General comments:

The study by Giraud et al. (2025) presents a novel modelling framework that enables to simulate plant growth and related C and water flow within the plant, in interaction with a soil model simulating the interactions between C inputs from roots and soil microbial dynamics. Using this new and exciting framework, the authors have investigated in silico the effect of drought on soil C dynamics in the rhizosphere of a young hypothetical cereal plant, taking into account the effect of dry spells on root C inputs and on their dynamics in the soil. Considering this impressive piece of work, authors have already done a good job in synthetizing the main features of the coupled models and of their simulation outputs, although the manuscript remains quite dense and demanding for a reader not familiar with the original models. Besides the detailed comments below, here are my main remarks:

• The present work is built on two main models described in Giraud et al. (2023) and Sircan et al. (2025), which have been further improved and coupled here. Given that both previous articles have already tackled some of the issues described here (e.g. effects of water stress on plant growth and exudation, C dynamics in the rhizosphere), I would recommend the authors to try to focus more on the benefit of the coupling when describing the simulation results or discussing them, i.e. to focus on the effect of drought on root-derived C and their effects on SOC dynamics in the rhizosphere, while reducing the length of other, less important parts of the manuscript.
• Only few details are given in the main manuscript regarding the soil model, although some are indicated in Appendix. I think it is especially important to mention in the Material & Methods which soil processes have been taken into account or not in the model (not necessarily the equations), and how soil water content and soil temperature may affect microbial activity, so that the reader is able to better interpret the simulation results. In particular, I understood that the dynamics of the bulk soil organic matter is not represented, but only the dynamics of dissolved C. In this regard, the discussion on rhizospheric priming effect is interesting, but may be limited if all the “native” soil organic matter is not included in the model but only its labile part.
• The study focuses on the effect of drought, but here and there a change in temperature is mentioned during the drought period, without information about this in the Material & Method. If temperature changed over time or among the scenarios, this should be clearly stated; if not, this should also appear explicitly in the M&M.
• I keep struggling to understand the link between macroscale voxels and microscale domains of root segments or outside root segments… As it seems to be an important feature of this work and could be inspirational for other similar modelling frameworks, I would recommend authors to illustrate this a bit more clearly in Fig. 1, using realistic volume dimensions and showing which volumes/segments are included within which types of voxels.
• Given the number of variables investigated, crossing three scenarios of drought with three sets of soil parameters makes it quite challenging to get a clear picture of the main results in the end. An idea to clarify things for the reader could be to formulate some hypotheses about the effects of drought on root-derived C inputs to the soil and their dynamics in the rhizosphere, and to use the simulation results to validate or invalidate them.

Detailed comments:

Title: “carbon stabilization by plant” is a bit confusing. Also, authors have only investigated the dynamics of root-derived C (not aerial residues). Maybe something more neutral: In silico analysis of carbon and water dynamics in the rhizosphere under drought conditions?

Abstract:

L8 (and throughout the text): I am not familiar with the use of “biokinetic” in this context; I would suggest only using “kinetic”

L11-13: The reader may also wonder whether the drought experienced in the soil affected soil microbial activity, independently on the indirect effect of drought on C input by roots

Introduction:

L18: “and as an intra- and inter-domain signalling carrier” is not very clear to me, please explain/rephrase

L23: A comma is missing after “exudation)”

L37: “Plants can also exert direct feedback effects on themselves (e.g., aboveground-belowground feedback)” : this could be rephrased and simplified

L41: What about nutrient concentration gradients in the rhizosphere?

L76-79: This study extends the work of Giraud et al (2023) that focused on water and C flow within the plant. It would therefore be useful to state a bit more explicitly that this new study focuses on the root-derived C dynamics in the rhizosphere, taking into account the previous modelling framework of Giraud et al. for integrating the retroaction between water flows and C inputs in the rhizosphere, and coupling it to another model of rhizospheric soil C dynamics. Also, stating here at the end of the Introduction some hypotheses linked to water spells that will be verified with this new modeling framework would help the reader to focus a bit more on the originality of this work.

M&M:

L100: Meunier et al. (2017). Rephrase “and the coupled the stomatal”.

L123-124: This could be mentioned earlier on in the Introduction.

L126-137 and Fig. 1 & 2: After reading this several times, I am still not sure that I really understood the spatial scheme. There are macroscale soil voxels that may or not contain microscale root segments. However, both appear with the same size on Fig. 1. The terms macroscale and microscale are perhaps misleading? And what is then the perirhizal zone described as microscale in Fig. 2: one full voxel containing at least one root segment? Perhaps this could be clarified in Fig. 1, e.g. if showing a spatial description of the 3D root segments and the voxelization around it with realistic dimensions, and explaining where materials are actually exchanged and where specific reactions may - or not - take place.

L175: I don’t understand what Ω\∂Ω means

L219: For simplicity

L225: It would be useful to remind to the reader what ξ is, even if it was introduced a few equations ago

L289: Remove bracket

L329-332: If a new calibration was introduced to better reproduce expected trends, this should be emphasized more in the discussion, e.g. if authors choose to discuss the validity of hypotheses from their simulation results.

L347: Again, an illustration of all these different scales in Fig. 1 would really help the reader to understand more quickly how these scales are interconnected

L373: I don’t think that oligotrophic and copiotrophic have been defined anywhere. For a reader not familiar with soil microbial ecology, it would be useful to define these terms, and explain what are the expected behavior of these two microbial pools.

L380: It would be worth adding to which class these tresholds correspond to Poeplau and Don, i.e. 0.65 (threshold between degraded soils and moderate soil quality), 0.83 (moderate/good soil quality) and 1.16 (good/very good soil quality). It would also be important to state that the pedotransfer function used here was developed for German soils. One may also wonder whether this study from Poeplau and Don at field scale across Germany is really relevant to identify hotspots of C in the rhizosphere, this could lead to additional comments in the Discussion.

Results:

L405: “an increasing concentration” compared to what or according to what?

L408-432: For brevity, I would remove this part. If these simulations results have already been presented and explained in Giraud et al. (2023), shouldn’t the focus be here rather on the exudation and mucilage secretion in response to drought, starting at L433?

L449-450: Shouldn’t this sentence be mentioned earlier in the paragraph, before showing the actual results for each soil parametrization?

L456-458: I am not sure this is a very important simulation result to emphasize, given that the variation of this maximum exudation rate per cm2 among the scenarios is quite small.

L464-465: I don’t understand. If there are fewer roots, why is there a higher maximum C concentration?

Fig. 8: I would suggest to increase the size of the figures and to add a title to each sub-graph with the name of the variable detailed in the caption

L492: I still struggle to understand the meaning of a variable perirhizal truncated volume among the treatements... Please try to better explain why it is important and which biological or physical information it actually brings.

L499 and after: Please give the full meaning of each concentration when used in the main test, and not only its symbol, as reading and understanding this part is quite challenging…

L519: “the negative effects of the low soil θ on microbial activation” - but this relationship was not introduced in the Material & Method. It’s really necessary to better explain how the SOC model works and how it depends on soil water content and soil temperature.

L531: “the relative volumes of the SOC hotspots” - I continue to be lost…

L540: cycling

L564: “can cause a the”

Discussion:

L598: for further optimizing

L616-617: “the virtual plant’s starch pool can be interpreted as representing both actual starch reserves and newly synthesised wall material”. I am not sure that I fully understand the conceptual difference between biosynthetic growth and expansion. Is the second type of growth independent on C? I thought that root growth was explicitly included here in the C balance. If so, why would a part of the root growth be included in another term with starch?

L645-647: Now I understand why authors developed the description of such results at L408-432. The present statement could therefore be made earlier, at L408.

L679: a ratio of dormant oligotrophs and what other variable?

L707: “and organic C-dependent soil hydraulic parameters” - I guess that the benefit of having simulated specifically mucilage secretion in this study would be linked to this s feedback on plant water uptake. Maybe it is worth explaining this?

L709-719: I find this paragraph very interesting. However I am surprised that authors do not link this heterotrophic respiration by soil microorganisms to root respiration simulated during the dry spells, as the modelling framework enables to do this, which is rather unique. Looking at how the ratio between the two sources of CO2 evolves over time and how the resulting total basal respiration evolves over drought may reveal interesting features.

L735-736: “The lateDry scenario led to the lowest plant growth but to a higher SOC hotspot volume, indicating a more resource-efficient root system exudation.” Why would an increase in the number of rhizospheric hotspots be considered more resource efficient? Do authors suggest that SOC hotpsots are associated to a better feedback for the plant (e.g. in terms of water or nutrient uptake)? Please explain.

L870-871: This definition of microbial pools is really needed in the main text.