Contrasting Roles of Microbial Heterogeneity and Sediment Heterogeneity in Controlling Hyporheic Nitrogen Removal

Xian, Yang; Wen, Zhang; Krause, Stefan

doi:10.5194/egusphere-2026-3760

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https://doi.org/10.5194/egusphere-2026-3760

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07 Jul 2026

| 07 Jul 2026

Status: this preprint is open for discussion and under review for Hydrology and Earth System Sciences (HESS).

Contrasting Roles of Microbial Heterogeneity and Sediment Heterogeneity in Controlling Hyporheic Nitrogen Removal

Yang Xian, Zhang Wen, and Stefan Krause

Abstract. Bacteria in streambed sediments reduce nitrogen pollution by performing chemical reactions that can transform pollutants. However, how differences in sediment types (like sandy vs. clay-rich layers) or the distribution of these bacteria affect the nitrogen removal in streambed sediments remains unclear. To explore this, we built numerical models to mimic real streambed conditions and explore how small-scale variations in sediment and microbial communities influence nitrogen removal. Our results show that the spatial changes in physical and chemical properties of sediments (e.g., permeability and organic matter content) have little impact on nitrogen removal. Instead, variations in the distribution of nitrogen-processing microbes are far more critical. This is because bacteria and the sticky substances they produce can slowly clog the sediment pores. This clogging limits the movement of pollution to the very top layers of sediments, making deeper sediment differences irrelevant to overall nitrogen removal. These results mean that future numerical models aiming to predict nitrogen removal should focus on mapping where these helpful microbes live, rather than overcomplicating simulations with too much detail about sediment variations. Simplifying sediment assumptions could make models more practical while still capturing the key role of microbes in cleaning streams.

Received: 25 Jun 2026 – Discussion started: 07 Jul 2026

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RC1:
'Comment on egusphere-2026-3760', Anonymous Referee #1, 27 Jul 2026 reply
The manuscript investigates the contrasting effects of sediment and microbial heterogeneity on hyporheic nitrate removal using coupled flow, reactive-transport, and biofilm-growth models. The topic is highly relevant, and the modelling framework is potentially valuable. The manuscript is generally well organized, but several points should be clarified before publication.
The comparison between the heterogeneous-growth and constant-biomass scenarios changes not only the spatial distribution of biomass but also microbial growth, biomass evolution, and bioclogging feedback. Therefore, the large differences in nitrate removal cannot be attributed exclusively to microbial heterogeneity. The authors should clarify this limitation and moderate statements such as “microbial heterogeneity plays a decisive role.”

The conclusion that sediment heterogeneity has a negligible effect is based on two selected small-scale sediment structures and the tested parameter ranges. This finding should not be generalized to all hyporheic zones. Please consistently qualify the conclusion as applying to the model configurations, heterogeneity scales, and environmental conditions considered here.

Please provide some additional information on model calibration and validation, particularly the parameters that were calibrated and the experimental observations used for comparison. Quantitative goodness-of-fit measures may also be included if available. A brief discussion of the limitations of applying the calibrated parameters to the present simulation scenarios would further improve the manuscript.

Please revise the Abstract into a more concise scientific style. Expressions such as “helpful microbes,” “sticky substances,” and “cleaning streams” are overly informal for a research article.

The manuscript requires careful language editing. Please correct grammatical and typographical issues, including duplicated brackets, subject–verb agreement, inconsistent abbreviations, and expressions such as “are called as” and “momentously enhances.”

Please clarify how the spatially uniform microbial biomass value was determined in the “Hetero. Sed. & Const. Bio.” scenario, including whether the averaging was performed over space, time, or both. This information is important for interpreting the comparison between the microbial scenarios.

Please briefly explain the rationale for selecting the two stream velocities and nutrient conditions. It would be helpful to indicate whether these values represent typical or contrasting conditions reported for natural streams.

Please moderate the statement “This study is the first to reveal...” unless this claim can be fully demonstrated. A more appropriate formulation would be “This study provides new insights into the contrasting roles of sediment and microbial heterogeneity in hyporheic nitrate removal.”

The current statement that all raw data are available upon request does not fully follow the HESS data policy. The model inputs, key simulation outputs, and data underlying the figures should be deposited in a reliable public repository with a persistent identifier. The authors are also encouraged to share the relevant model files or configuration information where possible. If any material cannot be made publicly available, the reason should be clearly explained in the Data and Code Availability section.

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Citation: https://doi.org/10.5194/egusphere-2026-3760-RC1
- AC1: 'Reply on RC1', Zhang Wen, 11 Aug 2026 reply
  
  The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2026/egusphere-2026-3760/egusphere-2026-3760-AC1-supplement.pdf
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  Citation: https://doi.org/10.5194/egusphere-2026-3760-AC1
RC2:
'Comment on egusphere-2026-3760', Anonymous Referee #2, 30 Jul 2026 reply
This manuscript presents a coupled numerical investigation of nitrate removal in heterogeneous hyporheic sediments. The modeling framework is compelling, and the findings offer valuable insights for improving the representation of biogeochemical processes in hyporheic zone models. However, before publication, the following points require clarification and revision:
Title Specificity: The title broadly refers to "nitrogen removal," whereas the study focuses specifically on nitrate removal via denitrification. Consider revising the title to "nitrate removal" or explicitly clarifying the scope of "nitrogen removal" in the introduction.

Homogenization Methodology: The equivalent homogeneous models utilize effective permeability tensors but employ arithmetic means for organic matter (OM) content. Please justify the use of arithmetic averaging for OM and clarify whether this approach conserves the total initial OM mass between the heterogeneous and homogeneous domains.

Boundary Condition Assumptions: The concentrations at the sediment-water interface remain constant throughout the 730-day simulation. Please confirm if the overlying stream is modeled as an infinite, well-mixed nutrient reservoir. A brief discussion regarding how this assumption might influence long-term nitrate removal estimates would strengthen the interpretation.

Microbial Biomass Representation: Both aerobic respiration and denitrification are simulated using Monod kinetics with oxygen inhibition. Clarify whether these processes share a single functional biomass pool or distinct microbial guilds. If a single biomass variable is used, please acknowledge this simplification and discuss its potential impact on the spatial distribution of biogeochemical hotspots.

Mechanistic Distinction: The interpretation heavily emphasizes progressive bioclogging near the sediment-water interface. Please more clearly differentiate between nitrate removal driven directly by enhanced microbial reactivity and that resulting indirectly from altered hyporheic exchange and extended solute residence times.

Dimensionality and Bedform Effects: The simulations are two-dimensional, representing repeating ripple structures. Discuss whether three-dimensional flow paths or non-repeating bedforms might introduce additional bypass routes around the clogged surface layer. This would clarify the applicability of the proposed mechanism to natural streambeds.

Sediment Stability: The model assumes fixed sediment structure and streambed topography over 730 days. Please explicitly state that sediment mobility, bedform migration, and biofilm detachment are neglected. Given that these processes often limit persistent bioclogging in natural systems, adding a statement regarding this limitation is crucial.

Section Numbering: Please correct the section numbering. "3 Results and Discussion" is followed immediately by "5 Conclusions," indicating that Section 4 is missing.

Definition of Metrics: Define the total nitrate removal metric (RN) more explicitly. Specify the calculation method, integration period, and the physical meaning of the unit "g m−1" within the context of a 2D model (i.e., per unit channel width).

Table 1 Corrections: Several entries in Table 1 require correction: (i) permeability units should be m2, not m s−1; (ii) transverse dispersivity is mislabeled as αL (longitudinal); (iii) clarify ambiguous range values and source labels; and (iv) remove the extraneous character in "1600c."

Notation Consistency: Ensure consistency in symbols and terminology across the text, tables, and figures. Address discrepancies such as OM vs. POC and X vs. Xh. All variables presented in Figs. 3–5 must be defined in the respective captions.

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Citation: https://doi.org/10.5194/egusphere-2026-3760-RC2
- AC2: 'Reply on RC2', Zhang Wen, 11 Aug 2026 reply
  
  The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2026/egusphere-2026-3760/egusphere-2026-3760-AC2-supplement.pdf
  Reply
  
  Citation: https://doi.org/10.5194/egusphere-2026-3760-AC2

Yang Xian, Zhang Wen, and Stefan Krause

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Yang Xian, Zhang Wen, and Stefan Krause

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Short summary

Streams naturally remove nitrogen pollution, but the main factors controlling this process remain unclear. Using computer models, we found that where bacteria are located is far more important than small differences in sediments. As bacteria grow, water moves more slowly through sediments, limiting nitrogen removal to shallow layers. These findings could simplify future prediction models by emphasizing bacteria rather than detailed sediment descriptions.


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