the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 08 Oct 2025
Modelling root exudation and plant-microbe interactions under CO2 fertilization in a mature forest
Abstract. Root exudation, defined as labile carbon (C) allocation into soils through fine roots, is a substantial yet often overlooked pathway of the terrestrial carbon cycle. Root exudation is likely to increase under rising levels of atmospheric CO2, but the implications of the increase in this flux are poorly understood. Increased labile C availability in soils may stimulate microbial growth and increase soil carbon storage but at the same time microbial nutrient acquisition could offset this accumulation by enhanced decomposition of soil organic matter
Here, we implement a dynamic representation of root exudation based on plant surplus carbon and nutrient limitation in the microbial explicit terrestrial biosphere model QUINCY-JSM (QUantifying Interactions between terrestrial Nutrient CYcles and the climate system). We evaluate the effect of elevated CO2 on root exudation and its consequences for microbial C, nitrogen (N) and phosphorus (P) cycling using observations from the Eucalyptus Free Air CO2 Enrichment (EucFACE) experiment in a soil phosphorus impoverished forest. In the experiment, more than half of additional gross primary productivity (GPP) under elevated CO2 (eCO2) could not be assigned to a measured vegetation flux.
With the explicit implementation of root exudation, our model predicted that elevated CO2 caused an increase in belowground carbon flux and an increase in microbial growth, but a limited effect on soil carbon storage. Root exudation was increased to 30 %, but more than half of this additional input was directly respired by microbes. As a result, root exudation gives a possible explanation for the not measured vegetation flux and the enhanced heterotrophic respiration under eCO2 observed in the experiment. Increased C input through root exudation also enhanced microbial growth, but in order to support this growth, microbes mostly gained nutrients from decomposition and mineralization of organic matter. As a consequence, increased decomposition negated build-up of microbial necromass. Our study emphasizes the role of root exudation and microbial activity for soil carbon sequestration under elevated CO2 and guides further research regarding plant-microbe interactions.
Competing interests: At least one of the (co-)authors is a member of the editorial board of Biogeosciences.
Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims made in the text, published maps, institutional affiliations, or any other geographical representation in this paper. While Copernicus Publications makes every effort to include appropriate place names, the final responsibility lies with the authors. Views expressed in the text are those of the authors and do not necessarily reflect the views of the publisher.- Preprint
(1760 KB) - Metadata XML
-
Supplement
(137 KB) - BibTeX
- EndNote
Status: final response (author comments only)
- RC1: 'Comment on egusphere-2025-4286', Anonymous Referee #1, 22 Nov 2025
-
RC2: 'Comment on egusphere-2025-4286', Anonymous Referee #2, 14 Jan 2026
The authors integrated root exudation into the QUINCY-JSM model to ascertain whether it would provide a plausible mechanism for the empirical inability to measure a vegetation flux that could account for the increase in GPP under elevated CO2 as well as explain why there was an increase in heterotrophic respiration without a concurrent increase in soil C at EUCFACE site. The core motivating idea behind this model-data synthesis paper is intriguing and the inclusion of root exudation in QUINCY-JSM is a significant model development. The model formulation of root exudation that depends upon the nutrient status of the plant presented in Figure 2 is also a simple but novel way to predict exudation fluxes in a dynamic manner. Overall, the manuscript presents a good idea, executes it in the model, and uses it to generate new hypotheses to explore to understand how elevated CO2 impacts ecosystem carbon cycling in P limited systems. However, the manuscript needs better structure, some cleaning up of grammar and sentence structure, a culling down of the presented results to give the reader the main points in a way that is easy to follow, and some clear discussion of the limitations and assumptions of the modeling effort and how they impact the conclusions. Below I provide the major concerns followed by more detailed line by line comments.
- Structure of introduction: The introduction could use some streamlining and focus. Some examples: The authors present four mechanisms to explain the fate of root exudates early in the introduction (one note here a conceptual pictorial model of this would be a great addition). Then there are three loose objectives that are presented at the end. However, these loose objectives are not tied to the four mechanisms that start off the introduction and would benefit from being clearly stated formal objectives or hypotheses. Another example is the paragraph that starts on line 120. I would split this into a simple clear description of the empirical results and then another paragraph that speaks to where models have failed in capturing these results.
- Results and figures: The results section is very hard to comprehend and follow. This seems to result from the authors presenting almost all the model data in the text and figures. My recommendation is to go through and pull out the relevant model results that meet the objectives and provide evidence for which of the four proposed mechanisms is operating at the site. As a reader of the results section, I found that there were too many fluxes, too many percentage changes, and many presented that didn’t inform the conclusions or the loose objectives in the introduction.
- Discussion of the model parametrization and assumptions: First, in Section 2.6, the authors provide a very brief overview of the model parameterization. One of the clear assumptions in the parameterization is that root exudation was parameterized to get the other fluxes right. What are the implications of this and can you provide more detail on how this was done.
Second, the model assumes that if you have roots they exude carbon. One big impact of this assumption is that there are exudate fluxes deep in the soil profile that lead to enhanced carbon storage at depth. At some level these deep roots are probably more important in water uptake than priming decomposition where nutrients and organic matter are scarce and more than likely are not exuding substantial amounts of carbon. Another big impact of this assumption is that with the model predicting a 33% increase in belowground production that is not matched in the empirical data that you have more roots exuding more carbon.
Finally, there also appear to be mechanistic assumptions in how microbial necromass is cycled in the model. The necromass appears to simply just get recycled as the microbes are using it to mine nutrients. Does the model assume that all necromass is readily available for microbial attack? What is the nature of the competition for necromass fate between sorption to mineral surfaces vs. microbial attack? It seems like the model assumes that necromass is always available for microbial attack which doesn’t parallel empirical mechanisms where microbes are living and dying in intimate contact with soil minerals so that they are preferentially stabilized on mineral surfaces.
All models have issues and the comments above are not meant to say that the model is wrong. Instead, there just needs to be a thoughtful discussion of how the model assumptions/issues impact the main conclusions.
- What about mycorrhizal fungi? Assuming that all the surplus C goes into root exudation ignores the fact that the eucalyptus is ectomycorrhizal and more than likely has high levels of colonization and biomass that could account for the missing vegetation pool as well. You should include this in your discussion of your results.
Line by line:
line 24: Need period
line 33: “not measured vegetation flux” is awkward and unclear.
line 57: change affect to determine or control
line 64-65: last clause in this sentence hangs. Could just switch comma for and
line 65: insert may between mechanism and regulate
line 70: maybe call this waste respiration like in Schimel and Weintraub 2003
line 75: maybe include something about sorptive capacity
line 88: I would make it obvious that this sentence pertains to all 4 mechanisms
line 96: remove where
line 98: it may be interesting to discuss Terrer 2021 Nature here
line 108: change for to in
line 116: remove P between widespread and globally and add a comma after globally
line 126: change did only invoke to only invoked
line 128: remove that between synthesis and done and remove :
line 133: What do you mean by trade mechanisms?
line 136: I would be specific here and speak to root exudation
line 141: decompose really isn’t the best word here
line 144-153: maintain active voice first person here and be consistent
Figure 1: What are the pools that start with as like asDOM and asRES?
Table 2: How did you validate these parameters? The description in section 2.6 is very brief.
line 303: Does this downward trend impact your interpretation?
Table B1: There are clear errors in NPP and soil C.
Table B2: These wider stoichiometric constraints would have a direct impact on the exudation flux. You should discuss this as well.
Table B3: You have more carbon coming into the system and more going to belowground production that is then exacerbated by the root exudation flux. How does this impact what you see in your results and what you state in your conclusions? Roots are a nutrient rich pool which would enhance microbial limitation.
Line 350: These numbers are fairly high compared to the Chari paper which you cite later and may want to cite here. Your flux may be high because you assume all roots exude, you have more roots, more GPP, and don’t account for mycorrhizae. You should acknowledge how this impact your conclusions.
Figure 3: You show soil C sequestration int his figure that is not observed at the site that is due to I think mostly the deep roots sending out carbon and the greater root production.
line 410: what assumption?
Line 416: are these deep roots really doing this or is this a model artifact?
Line 435: I think this is clearly wrong and you mean a high C:N ratio. In the same vein, it seems like the exudate C:N is a big driver of your microbial limitation. Basically you are pumping a bunch of C into the soil and it drives nutrient limitation. What if you varied the C:N ratio like JE Drake 2013 Biogeosciences.
Line 450: Why is this fixed and how does it impact the necromass results?
Line 520: Is this true? You have a lot of things that aren’t quite right. I would soften this language and again talk about the big conclusion but also the things that aren’t quite right in the model. I think there is a compelling case that this is important to explain the EUCFACE results but what is presented here is a first pass and it generates important hypotheses and questions. It doesn’t really solve the case of the missing carbon for good.
Line 535: I disagree with this statement as you don’t account for mycorrhizae which could take up a big chunk of this carbon and the deep root issue.
Line 568: This contradicts what I think is wrong in 435 and also raises an important question. What if the C:N was different?
Line 608: Why did it enhance necromass desorption?
Line 696: Your results and model efforts do not support a grand global statement like this. As stated above, there are issues with this model exercise and as such you are raising cool hypotheses and potential mechanisms but there is not nearly enough evidence for statements like this.
Citation: https://doi.org/10.5194/egusphere-2025-4286-RC2
Viewed
| HTML | XML | Total | Supplement | BibTeX | EndNote | |
|---|---|---|---|---|---|---|
| 440 | 185 | 24 | 649 | 64 | 22 | 21 |
- HTML: 440
- PDF: 185
- XML: 24
- Total: 649
- Supplement: 64
- BibTeX: 22
- EndNote: 21
Viewed (geographical distribution)
| Country | # | Views | % |
|---|
| Total: | 0 |
| HTML: | 0 |
| PDF: | 0 |
| XML: | 0 |
- 1
This manuscript presents an interesting and timely study that contributes to the overall understanding of carbon allocation and transfer via root exudates, and how these processes interact with nutrient cycling under elevated CO₂. The work highlights the importance of root exudation from a modelling perspective and provides valuable recommendations for improving the representation of root exudation, microbial dynamics, and plant-microbe interactions in global ecosystem models.
The authors implemented a dynamic root exudation module within the QUINCY-JSM model and applied it to the EucFACE experiment, a P-limited mature eucalypt forest. The goal of quantifying competing soil mechanisms that regulate carbon storage under changing root exudation fluxes at elevated CO₂ is both relevant and timely, particularly given the current uncertainties surrounding belowground carbon dynamics and their coupling to nutrient availability under future conditions. The model appears to be a meaningful advancement in simulating carbon and nutrient dynamics by explicitly incorporating exudation fluxes. Although the exudation flux is not validated, I appreciate that the authors transparently discuss model limitations and outline thoughtful directions for future development.
Major Comments
Overall, this is a valuable and timely contribution that substantially advances modelling efforts related to root exudation and belowground carbon–nutrient interactions. With improved focus, clearer terminology, and a more structured introduction, the manuscript will be significantly strengthened.
Specific line comments: