the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 31 Mar 2025
Bacterial community composition changes independently of soil edaphic parameters with permafrost disturbance
Abstract. Microbial degradation of frozen organic carbon increases with permafrost thaw, resulting in greater fluxes of the greenhouse gases CO2 and CH4. To examine the effect of disturbance-induced permafrost thaw on microbial communities, we assessed the microbial diversity of soils near a gold mine where thaw was induced by stripping the vegetation and topsoil at Dominion Creek, Yukon, Canada. Bacterial metabarcoding and soil physicochemical parameters were assessed across this disturbance including surface samples and three cores which included active layer and permafrost horizons. Bacterial communities changed in the absence of physicochemical parameter shifts after only 6 weeks of thaw, with a high proportion of active layer indicator species becoming more abundant with permafrost thaw. Three distinct communities emerged: (1) undisturbed active layer, (2) lower active layer, disturbed active layer, and disturbed permafrost samples, and (3) intact permafrost. Community composition shifts correlated with pH, Zn and community cohesion. These results suggest that active layer communities rapidly colonize thawed permafrost, combining with and replacing many resident permafrost taxa. Disturbances may induce a strong microbial community change in permafrost-affected soils before soil physicochemical parameter shifts.
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Status: final response (author comments only)
- RC1: 'Comment on egusphere-2025-224', Wang Minxiao, 05 Jun 2025
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RC2: 'Comment on egusphere-2025-224', Claudia Bruhn, 28 Oct 2025
Overall impression:
Most of the manuscript reads well and it has interesting findings that are worth being told. However, several aspects require clarification and revision. In particular, it is unclear how changes in the community within six weeks of soil disturbance can be characterized without pre-disturbance samples for comparison. If such data exist, this should be clearly explained. The findings of biotic influence being more important than edaphic influences is quite interesting.
Scientific remarks:
Line 59: 2018 and 2014 are not very “recent”.
Line 64: It would be great to define microbial activity before stating the examples in this paragraph, there is a plethora of different approaches (ATP quantification, enzymatic activity as in FDA assays, growth, viability,...). You are showing examples for different approaches (respiration etc.), but in the following it's not always clear which measurements are used.
Line 66: What is meant with transcriptionally active? Does this mean that they have a higher total amount of RNA? Or just more of the gene of interest is transcribed?
There is even evidence that RNA levels go down with warming as in Söllinger et al. 2024 https://pmc.ncbi.nlm.nih.gov/articles/PMC11126301/ , although this doesn't seem to be from frozen soils.
Line 71: Does this refer to (seasonally) frozen temperate soils or just "regular" thawed temperate soil?
Lines 82 ff: The phrasing suggests that the Tibetan Plateau is in the Arctic. Of course, both are examples of permafrost harboring environments, but it could have been made a little bit more clearly here.
Line 90 ff: Present the Canadian study site a little bit more in a manner that it is exemplary for permafrost studies. It is only implied through context that it has permafrost.
Line 96: While I am sure that the study will help with understanding future findings, the statement of this study being crucial overstates the study’s implications.
Lines 100ff: The paragraph doesn’t explain how/that the samples were taken after disturbance, which is the premise of the manuscript.
Line 108: The names of the sites are confusing. First, Core site 2 and Core site 3 are mentioned, but no Core site 1. Later on, surface samples from sites A to F are mentioned. It would be good to have an overview about how many sites were sampled and what is meant by Core site 1-3 and A-F, because they are all called sites. Figure 1 also does not help much in the distinguishing between sites 1-3 and A-F.
Line 115: Was the spade also disinfected? How else was assured that no contamination took place?
Line 124: How deep was the active layer before it was removed?
Line 126: A depth of 1m measured from where?
Line 131: Haven't they already been thawed because of the season? Or were they seasonally frozen? The maximum active layer depth is typically in September. How did you distinguish between seasonally frozen soil and permafrost?
Line 133: How long have the samples been stored frozen before being processed? Assembling has been done in 2016 and the paper is now under review it makes you wonder how long everything has been frozen before being analyzed.
Line 142: I would replace "section 1" with "the first section", as they are not specifically named. Likewise with Section 2 and 3 later on. I think it would be clearer to just describe and not name everything.
Lines 181ff: I think this paragraph can be shortened with the reference to the source that you've already put in.
Line 202: How many samples were without the negative extractions and blanks? I think this is the more important number.
Line 214: The usage of OTUs in contrast to ASVs should be explained.
Line 235: It is not necessary to explain which specific plots were done, because they can just be presented in the results. This sentence also doesn't seem to have a good syntax.
Line 260: How did this not result in the lysis of many cells? But I guess at least they are all lysed in the same manner and thus comparable. Is there a reference that shows that this method is proven?
Line 275: How were they grouped? Per core or per depth, or something else?
Lines 280-290: This is what I meant in line 90. This also seems to belong to a separate paragraph in the Material and Methods section, which you could name "study site". It is not a result.
Line 289: Is there a reference that a water table correlates with the permafrost depth?
Line 310: Which specific edaphic parameters were used for this statement? Also state which NMDS method was used for this.
Lines 316f: This would be part of the discussion.
Line 330: Does that mean that the active layer and sample C and D are the same grouping, because of the letter a that is on top of them? This is not clear enough for me.
Line 372: How do you know that it changes after being disturbed? If I understood this correctly, it has only been sampled once.
Line 387: I don’t think it makes sense to name the Clusters (1 – 3) if you only use the cluster names in this figure description. Rather describe which samples cluster together.
Line 396: Do you mean Zn concentration?
Line 405: “This indicates” should be part of the discussion.
Line 419: Which samples have been the basis for assigning the indicator OTUs?
Line 444: All bacterial communities combined?
Line 460: axis labels
Lines 497ff: Link the expected changes (pH, mineral N, C,…) better to the literature that you cite. How do the other findings relate to your assumptions?
Lines 511f: How can this be said without knowing how the soil has been before disturbance? There might have been general spatial variation. This possibility should at least be acknowledged or refuted – maybe in the M&M section.
Line 520-523: Reference? Or do you refer to the presented study?
Lines 524 ff: It would be nice to have more than one reference for the hole paragraph.
Are there more in situ thaw experiments from other study sites that you refer to in the text? Because they are in plural.
Line 556ff: “permafrost and active layer community clusters could not differentiate between permafrost and active layer community clusters.“ This doesn’t make sense
Lines 565-576: Really interesting findings!
Lines 609-613: Please link this more to your findings. Also, be careful with the statement of “activity”, because I don’t recall you measuring something in the direction of activity of the cells. In general, what counts as “active” is also not that clear.
Refrences: Could possibly be updated with more recent literature.
Formal remarks:
General: Sentences shouldn't be started with abbreviations.
Line 110: Numbers until twelve should be written as words and not digits
Line 165: No brackets around the reference, but only the year. "performed as described by Saidi-Mehrabad et al. (2020)."
Lines 392ff: Avoid putting crucial explanations into brackets.
Line 584: aerobic in lower case
Line 596: functionality?
Line 648: Space missing after comma.
Lines 482ff: awkward syntax
Citation: https://doi.org/10.5194/egusphere-2025-224-RC2
Data sets
NCBI Sequencing Submission of Raw Sequence Reads Patrick Neuberger https://www.ncbi.nlm.nih.gov/bioproject/PRJNA999916
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- 1
This manuscript assessed the microbial diversity of soils near a gold mine. It showed a very interesting conclusions on the influence of disturbance-induced permafrost thaw on microbial communities. This research may provide valuable information on the possible environmental influence of permafrost thaw. However, data from six sites in this study seems actually not representative and more extensive environmental data is needed to confirm the findings. The close spacing of sampling stations may limit their representativeness. Given that the article's focus is on the relationship between environmental parameters and microorganisms, several environmental parameters were measured. However, the paper lacks figures/tables to visually present key environmental data. Moreover, the mechanisms underlying the influence of environmental factors are not thoroughly analyzed—for example, the relationship between microbial communities and Zn mentioned in the abstract. It would be valuable to include key parameters in future research. More convincing conclusions could potentially be drawn by measuring more environmental parameters (such as measurements of soil redox potential) or conducting analyses over longer time scales. While the paper's title and conclusions present interesting perspectives, they might benefit from additional supporting analysis or a more precisely framed title to accurately represent the study's scope. Thus, I think major revisions are needed. Additional specific comments are given below:
L280-290 It is repetitive. The information has been given in the method.
What is the possible functional shift during your thaw experiment?
Figure 5: Why does the accumulation of active layer bacterial indicator species and permafrost bacterial indicator species exceed 1?
What were the original differences between the communities of ABCDE before they thawed?
585 Have you measured gaseous geochemical parameters like methane?