbial decomposition...
- ....flooding (Reference needed).
Page 3
72 perhaps: ... mechanisms driving variation in soil respiration within and between these two ecosystems....
- ... delete ‘permafrost areas’
- Are’nt they disturbed sites not just disturbed soils.. E.g. the vegetation is very different in composition and density.
- Do we know that the ‘disturbed site’ was similar/identical to the undisturbed prior to the trail building and wood harvesting......Any evidence.. historical photos maybe. Presumably the sites are identical in terms of topography, parent material (i.e. the state factors) – say so in the manuscript.
- Is 10 m apart really sufficient? Are you confident that the two sites are independent of each other in terms of functioning. Any evidence.. Otherwise there must be concerns about shading, leaf litter, and even root penetration across the ecotone/boundary. 10 m seems pretty close.
Page 4.
96-100. Reader really deserves to see photos of the two sites,..... to gauge the vegetation difference, the birch density. I suggest you add multiple photos to the supplementary files.. including soil profiles to see the overlying organic layer and the deeper mineral layer.. and where exactly is the permafrost – photos? And why is there so much more soils info given for the disturbed site.. seems unbalanced description.
Section 2.2 and 2.3 Woefully inadequate description of this critical methodology
How far apart were the collars – a map in the supplemental file would help... one that combines the disturbed and undisturbed sites.. are they really separate sites, or just zones??
Were the CO2 flux plot measurements continuous, 3 per hour 3 per week... there’s no information at all. For how long was each measurement period. Were there checks for leaks, and for adequate seal. The data presented in Fig 6 are grand cumulative totals per season... but the reader needs to know the details of how these totals were reached. Were there similar numbers of measurements per day week etc in winter as in summer.
Page 5.
147-149.The temperature probes for topsoil and subsoil seem to be at different depths in the disturbed versus undisturbed... although the vegetation cover depth differences may accoiunt for this. Otherwise, this difference alone could explain the temperature differences observed in Fig.2
Page 6.
159-163 – What depths exactly were the soil samples taken... and did those sampling depths differ between winter and summer/spring? You need to at least give the range of depths at each sampling time. And depth from what exactly.. the top of the organic soil surface, or the vegetation.....
- All soil samples for microbiological analysis were placed ina freezer on collection. This is routine practice, but is there not a concern that the summer soil community will be impacted by freezing resulting in an altered microbial community composition?At least cite references to support this practice.
Page 7.
184.. ...soil pH were each statistically....
Page 9.
- Presumably the winter soil temperatures were warmer in the undisturbed site because there was deeper snow accumulation there.Give info on snow depth comparison between sites... and here is a variable that might well be influenced by the very close proximity between the sites.
267 and other graphs. How exactly were outliers determined?
Page 10
- This is a comparison between sites. There was no ‘treatment’ enacted by the authors..and so I think this term should be removed entirely from all locations in the manuscript. Likewise, the statistical comparison is really between ‘sites’, and so the 5 uses of the word disturbance in Fig 4 should all be replaced with Site. And likewise for the 4 uses in Fig 5.
283 and 287 and 290. The variable being reported in soil concentration of C or N, not content which would require multiplying the concentration by the bulk density. Please correct throughout.
283-285 is duplicated at 290-292.
286 and elsewhere (not significantly different)
Page 11
309 Perhaps: We compared microbial community composition and diversity between the disturbed and undisturbed sites.
Page 12.
327... there’s no disturbance regime.. this is a site comparison
Page 13.
Section 3.4. This text is written in a way that makes it very hard to determine whether respiration rates differed between the two sites... and exactly what the respiration variable is. But it seems only the summer daily rates were different (line 345). And are these comparisons only of the peak daily rates in each season.. it is all quite unclear. The final sentence (line 352) clearly indicates that there are overall whole season differences for the winter and for summer seasons.
One fundamental methodological issue concerning winter is that tables were used to cover over and keep the snow from building up on top of the CO2 measurement enclosures. I understand the methodological necessity of doing this to allow the flaps to operate, but did it not result in confounding effects on soil temperature because there was no insulating snow cover there. Could this mean that the winter measures are likely underestimates of actual daily and seasonal rates?
Page 14.
- Are these daily (ie. daytime only) or diel (full 24 hour) means??
365-367. Perhaps: The relationships between soil efflux and the aforementioned variables did not differ significantly between the two sites (p...).
Page 17.
418 ...soil were markedly....
- That there were site differences in soil organic layer thickness was not apparent to me.In fact I don’t think those depths were reported, and should be. And what is the topsoil layer.. does that include the OeOa organic layer right at the surface – directly beneath the mosses (at least in the undisturbed site). And what about in the disturbed site.. presumably it is thinner?
426-429. Okay if there’s a thicker layer of organic soil right at the surface that might help. But surely the snow depth and density are both distinctive to the undisturbed site in terms of providing thermal insulation against severe air temperatures. Add the relevant data and maybe photos of the site through each of the seasons if available.
- again relating to snow cover depth and density may possibly explain why air temp was the best predictor variable... in the sense that only marked changes in air temp would influence the soil temp because of the snow insulation layer. One alternative explanation for the soil temperature being a better explanatory variable of flux from the disturbed site is that soil respiration there is primarily from deeper depths within the soil because the surface organic soil C is relatively low/depleted.
Page 18.
461-463. Is this novel and therefore the study has contributed new insights? If so, then the manuscript should be clearly structured around that conclusion.
I sincerely hope these comments and suggestions are useful to the authors.
Citation: https://doi.org/10.5194/egusphere-2025-1204-RC2 -
EC1: 'Comment on egusphere-2025-1204', Krystyna Kozioł, 20 Nov 2025
Dear Authors,
an additional set of Reviewer's comments has been made available to us very recently. I believe for the more comprehensive discussion, it is beneficial to include them in the review process as well. They are attached as a supplement. Please consider them in the Authors' responses.
Kind regards,
Krystyna Kozioł
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The topic and data are interesting. However, data analysis and presentation are poor. Therefore, substantial revisions throughout the manuscript are required. For example:
1) Why did the authors consider only microbial respiration when they measured total respiration, including plant root respiration?
2) Why did the authors evaluate only the linear relationships between soil CO2 efflux and environmental variables, when they can be related non-linearly to each other? I think the authors should present and describe relations between soil CO2 efflux and potentially important variables (i.e., temperature and VWC) in more detail before applying the simple analyses with linear correlations and random forest models.
3) How did the authors determine the microbial activity from microbial abundances based on DNA amplicon analysis? The amplicon analysis just provided microbial abundances but never microbial activity. Presenting data of microbial species composition in the main text but not in the supplemental is required.
4) Why did the authors refer only to carbon dynamics studies on non-permafrost regions in their introduction (L49-L60)? Referring to those studies on permafrost regions is essential to clarify the position of the present study within the scientific context of this research field.
It is super challenging to summarize concisely all the issues of the manuscript. Therefore, substantial self-efforts by the authors are essential in thoroughly revising the manuscript.