the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 11 Mar 2024
Impacts of soil storage on microbial parameters
Abstract. This review aims to determine the impact of soil storage on microbial parameters (abundance/biomass, activity and various diversity metrics). We analysed the literature dealing with the impact of storage practices (cold, freeze, dry, freeze-dry and ambient storage) on soil microbial parameters. A total of 73 articles were included in the analysis, representing 261 basic data (impact of a given storage practice on a microbial parameter). Globally, 74 % of these data showed significant impact of storage on the measured microbial parameters, as compared to those measured on fresh, non-stored soil samples. The storage practices showed various effects on the soil microbial parameters, with sometimes opposite effects across different soil types. For instance, various soil enzyme activities did not respond the same way to storage practices, even in a given soil type. There are currently too few studies to draw recommendations, but some studies suggest that the pedoclimatic context could be useful for choosing the best storage option, with soils that regularly undergo drought or freezing being less impacted by dry and freeze storage, respectively. I conclude that storage practices for soil samples, when unavoidable, should be carefully selected according to conditions that prevail in the native soil environment, to microbial parameters that are analysed (even though there is no consensus for a best practice), and with different storage practices for different microbial parameters if necessary.
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RC1: 'Comment on egusphere-2024-411', Anonymous Referee #1, 13 Jun 2024
This review addresses storage, a very important methodological aspect in soil biology which has not received enough attention. As this work shows, we should take more account of the artefacts that storage could introduce to data. This is clearly a relevant topic and falls within the scope of SOIL. However, while this assembly of data is a strong starting point, in my view the analysis suffers from some crucial flaws, such that this contribution falls short of its potential and does not generate well-supported conclusions.
- The manuscript places considerable emphasis on the significance of the storage impacts, not just in the discussion of the results but fundamentally in the way the data were scored and collected from the underlying literature (line 140-150). However, the more important question is how big the effects are, and whether this can be so large as to seriously bias the conclusions of a study. In other words, the analysis would be much more relevant if it focused more on effect sizes and less on significance.
- Another problem with the focus on significance is that the analysis essentially follows a vote-counting approach (counting up the number of studies that found a significant effect in one direction or another). This sort of approach has been long recognized as statistically flawed and potentially misleading (e.g. Koricheva et al. 2013 Handbook of Meta-analysis in Ecology and Evolution). There are stronger statistical methods for meta-analysis that could be better applied in this situation.
- A review in my view should not only summarize results from the literature (which this manuscript has done) but also add something new to the literature through the analysis or interpretation of these results to create new knowledge. I don’t think the manuscript has done enough to achieve this. The Discussion concludes that the effects are concerning and highly variable, but I would really like to hear something deeper: what might be causing the variation? What parameters of storage or removal of storage might be influential? When does it matter and when not? The Conlusions state that storage practices need to be adapted to the microbial parameters and soils being studied, so what guidance does the assembled data provide on how to do this?
- The analysis is not up to date, not including literature from the last three years (line 159) and excluding relevant recent work (l. 228). Such a meta-analysis should really be as current as possible.
- The manuscript touches on the bias of effects (i.e. does storage affect all samples the same, so that experimental conclusions might still be valid even if absolute values are shifted?) but it doesn’t provide a robust and transparent analysis on this point. This would be very valuable, because many workers defend even large experimental artefacts as acceptable if all samples are treated the same. Line 461 in the Conclusions supports this argument, but it is not clear what data this conclusion is based on.
- The presentation of results provides a raw summary of results from numerous papers, but is very dense reading without a clear line of argument. This would benefit greatly from summarizing the various findings in a figure and highlighting only the important points in the text.
- The Discussion section does provide a few conclusions, but to a large extent introduces new observations from the literature (e.g. lines 371-403) rather than discussing deeper trends or conclusions available from what was presented in the Results section.
- Other comments
It is not clear what the conceptual difference is between measurements of community composition and structure (l. 133-4)
The abbreviation “qPCR” is preferable to “RT-PCR”, since the latter is ambiguous (“real time” or “reverse transcription”). In line 215 they are both given, increasing the confusion.
line 244 not clear what “failed to report” means: didn’t investigate; didn’t show results; or found no significant effect?
Would Table 1 not be better presented as a figure (e.g bar or line graph)?
Citation: https://doi.org/10.5194/egusphere-2024-411-RC1 -
RC2: 'Comment on egusphere-2024-411', Anonymous Referee #2, 27 Jun 2024
In this review, Fromin highlights the necessity and potential pitfalls of various soil storage methods for understanding different microbial parameters. This analysis is an important piece in improving our ability to gain inference from soils that cannot be analyzed immediately after collection. Unfortunately, the analysis here feels quite incomplete for two major reasons:
- The “yes or no” style aggregation of the studies considered in this analysis is not particularly helpful in finding the degree to which soil storage influences microbial parameters. It seems relatively straight forward to intuit that some storage will likely alter the microbiomes in soils, but the important question is “How much?”. We must store soils, but understanding if these storage conditions fundamentally change the inference we can gain from them is the critical piece of using these methods. Soil storage may decrease diversity (or some other metric) globally, but if it does this similarly for treatment A and treatment B, that is still a valid method for experimentation. While the author discusses some attributes of effect size in the discussion, greater effort must be taken to quantitatively incorporate (preferably with statistics) effect sizes from these studies into the overall results of this meta-analytical approach.
- The author states several times that the number of studies is too low, however a significant number of papers focusing on this exact issue have been published since 2021. Some of these are referenced in the text but not included in the synthesis. The literature search should be updated to achieve a greater number of studies with which to do analysis and to provide a more compressive, up-to-date view of this field’s state.
Minor comments:
50: *can
64: this sentence is a bit difficult to read, could it be broken up?
Why are some references using names and some numbers?
80: Could help to mention here that DNA is relatively recalcitrant, thus potentially less susceptible to storage effects than other microbial parameters
Table 1: This information might also be more useful as a figure, maybe a bar graph with date as the X axis and number of studies as the Y, exp as you have the same info in Table 2.
Table 2: I believe this info would also be more digestible in some graphical context
361: *are preserved
366: Difficult sentence, too many clauses
446: Storage cannot be avoided. It is impossible to measure these characteristics in situ, thus, this is not a realistic or helpful recommendation for from this analysis.
Citation: https://doi.org/10.5194/egusphere-2024-411-RC2
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