the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 26 Aug 2026
A physico-chemical framework for explaining the generation mechanism of Nocturnal Soil CO2 Uptake in Deserts
Abstract. Nocturnal soil CO2 influx (Fs) has been widely documented in global deserts, while the underlying mechanisms remain unclear. Based on 563 observations from 30 published studies across five major desert regions in the world, we employed multiple linear mixed-effects models (LMMs), random forest (RF) regression, polynomial regression, and structural equation modeling (SEM) to quantify the effects of air‑soil temperature difference (ΔT = Ta - Ts), soil water content (θv), soil pH, and ln(clay/sand) on soil nocturnal CO2 influx (Fs), and to establish a physico-chemical framework for explaining the generation mechanism of Fs. The results displayed a global mean Fs of −0.195 μmol m-2 s-1, with the strongest CO2 uptake occurring in the Central Asian Desert Area and the weakest in the North American Desert Area. Fs showed a significantly positive correlation with ΔT and negative correlations with θv, pH, and ln(sand/clay). SEM revealed that ln(sand/clay) and θv influenced Fs both directly and indirectly. The relationships of ΔT, θv, pH, and ln(clay/sand) with Fs suggested exerted pronounced effects on nocturnal CO2 influx in desert soils. The correlation analysis demonstrated that these environmental factors may serve as important drivers in the generation of nocturnal soil CO2 influx. Integrating our results ad previous studies, we proposed a comprehensive physico‑chemical mechanism framework. In this framework, thermal convection driven by the temperature difference served as the physical driving force, continuously transporting atmospheric CO2 into soil. One fraction is temporarily stored as gas in soil pores, and the other fraction enters chemical reactions under alkaline conditions. The above physico‑chemical processes generated the nocturnal CO2 influx process in desert soils.
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Status: open (until 16 Nov 2026)
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CC1: 'Comment on egusphere-2026-4692', Wu Xiao, 22 Sep 2026
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CC4: 'Reply on CC1', Jia-Bin Liu, 08 Oct 2026
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Thank you for your valuable time and constructive comments on our manuscript.
Comment 1:Line 15,16 The ratio is written as both ln(clay/sand) and ln (sand/clay) in different places. Please standardize.
Re: The corresponding part has been modified.
We have standardized the soil texture index as ln(clay/sand) throughout the entire manuscript. Modification locations: Abstract, Section 2.2, Section 3.2 (Pearson correlation, RF variable importance, partial dependence plots, hierarchical partitioning), Section 3.4 (SEM), and all relevant figure captions.
Comment 2:Line 36-40, the second paragraph lists previous single factor studies but does not clearly summarizethe major research gap (lack of cross‑site, multi‑factor interaction analysis).
Re: The core research gap has been explicitly supplemented at the end of the second paragraph in Introduction.
“Furthermore, most hypotheses come from long-term monitoring at single sites, where soil texture and pH vary little and their effects cannot be reliably separated from site-specific conditions. As a result, they cannot fully explain how uptake responds to changing environmental conditions.” (Line 41-44)
Comment 3:Duplicate section heading (Section 2.2)– There are two sections labeled "2.2 Data Extraction." The second should be renumbered as "2.3 Statistical Analyses" （or similar）, with subsequent sections renumbered accordingly (currently 2.3 → 4, etc.).
Re: The duplicate section heading has been corrected and the section numbering has been adjusted. The second data extraction section has been renamed as Statistical Analyses.
“2.3 Statistical Analyses” (Line 102)
Comment 4:line 83, the article emphasizes abiotic/nocturnal CO2uptake, but in the Methods section, it links texture with "supporting microbial activity". If the article does not have data such as microbial biomass, respiration, and enzyme activity, it is best to avoid giving readers the impression that microbial activity is the direct mechanism of Fs.
Re: The reference to microbial activity has been removed from the description of the soil texture index.
“We therefore used the log-ratio of clay to sand content, ln(clay/sand), as an index of soil texture fineness to represent the capacity of soils to retain moisture.” (Line 83-85)
Comment 5:Figure 2 presents the average Fs and their confidence intervals for the five regions. However, the main text does not clearly state how many observations, sites, and studies are included in each region. This is very important because regions such as the Antarctic Desert Area may have significantly smaller sample sizes than the Central Asian Desert Area. It is recommended to report in Figure 2 or the Supplementary Table as: n observations / n sites / n studies. This will make the comparison between regions more transparent.
Re: We have added the sample size information for each of the five desert regions in the text of Section 3.1. We have also updated the caption of Figure 2 to explain this sample size notation.
“Fs among five major desert regions. Points represent means with 95% confidence intervals. Values in parentheses indicate the number of studies for each region. Different letters indicate the obvious discrepancy across different areas.” (Figure 2 caption)
Comment 6:Partial dependence plots illustrate the marginal predictive relationship under the model conditions and cannot directly prove causal relationships. Therefore, expressions such as "confirm" or "driving" in the text can be appropriately weakened and replaced with "suggest" or "indicate", especially in the research framework of observational synthesis. For example, line 266 could be changed to "favourable for the progress of the reaction".
Re: Overstated causal expressions have been weakened throughout the text.
“These patterns indicated that the effects of ΔT and θv on Fs are predominantly nonlinear or threshold-dependent, which linear models cannot adequately capture.” (Line 178-179)
“These results suggested that nocturnal CO2 uptake in dryland soils was a multi-factor synergistically regulated process, whose core driving forces can be attributed to two main mechanisms: physical and chemical.” (Line 258-259)
Comment 7:The manuscript proposes that the air-soil temperature difference drives thermal convection, and further regards it as the main driving force in the physical process. However, the current data mainly come from statistical relationships and do not directly measure the pressure gradient within the soil, the gas velocity, or the CO2concentration gradient. Therefore, it is suggested to clearly define this mechanism as "supported hypothesis/conceptual mechanism", and further emphasize in Discussion 4.3 that there is currently a lack of direct process observation evidence.
Re: The proposed mechanism has been explicitly defined as a physico-chemical conceptual mechanism framework. We emphasized the lack of direct in-situ process observation evidence and proposed future validation approaches.
“By integrating the results of our analysis with previous findings, we proposed a comprehensive conceptual physico‑chemical mechanism framework to elucidate the possible generation processes of nocturnal atmospheric CO2 uptake by dryland soils （Fig. 10）.” (Line 297-299)
“Direct in-situ measurements of soil pore pressure gradients, gas flow velocity, and vertical CO2 concentration profiles are still lacking, which are critical to directly verify the physico- chemical process. Future research could combine high-frequency pore gas monitoring and 13C isotopic labeling to test this framework under controlled conditions of temperature difference, moisture, pH, and texture.” (Line 309-312)
Comment 8:Line 207, the text states that SEM is "based on a priori hypotheses informed by the RF and VPA results", but in the Methods section, HP is actually introduced, while VPA is not.
Re: The terminology inconsistency has been corrected. "VPA" has been replaced with "hierarchical partitioning (HP)" to be consistent with the method description in the Methods section.
“To disentangle the causal pathways through which environmental factors influence Fs, we constructed a structural equation model (SEM) based on a priori hypotheses informed by the RF and hierarchical partitioning (HP) results.” (Line 207-208)
Citation: https://doi.org/10.5194/egusphere-2026-4692-CC4
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CC4: 'Reply on CC1', Jia-Bin Liu, 08 Oct 2026
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CC2: 'Comment on egusphere-2026-4692', Zhen Liu, 23 Sep 2026
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This manuscript compiles 563 observations of nocturnal soil CO₂ flux (Fs) across global deserts and proposes a physico-chemical framework involving physical transport and chemical fixation. The topic is relevant, the dataset is valuable, and the proposed framework is potentially novel. However, several issues concerning variable definitions, sign conventions, statistical reporting, figure captions, and terminology need to be clarified. I recommend minor revision.
1. The Methods define ln(clay/sand)ln(clay/sand), whereas the Abstract, Results, and Fig. 8d often use ln(sand/clay) and ln(sand/clay). This inconsistency makes the direction of the correlation difficult to interpret. Please use one index consistently throughout the manuscript and clearly state whether an increase represents finer texture or higher sand content. Also check that the signs in the Pearson correlation, RF, HP, and SEM results are consistent with this definition.
2. The overall research objective does not pertain to any specific global region. Therefore, if there are no data for South America and Australia, it is recommended to remove the colors.
3. Line 209, soil pH had a direct effect of -0.44 on Fs and an indirect effect of -0.092 via soil water content. The indirect effect here does not match that shown in Figure 9.
4.Line 253, Variable importance in the random forest model (Fig. 5), but the RF variable importance graph is Fig. 4, and Fig. 5 is a partial dependence plot. The citation here should be changed to Fig. 4.
5. Line 221, Please check the superscript on the entire text.
6. The method mentions using parameters such as AIC to evaluate SEM, but no relevant results are provided in the outcome.
7. Line 254, It states its independent contribution in VPA analysis, but in the method, hierarchical partitioning (HP) is used instead of VPA. Please unify it to HP, or explain that VPA is a different name for the same analysis.Citation: https://doi.org/10.5194/egusphere-2026-4692-CC2 -
CC3: 'Comment on egusphere-2026-4692', Xue Yang, 28 Sep 2026
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Major comment
The topic is relevant to the Earth and environmental science community served by EGUsphere because nocturnal CO₂ uptake remains poorly constrained in dryland carbon budgets, and a cross-site synthesis could make a useful contribution. The manuscript also assembles a potentially valuable dataset and attempts to connect physical and chemical controls.
The present analysis, however, does not yet support the title’s claim that it explains a generation mechanism. The evidence consists of observational data extracted from heterogeneous studies, many predictors vary mainly between studies or sites, and several analyses appear to treat clustered observations as independent. Contradictory definitions and sign interpretations for ΔT, Fs, and the texture ratio further prevent a stable interpretation of the reported effects. The annual carbon calculation also appears to apply a full-year, 24-hour multiplier to a nocturnal flux. These issues affect the principal conclusions and require substantial reanalysis and reframing.
- lines 8–23; Discussion, lines 243–307: Could the authors describe the proposed physicochemical mechanism as a conceptual framework supported by cross-study associations, rather than as a demonstrated causal mechanism, and revise the title, abstract, and conclusions accordingly?
- lines 65–126: Could the authors add the search date, screening procedure, data-selection rules, study/site hierarchy, and complete model settings so that readers can understand how the 563 observations were selected and analysed?
- lines 145–211 and, lines 243–285; Figs. 3, 5, 8, and 9: Could the authors use one texture variable throughout, either `ln(clay/sand)` or `ln(sand/clay)`, and check all signs and interpretations of ΔT and negative Fs so that “stronger uptake” has one consistent meaning?
- lines 220–236: Could the authors correct the annual conversion of nocturnal Fs, state the assumed number of nighttime hours and uptake days, and present the NEE and soil-respiration comparisons as illustrative estimates unless the quantities are directly comparable?
- Lines 310–314; Supplement, Table I: Could the authors provide a machine-readable dataset and analysis code, reconcile the supplement with the reference list, and use one consistent Data and code availability statement?
Minor comment
- Lines 18–20，Revise “suggested exerted pronounced effects” and “results ad previous studies”; both phrases are grammatically incomplete.
- Line 100，Rename Section 2.3 because the heading repeats “Data Extraction”; “Statistical analysis” would be more accurate.
- Lines 124–126，Correct “Fisher ‘s C” and list and cite all R packages used for the LMM, RF, hierarchical partitioning, and SEM.
- Lines 139–140，Replace “obvious discrepancy” with “statistically significant differences.”
- Lines 153–156，Correct the Fig. 3 caption because the displayed legend uses red for positive correlations and blue for negative correlations.
- Lines 164–168，Describe `%IncMSE` as predictive variable importance rather than “explanatory capacity,” and state whether it was calculated from out-of-bag predictions.
- Lines 180–182，Correct the Fig. 5 caption to match the panel order and use the same soil-texture ratio as the figure.
- Lines 193–195，Remove the stray “(c)” after “subsequent analyses” and identify the test used for EC.
- Lines 209–213 and 279–285，Reconcile the ΔT path coefficient, which is 0.249 in the Results and Fig. 9 but 0.2741 in the Discussion.
- Lines 223–225，Correct “NEE acrossed” and use either `yr⁻¹` or `a⁻¹` consistently.
- Lines 228–230，Correct the soil-respiration unit from `s⁻¹¹` to `s⁻¹`.
- Lines 257–266，Standardize the chemical notation, charges, subscripts, equilibrium arrows, and reaction numbering.
- Lines 306–309，Correct “labelingto” and specify which carbon pools the proposed ¹³C experiment would measure.
- After line 309，Add a concise Conclusion that answers the stated objectives and distinguishes observed associations from proposed mechanisms.
- Lines 316–319，Reconcile “Yao Gao” in the author list with “Yang Gao” in the contribution statement.
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This paper focuses on the nocturnal CO2 absorption process in desert soil, based on global multi-regional observational data. It comprehensively employs methods such as LMM, RF, HP, and SEM to analyze the effects of environmental factors, and further proposes a physical-chemical coupling mechanism framework. The research is novel and has ecological significance, and the data integration and multi-method analysis are relatively comprehensive. Overall, the manuscript has the basis for publication, but it still needs further improvement in terms of statistical analysis consistency, and some mechanism explanations. It is recommended to be accepted after minor revisions. Specific comments are as follows: