the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 13 Oct 2025
Technical note: Lys-clim, a combination of lysimeters and an atmospheric conditions simulator to study biogeochemical processes in the shallow critical zone
Abstract. Studying the Critical Zone (CZ), i.e. the outermost envelope of Earth, and its bio-geochemical processes requires an interdisciplinary approach. The deployment of critical zone observatories has led to significant scientific advances but does not offer the possibility of comparing treatments or apprehending different climatic scenarios. Conversely, mesocosm studies are often discipline-specific and can be limited in scope. Here, we propose a complementary approach that relies on the combination of 15 lysimeters and a climate chamber. The lysimeters have been equipped to allow for a detailed monitoring of the water flow, which connects most biogeochemical processes in the critical zone. This monitoring relies on scales, tipping buckets, soil moisture sensors and a facilitated high frequency sampling of discharge water. Besides, in-situ continuous gas analysis is enabled by a 45-channel manifold. The climate simulator is a 81 m3 isolated chamber that enables regulation of temperature; atmospheric CO2; relative humidity; quantity and quality of irrigation water and quantity and quality of light. We evaluate the design in terms of its ability to assess the interactions between CZ processes. The main advantages of this set-up are as follows: it allows for the simulation of future climates or extreme events; it enables replication and the application of different treatments, facilitating the isolation of processes and the assessment of anthropogenic impacts; and it provides automated data acquisition.
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Status: final response (author comments only)
- RC1: 'Comment on egusphere-2025-4243', Anonymous Referee #1, 21 Nov 2025
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RC2: 'Comment on egusphere-2025-4243', Kevin Bishop, 28 Jan 2026
This paper presents an innovative mesocosm approach to simulating changes in the crucial zone with an emphasis on climatic factors. The paper is well-written and appropriately detailed in the presentation. As such it provides the critical zone community with a useful overview of this infrastructure.
Major concern:
I lack information on the possibility for researchers to make use of this facility. Is there a possibility for the scientific community to make use of this infrastructure? Or is the presentation more an inspiration for others to try to create their own mesocosm since the one presented in this manuscript is not going to be accessible for testing new ideas from people not already involved in this in this particular mesocosm.
Minor comments
Figure 5: There is platueau in cumulated discharge, and a gap in conductivity data between hours 10-25 from start of the drainage. Please explain if this is an experimental artefact or a feature of the planned experiment.
Line 264. Please consider adding “or downslope changes along a soil catena” after the workds “... vadose zone, such as preferential flow”
Citation: https://doi.org/10.5194/egusphere-2025-4243-RC2 -
RC3: 'Comment on egusphere-2025-4243', Anonymous Referee #3, 02 Mar 2026
In the Technical Note, the authors describe the configuration of the new CEREEP-Ecotron Ile de France facility. Such experimental facilities are important for improving our understanding of processes and investigating how they change in the context of changing climatic conditions. This contribution is highly relevant, as the CZ observatories' manipulative experiments can complement and accompany it. The Technical Note will be of interest to other readers who would like to set up a similar facility or who might use it for experiments in future.
However, I recommend providing more detail on the facility's framework conditions, e.g. which lower boundary condition was used and what potential ET can be set by the climatic conditions. It is also important to specify the respective minimum ranges for the variables that can be controlled. The results section would benefit from a clearer presentation of the data, rather than so many small examples for different compartments, and the discussion could also be improved. Please refer to the specific comments for more detail.
Specific comments:
L11-13: The setup uses one climate chamber, so my question is how it enables the evaluation of future climates and extremes when it is not possible to use a reference scenario or other treatments. It would be possible to run different scenarios one after the other, but this would considerably extend the overall study period and preclude longer experiments. For example, five years per scenario would require 15 years for a reference scenario and a second scenario. I recommend providing a clearer explanation of the types of experiments that can be conducted in this facility.
L45: This is an important point. The question is how this experimental data from a simulator can be related to the field. I suggest adding to this discussion later, as experiments often have specific limitations. It would be useful to clarify what can and cannot be done.
L Fig.1: Looking at Figure 1b, I am wondering why the lysimeter cylinders and isolation foam were chosen to be black. Due to their low albedo, they will perfectly absorb energy and lead to enhanced evapotranspiration and soil temperature.
L65: What about wind speed? This is an important factor affecting the atmosphere's demand for evapotranspiration. Also, how is air pressure controlled?
L70-75: Please report the temperature range that can be set by this controlled circuit here. How are the fans located and distributed across the chamber to avoid creating a localised source of air exchange over a specific lysimeter that could affect surface-atmosphere interactions? I recommend adding this information to the technical view in Figure 1a. It would also be useful to know how long it takes to adapt to new temperature conditions, or whether there is a specific delay in the technical setup to match the climate conditions of a scenario, e.g. reaching XX°C in one hour. Please clarify this.
L76-81: Is this measured by only one sensor in the entire chamber? Wouldn't it be necessary to use several sensors to ensure homogeneous conditions for the different lysimeters and prevent inhomogeneous mixing? Could you also please report the RH range that can be achieved by the system, e.g. 5% to 110%?
L82: One limitation of this set-up is that potential greenhouse gas (GHG) emissions between different mesocosms cannot be defined.
L83: Please also provide the system's minimum and maximum CO2 values here. This information is important for general knowledge and for anyone else who might request to use this setup.
L90: Could you please explain in more detail how the lysimeter is distributed across the surface? How homogeneous can water infiltration be when using these six drippers? Could you also provide the minimum amount that could be added to the surface by this dripping system? Another point to consider is that, due to drip irrigation, intercept evaporation is neglected. Also, plants can transpire during irrigation events, which requires weight measurements to be taken at a high temporal resolution to avoid losing information.
L96: Please provide information on the intensity of light reaching the surface and the top of a canopy, for example at a height of 1.5 m above the soil. What about the light spectrum? Please also provide the light spectrum that is crucial for plant growth.
L103: Please also describe the surface area of the system. The dimensions of the lysimeter column are crucial for determining the type of vegetation that can grow. I hope this will be covered later in the discussion.
L110: What about the possibility of direct upward water flow? This is usually found in sites with a shallow groundwater table, but it is also important in spring and summer, as water from deeper soil depths in the field can be used for ET. Could you please explain why such an important feature is not included in the setup? This is especially important for a setting which a relative shallow soil column.
L110-118: Why not use the lysimeter weight directly to obtain components of the water cycle? By e.g. using algorithms developed to interpret lysimeter weight data (Hannes et al., 2015; Peters et al., 2017) as described in Schrader et al. (2013).
What is the temporal resolution of the weighing system? In general, the subsection is highly fragmented. Perhaps it would be worth merging some parts and information to improve understanding of the water balance. For example, temporal resolution is required, not just weighing resolution.
L100: It is unclear how biomass can be monitored here with a resolution similar to that of the water balance components. As the plant grows inside the lysimeter, water is only redistributed into the plant from the soil. Therefore, I still don't understand why biomass is included.
L116: That’s very vague, and the microclimatic conditions close to the surface will differ from those measured above the lysimeter in the chamber. These conditions are crucial for dew formation. Perhaps a setup with a leaf wetness sensor could help to distinguish between rainfall and non-rainfall more effectively (Binks et al., 2021; Groh et al., 2026).
L135: I am wondering about the acquisition frequency of the mesocosm weight. Why is it measured at 75-second intervals and not at least every 60 seconds, and how can this be combined with discharge observations (tipping buckets)? Later, the authors describe that the water cycle is analyzed on a 5-minute basis. It remains unclear to me why such a great system reduces its ability in high temporal resolution analysis.
L141: Could you please explain how water is extracted from the soil via the suction cells? Also, please clarify whether this is a permanent process or only occurs during specific periods.
L145: It is unclear whether a classical seepage face or a suction-controlled system is being used here. If the former, please explain how the bottom was prepared to enable this. This could also be a significant limitation, particularly with regard to water flow and solutes, since seepage face boundaries only release water when the gravel layer is saturated, which has an impact on solutes (anaerobic conditions). Please take a closer look at, for example, Abdou and Flury (2004) or Boesten (2007)
L145: Using an autosampler is very helpful. However, removing 24 samples, especially during periods of high water content in the column and at weekends, may restrict the frequency with which soil water can be measured. I am just curious about how the later sample can be automatically related to a specific time period, and what would happen if more than 50 ml of water were required for the analysis of solutes.
L154: Are those the min and max values that can be set for the simulator?
L179-188: A more thorough test of different situations and combinations of conditions would be useful for capturing its ability to simulate predefined climatic conditions, especially with regard to air temperature and relative humidity (RH). It is also unclear which atmospheric demands are set for plants due to temperature, RH and light, as these are crucial in combination for plant transpiration and evaporation. I therefore recommend providing an estimate of reference evapotranspiration based on climatic conditions.
L185: 450 µmol m -2 s -1 is very low. For growth of major crops much higher values are of need. This could be a major limitation of the system. Please clarify this
L190: I'm just wondering why only 14 water samples with enough water (50 ml) to measure EC were collected during an event with 277 mm of rainfall in 42 hours. I would have expected a much higher frequency of measurements.
L206: I would also recommend showing a figure illustrating the diurnal pattern of lysimeter weights, temperature, relative humidity and seepage. After all, the system itself should be evaluated, not just parts of it.
L208: Please add also the reference or potential ET in the plot (e.g. Medicago Sativa + fertilization up to 13%). Another point is that the daily ET seems for the treatment with fertilization very high with ~10 mm (225 mm over 23 days)
L208: What causes such large deviations between replications over such a short period of time?
L209-211: Please explain why ET was negative. For the review process, please provide a figure showing the lysimeter weights, seepage water and climatic conditions at the time when negative ET was detected. Single peaks and longer negative ET values are visible after irrigation events. Was the presence of dew neglected during this time? To get a complete picture, please also add other variables, i.e. humidity and temperature during this time, as well as seepage.
L213: So please use such smoothing filter when showing the water balance components. I suggest using a more sophisticated method e.g. AWAT (Peters et al., 2014; Peters et al., 2017) or method suggested by Hannes et al. (2015).
L227-231: A review paper by Breuer et al. (2003) on rooting depth found that crops had an average maximum rooting depth of 1.43 m, while grasses, forbs and herbs had an average maximum rooting depth of 0.93 m. This is a major limitation of the facility, and it remains unclear which plants can grow without their rooting space being artificially limited. Table 6 provides more details on specific crops and grasses, showing that only 16% of the crops, grasses, forbs and herbs have a maximum rooting depth below 75 cm.
L234: The water observed leaving the lysimeter is seepage at 75 cm.
L234: Please bear in mind that seepage water collected at 75 cm cannot be directly related to groundwater recharge. It would also be worth briefly discussing this, especially given that no water can move upwards in this setting.
L243: A recent overview of CZ across the globe, including the respective land cover types, has been published by Arora et al. (2023).
L263: It is not clear why the size should reduce the occurrence of preferential flow.
L266-268: Another major limitation is the water required for ET processes and its implications for ecosystem services.
L269: There is also no possibility to control the temperature boundary condition.
L290: I'm not sure if this section is necessary for the technical note. I would suggest focusing more on the setting, and discussing the opportunities and limitations more broadly.
297: How can the authors quantify the difference between treatments with and without ERW when CO2 release over time cannot be differentiated? Please clarify this.
L304: As it was unclear which boundary conditions were used for the lysimeter, please clarify this setting, as it may have a significant impact on solutes, given that water only leaves the system under saturated conditions, which affects biogeochemical processes.
L316: The wall effects appear here for the first time. I am not sure if this is the right place to discuss it, but I suggest doing so earlier.
Abdou, H.M., Flury, M., 2004. Simulation of water flow and solute transport in free-drainage lysimeters and field soils with heterogeneous structures. European Journal of Soil Science, 55(2): 229-241, 10.1046/j.1365-2389.2004.00592.x.
Arora, B., Kuppel, S., Wellen, C., Oswald, C., Groh, J., Payandi-Rolland, D., Stegen, J., Coffinet, S., 2023. Building Cross-Site and Cross-Network collaborations in critical zone science. Journal of Hydrology, 618: 129248, 10.1016/j.jhydrol.2023.129248.
Binks, O., Carle, H., Coughlin, I., da Costa, A.L., Meir, P., 2021. Measuring the vertical profile of leaf wetness in a forest canopy. MethodsX, 8: 101332, https://doi.org/10.1016/j.mex.2021.101332.
Boesten, J.J.T.I., 2007. Simulation of Pesticide Leaching in the Field and in Zero-Tension Lysimeters. Vadose Zone Journal, 6(4): 793-804, 10.2136/vzj2007.0067.
Breuer, L., Eckhardt, K., Frede, H.-G., 2003. Plant parameter values for models in temperate climates. Ecological Modelling, 169(2–3): 237-293, 10.1016/S0304-3800(03)00274-6.
Groh, J., Vanderborght, J., Pütz, T., Vogel, H.J., Gründling, R., Rupp, H., Rahmati, M., Sommer, M., Vereecken, H., Gerke, H.H., 2020. Responses of soil water storage and crop water use efficiency to changing climatic conditions: a lysimeter-based space-for-time approach. Hydrol. Earth Syst. Sci., 24(3): 1211-1225, 10.5194/hess-24-1211-2020.
Groh, J., Pütz, T., Beysens, D., Cuxart, J., Agam, N., Küpper, W., Colaizzi, P.D., Vereecken, H., Gerke, H.H., Amelung, W., 2026. Land cover influences microclimate and non-rainfall water inputs in temperate agricultural environment. Journal of Hydrology: 135040, https://doi.org/10.1016/j.jhydrol.2026.135040.
Hannes, M., Wollschläger, U., Schrader, F., Durner, W., Gebler, S., Pütz, T., Fank, J., von Unold, G., Vogel, H.J., 2015. A comprehensive filtering scheme for high-resolution estimation of the water balance components from high-precision lysimeters. Hydrol. Earth Syst. Sci., 19(8): 3405-3418, 10.5194/hess-19-3405-2015.
Peters, A., Nehls, T., Schonsky, H., Wessolek, G., 2014. Separating precipitation and evapotranspiration from noise - a new filter routine for high resolution lysimeter data. Hydrol. Earth Syst. Sci. Discuss., 18(3): 1189 - 1198, 10.5194/hess-18-1189-2014.
Peters, A., Groh, J., Schrader, F., Durner, W., Vereecken, H., Pütz, T., 2017. Towards an unbiased filter routine to determine precipitation and evapotranspiration from high precision lysimeter measurements. Journal of Hydrology, 549: 731-740, 10.1016/j.jhydrol.2017.04.015.
Pütz, T., Kiese, R., Wollschläger, U., Groh, J., Rupp, H., Zacharias, S., Priesack, E., Gerke, H.H., Gasche, R., Bens, O., Borg, E., Baessler, C., Kaiser, K., Herbrich, M., Munch, J.-C., Sommer, M., Vogel, H.-J., Vanderborght, J., Vereecken, H., 2016. TERENO-SOILCan: a lysimeter-network in Germany observing soil processes and plant diversity influenced by climate change. Environmental Earth Sciences, 75(18): 1-14, 10.1007/s12665-016-6031-5.
Schrader, F., Durner, W., Fank, J., Gebler, S., Pütz, T., Hannes, M., Wollschläger, U., 2013. Estimating Precipitation and Actual Evapotranspiration from Precision Lysimeter Measurements. Procedia Environmental Sciences, 19(0): 543-552, 10.1016/j.proenv.2013.06.061.
Citation: https://doi.org/10.5194/egusphere-2025-4243-RC3
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This paper presents a new research facility that combines fifteen small lysimeters (surface area of 0.1 m², depth of 72 cm) within one climate chamber. This allows the lysimeters, including growing plants, to be operated under identical climatic conditions. The paper describes the technical design, instrumentation, and modus operandi of the system. The paper also presents test data on temperature, air humidity, PPFD, and the spectral composition of light provided by the LED lighting system. The lysimeters can be semi-automatically irrigated; soil pore and seepage water can be collected; and soil gas concentrations of CO₂ and O₂ can be measured through gas-permeable membrane tubes at three different depths within each lysimeter. Additionally, soil temperature and moisture can be measured at four different depths within each lysimeter.
The system is innovative and allows for targeted process studies under controlled conditions. Its strengths include the ability to monitor the total water balance, pore and seepage water quantity and quality, and soil gas concentrations, as well as the ability to modulate environmental conditions over a wide range. The system's weaknesses are the small size and shallow depth of the lysimeters; the lack of soil temperature control, which prevents a natural vertical soil temperature gradient; the inability to freeze; and a lighting system that provides only about 25% of full sunlight intensity.
This paper will be of interest to readers who use or plan to use ecotrons and lysimeters for experiments or intend to use data from such experiments for modeling purposes. While the paper is generally easy to understand, it lacks some detail regarding technical specifications and equipment. The data presented in the Results section seem somewhat arbitrarily selected. It would be helpful to include example data from different climatic conditions. The discussion highlights the system's potential and limitations. However, it also includes a section about perspectives that is a bit far-fetched. Overall, this is an interesting paper, but it requires revision before publication can be recommended. I have made specific comments and edits in the attached annotated manuscript.