Reviews and syntheses: The mechanisms underlying carbon storage in soil

Basile-Doelsch, Isabelle; Balesdent, Jérôme; Pellerin, Sylvain

doi:https://doi.org/10.5194/bg-17-5223-2020

Articles | Volume 17, issue 21

https://doi.org/10.5194/bg-17-5223-2020

© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.

https://doi.org/10.5194/bg-17-5223-2020

© Author(s) 2020. This work is distributed under
the Creative Commons Attribution 4.0 License.

Articles | Volume 17, issue 21

Reviews and syntheses

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30 Oct 2020

Reviews and syntheses | Highlight paper |

| 30 Oct 2020

Reviews and syntheses: The mechanisms underlying carbon storage in soil

Isabelle Basile-Doelsch, Jérôme Balesdent, and Sylvain Pellerin

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Final revised paper (published on 30 Oct 2020)
Preprint (discussion started on 19 Feb 2020)

Interactive discussion

Status: closed

AC: Author comment | RC: Referee comment | SC: Short comment | EC: Editor comment

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RC1: 'My review', Anonymous Referee #1, 24 Mar 2020
- AC1: 'Reply to referee#1', Isabelle Basile-Doelsch, 25 Jun 2020
RC2: 'review of "Reviews and synthesis: The mechanisms underlying carbon storage in soil', Anonymous Referee #2, 11 May 2020
- AC2: 'Reply to Referee#2', Isabelle Basile-Doelsch, 25 Jun 2020

Peer-review completion

AR: Author's response | RR: Referee report | ED: Editor decision

ED: Reconsider after major revisions (26 Jun 2020) by Sara Vicca

AR by Isabelle Basile-Doelsch on behalf of the Authors (29 Jun 2020) Author's response Manuscript

ED: Referee Nomination & Report Request started (02 Jul 2020) by Sara Vicca

RR by Anonymous Referee #2 (07 Jul 2020)

Suggestions for revision or reasons for rejection

The manuscript is the revised version of an earlier submission. The reviewers thoroughly revised the manuscript according to the reviewers' suggestions. Only a few minor points remain to be improved, as detailed below. All line numbers refer to the final version without the track changes mode, and I completed the line numbers > 100 (the first digit was not visible in the pdf).

detailed comments:

- lines 76-82: In this section, harvesting of aboveground biomass is mentioned as a general reduction of carbon inputs. Although in a way, this is true as this amount could also be set to zero, I suggest to indicate in the text that this is not a natural process but is there because of anthropogenic activities, i.e. land use.

- lines 84-90: Similarly, here the harvest index is introduced, which only makes sense in agricultural settings, but not in general.

- lines 131-132: Organic amendments such as manure or slurry most probably also contain animal-derived organic compounds (in addition to plant and microbial molecules).

- lines 176-177: In this sentence, somehow two steps of organic compound degradation are mixed together: Macromolecules need to be depolymerized (mainly hydrolytic reactions) to reduce the molecular weight (and size) until they can be transported into the cells. In the cells, catabolic reactions mainly are oxidative reactions with the final products CO2 and H2O.

- line 182: As the authors stated in their answers to the earlier reviewer comments, growth would allow for increasing the possibility of substrate/enzyme contact for fungi, but not so much in the case of bacteria. Similarly, most fungi are not motile and thus mobility is more a factor for bacteria. It would be nice if this could be indicated more clearly.

- line 190: It would be nice here to have an indication about the molecular weight cutoff for transport through microbial cell membranes. Of course, this will not be an exact number, but vary depending on organism and molecular geometry, but maybe some indication or range could be given here.

- lines 193-194: In addition to the loss of the depolymerized substrate molecules by abiotic processes such as dilution or sorption, there might also be "cheaters" around who do not produce the extracellular enzymes necessary for depolymerization but rely on other organisms to do so. These organisms might also take up part of the low-molecular weight substrate molecules produced.

- line 247: I do not agree that the concept of humification, humic acids etc. should not be showcased in teaching. This concept has severe limitations and recent scientific progress has proven it unsuitable, but it has been one step in the development of the knowledge on soil organic matter. It should be presented in courses as such a step and in the light of the time when it was developed and when the analytical facilities were not as sophisticated as today.

- line 353: The description of the "microsites" in this section suggests that the authors are talking about micropores here. Although micropores are microsites, not all microsites have to be located in micropores. The term just describes the fact that in a heterogeneous soil, the average conditions are not relevant to microbes, but the conditions in their very close surroundings, at the scale of micrometers. As a consequence, not all microsites are oxygen-deficient as suggested by the authors here.

- lines 360-361: It is not only the number and availability of parameters at the relevant scales. Modelling each and every process in all the microhabitats and microenvironments and upscale to the plot scale by integrating all these calculations would be computationally too demanding even for the fastest computers.

- lines 381-383: The sentence about OM loss due to leaching with DOM seems a bit lost in this section which mainly addresses erosion. As I think export with DOM is an important loss pathway, I suggest to provide a little bit more context and a nice transitory sentence to better integrate the DOM part into this section.

- lines 423-428: All values given here assume steady state or describe an average over time. Also a short explanation should be given to indicate how the average age of the C (42 years) was derived.

- line 507: The doubling of mineralization rates with every 10 K temperature increase is only valid in the physiological temperature range. At very high temperatures, microbial activity breaks down quickly.

- line 543: The reference for the "reported C:N:P ratios" needs to come a bit earlier, as it is not well connected now. It is also a bit strange to oppose topsoils to pasture which is due to different original publications comparing different things.

minor editorial remarks:

- check the correct use of brackets for in-text citations throughout the manuscript. For example, in line 418 the opening bracket is dublicated, and in line 448, the two citations should be in a single pair of brackets.

- line 33: What are "downstream ecosystems" in the context of soils, atmospheric CO2 and climate change?

- line 43: reword "political opportunity ... renewable forms of energy" to something like "potential for political delay of transition to renewable energies"

- line 84: I struggle a bit with the term "restitution" which could be replaced by "aboveground litter input", for example.

- line 94: replace "are" (last word of the line) by "is"

- line 95: "contribute more to soil organic matter" needs a comparison

- line 133: reword "charcoal production site" to indicate a material (e.g. "charcoal production residues")

- lines 193-194: "While on the other hand...organic or mineral compounds": This is not a complete sentence, please rephrase.

- line 227: Rephrase "Some organic compound functions are also pH dependent" to read "The speciation of some functional groups of soil organic matter is also pH dependent."

- line 274: Delete "However,"

- line 287: add missing space between "DOM" and "(Kleber et al., 2015)

- line 288: Rephrase to read "but experimental data on DOM mechanisms and processes in agricultural soils are still sparse (Gmach et al., 2020)"

- line 298: delete "the" between "are" and "most"

- line 310: rephrase to read: Adsorption sites are not evenly spread over mineral surfaces"

- line 352: rearrange to read "nanometric to micrometric"

- line 385: replace "compounds" by "products of OM degradation"

- line 390: move "is" to after "for a given substrate,"

- line 406: k is the "mineralization rate constant"

- line 408: Obviously, "dC/dt = 0 and I = kC" are equivalent and describe the equilibrium. Steady state would require I = constant and kC = constant.

- line 582: replace "consists" by "consist"

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RR by Olga Vindušková (15 Jul 2020)

Suggestions for revision or reasons for rejection

Authors made significant improvements to the manuscripts that I’m happy with. I still found unclear parts or mistakes/typos that need to be dealt with but I think we’re almost there. Congratulations!
Detailed comments (also see the attached PDF for minor corrections):
Page 1 L28 use “these” instead of “the”
L20 consider using “carbon turnover time” instead of “residence time” throughout the text since later you now argue that this term is ambiguous and should be avoided…
L22 I recommend to use “particle size” instead of “grain size” throughout the text
L29 term “action levers” doesn’t sound right, would this work too? “could provide future levers of action for C sequestration in soil.”
Page 2 L34 “interest in” instead of “interest on”
Page 3 L78: (copying the discussion here)
R1: this sentence is true only for cropland and ecosystems in which you assume constant standing plant biomass
Authors: We don’t really understand this comment.

….> my comment relates to this sentence: “The soil carbon input flux is the net primary production of the ecosystem minus the exported production, herbivore production and respiration.” This statement is true in agricultural soils but for example in a young forest some part of annual NPP is just translated into standing biomass growth (=trees grow bigger), thus this C is neither exported nor consumed by herbivores nor enters the soil.

Page 3 L84 the term “restitution” still needs to be explained when first used, maybe introducing it in the previous paragraph (L78) could work “via unharvested aboveground plant parts (hereafter “restitution”) ”
Page 3 L84: the sentence doesn’t seem to have changed (?), even though authors seemed to like my suggestion below :) (copying the previous discussion below)
R1: explain what do you mean by “estimators of soil restitution fluxes” would “Soil carbon input can be estimated based on” work too?

Authors: Yes, that works too and is even better, so we suggest changing the sentence to:
Estimators of soil restitution fluxes are often based on plant carbon allocation equations (allometric relationships) combined with carbon models.

Page 5 L44 I’d recommend to leave out “microbiota”
Page 8 L66 missing period at the end of sentence
L75 better “belong to different” instead of “are placed into”
L80 maybe better “either free or adsorbed” instead of “free, but may also include adsorbed”\

Page 9 L10 “uneven” instead of “unevenly” (sorry!!, I know I’m correcting myself now :o) )
Page 12 L8 just noticed it is not very clear whether you define equilibrium and steady-state as two different states (I actually thought that steady state and equilibrium are synonymous terms but that may be very well my ignorance), please double check these definitions and maybe move the equations in brackets to the preceding sentence about equilibrium in which it fits better? Because this way it seems you are repeating the same statement twice. I guess the correct mathematic representation to the second sentence in its current form would be dI/dt=0, dkC/dt=0…
L18 delete extra bracket
L87 missing space before bracket
Page 13 L48 merge brackets
L50 remove first comma
Page 14 L94 add “and” instead of comma before “an increase when forests”
Page 15, L20 use “enriched in” instead of “enriched with” – “enriched with” implies something has been artificially added. Fix throughout the manuscript. https://english.stackexchange.com/questions/426564/enriched-in-vs-enriched-with
Page 16
L48 missing period after “etc”.
L76 this sentence doesn’t sound quite right in terms of English, would the following work? “Although previous research has mainly focused on the 0-30 cm horizon, it has been recently shown that …”
L78 better “time” than “date”, maybe leave out “thus”
Page 17 L80 better “belowground” than “underground”, maybe rephrase to:
“biotransformation of (mainly belowground) plant inputs”
L82 “consist” instead of “consists”
L85 “through” instead of “though”
L87 “a term” instead of “this formulation is”
L89 I miss fauna here – could this be rephrased to something like: “The activity and biodiversity of soil biota, ” (also I didn’t notice that main text would discuss the effect of plant biodiversity)
Table 1, 2, Fig 2 and 3 typos to be fixed, see attached PDF with comments
Figure 4 legend, better: Nature, size range and indicative proportions of organic matter in <2 mm soil
Better: “microbial activity” instead of “microorganisms activity”

Referee Report: PDF

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ED: Publish subject to minor revisions (review by editor) (19 Jul 2020) by Sara Vicca

AR by Isabelle Basile-Doelsch on behalf of the Authors (26 Aug 2020) Author's response Manuscript

ED: Publish subject to technical corrections (03 Sep 2020) by Sara Vicca

Short summary

The 4 per 1000 initiative aims to restore carbon storage in soils to both mitigate climate change and contribute to food security. The French National Institute for Agricultural Research conducted a study to determine the carbon storage potential in French soils and associated costs. This paper is a part of that study. It reviews recent advances concerning the mechanisms that controls C stabilization in soils. Synthetic figures integrating new concepts should be of pedagogical interest.