the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
The community-centered aquatic biogeochemistry model unified RIVE v1.0: a unified version for water column
Shuaitao Wang
Vincent Thieu
Gilles Billen
Josette Garnier
Marie Silvestre
Audrey Marescaux
Xingcheng Yan
Nicolas Flipo
Abstract. Research on mechanisms of organic matter degradation, bacterial activities, phytoplankton dynamics, and other processes has led to the development of numerous sophisticated water quality models since one of the first in 1925, based on first order kinetics for organic matter degradation. The community-centered aquatic biogeochemistry model RIVE was initially developed in 1994 and has since been integrated into several software programs such as Seneque-Riverstrahler, pyNuts-Riverstrahler, ProSe/ProSe-PA and Barman. After 30 years of research, the use of different programming languages including Qbasic, Visual Basic, Fortran, ANSI C and Python, as well as parallel evolution and the addition of new formalisms, raise questions about their comparability.
This paper presents a unified version of the RIVE model for the water column, including formalisms for bacterial communities (heterotrophic and nitrifying), primary producers, zooplankton, nutrients, inorganic carbon, and dissolved oxygen cycles. The unified RIVE model is open source and implemented in Python 3 to create pyRIVE 1.0, and in ANSI C to create C-RIVE 0.32. The organic matter degradation module is validated by simulating batch experiments. The comparability of the pyRIVE 1.0 and C-RIVE 0.32 softwares is verified by modeling a river stretch case study, which considers the full biogeochemical cycles (microorganisms, nutrients, carbon, and oxygen) in the water column, as well as the effects of light and water temperature. The results show that the simulated concentrations of all state variables, including microorganisms and chemical species, are very similar for pyRIVE 1.0 and C-RIVE 0.32. This open-source project highly encourages contributions from the aquatic biogeochemistry community to further advance the project and achieve common objectives.
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Shuaitao Wang et al.
Status: open (until 21 Oct 2023)
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RC1: 'Comment on gmd-2023-135', Anonymous Referee #1, 02 Oct 2023
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The paper titled "The community-centred aquatic biogeochemistry model unified RIVE v1.0: a unified version for water column" presents a unified version of the RIVE model for the water column, which includes formalisms for various ecological and biochemical components such as bacterial communities, primary producers, zooplankton, nutrients, inorganic carbon, and dissolved oxygen cycles. The unified RIVE model is open-source and has been implemented in Python 3 to create pyRIVE 1.0, and in ANSI C to create C-RIVE 0.32. The paper also discusses the validation of the organic matter degradation module through the simulation of batch experiments and compares the comparability of pyRIVE 1.0 and C-RIVE 0.32 by modelling a river stretch case study. The RIVE model described in this paper is state-of-the-art, the model description is generally very detailed, and the open-source implementation of the model in different programming languages is very meaningful and useful for geoscience modellers. As the importance of process-based models is increasingly recognized to uncover the underlying mechanisms behind water quality metrics, this study and its described model are very timely and valuable. While the model code and its metadata are well organized (which is the most important for a model development paper), the model descriptions and some details (text, equations, figures, and language) in the manuscript need to be improved (see my comments below). I therefore suggest minor revisions before acceptance for publication.
Major comments and questions:
- RIVE is one of the most state-of-the-art water quality models in the world, with its particularly strong functions in simulating biogeochemical processes, multiple variables together, spatio-temporal changes, and changes with different factors. Some recent studies propose the idea that some conventional water quality models may be too complex, e.g. Jackson-Blake et al. (Water Resource Research). Although I myself fully believe the complexity and strengths of the RIVE model go hand in hand, I was just wondering: do you have some existing test or experimental examples, to roughly show that the processes/kinetics/environmental factors/or variables built in RIVE are necessary or important or advantageous for a better performance? Or show the contrary, that omitting some of them will cause poorer simulations/performance/understanding? If this is possible, can you add a paragraph for this in the discussion?
- Given the complexity of the model, user-friendly documentation and tutorials would be helpful for users who are new to this field or the model. Can you possibly include the documentation in the archive of the model? For example, are you going to add the publication of this paper to the archive of the model?
- Is phytoplankton dynamics in the RIVE also dependent on temperature? If so, please mention it in a suitable place, e.g. Line 40 and section 2.3.1. Similar questions for other processes: do you also consider temperature? This should be mentioned earlier in the text to better inform readers.
- I guess “state variable” means evaluating output variables from elemental and process balances. Or maybe I misunderstand this? This needs to be explained at the beginning of the text.
- Section 2 Line 92-101: Can you clarify whether the community-centred RIVE simulated different dynamics across different locations and times/periods? This information is not mentioned, so not clear to readers.
- Some terms used in equations are not explained in terms of their meaning and unit. Please thoroughly check and add explanations incl. units for all terms used in all equations.
- Please consider revising the expression of ions in all flowcharts. In these flow charts, gas forms (e.g., “O2” and “CO2”) and ions (e.g. “NO2” and “NO3”) are used together, but in fact “NO2” can mean a gas form, but obviously here “NO2” is only used to mean “NO2-” in this paper.
- The sentences of this manuscript are generally too long and a bit hard to read, particularly for those who may not be so familiar with this model. Some examples: The 1st sentence of the abstract is as long as three lines: “Research on mechanisms of organic matter degradation, bacterial activities, phytoplankton dynamics, and other processes has led to the development of numerous sophisticated water quality models since one of the first in 1925, based on first order kinetics for organic matter degradation”. The 2nd and the 3rd Another typical example is a 4-line sentence spanning Line 25-28: “While the role of microorganisms in the degradation of organic matter has been acknowledged since the end of the 19th century, an important limitation of this type of representation is that the microbiological nature of the organic matter degradation process and the bacterial population dynamics intrinsically involved are completely obscured, being implicitly taken into account only through a biodegradability constant of OM and its dependence on temperature.”. I suggest revising each of such long sentences into 2-3 short ones throughout the entire manuscript, to make the text more readable.
Minor comments:
- Title and Line 19: The tile mentions “aquatic biogeochemistry model”. “Aquatic” can be broad and include freshwater, coastal and marine water. Does this model version simulate both freshwater and marine biogeochemistry? If only for freshwater, I suggest changing this term in the entire paper.
- Line 4: This sentence is a little confusing: RIVE is certainly community-centred now, especially via this paper. However, this sentence reads like RIVE has been community-centred since its development in 1994...
- Line 5: "has since been integrated ..." should be changed to either "has since then been integrated ..." or "has subsequently been integrated ..."
- Line 8 (and elsewhere in the manuscript): Do you mean merely “comparability”, or “comparability and compatibility”?
- Line 19: add “and” or “or” between “lake” and “reservoir”; same for Line 62.
- Line 40-41: please add “of phytoplankton” before “growth” to make it more clear.
- Line 46-60: Since there is a Table A1 that summarizes RIVE applications, please cite the table in this paragraph.
- Line 53: Please add ”simulating” before “hydro-biodynamic functioning”
- Line 75: please add the reservoir/river basin name or location for the stagnant systems here,
- Line 80: “Python 3” is mentioned here. Or does it work for all Python 3 versions? If not, could you please add more information here? like “Python 3 (py3.x-py3.y)”, Because Python 3.9 has been quite different from previous versions in many aspects.
- Line 89: Can you clarify here which aspects are evaluated among different implementations? e.g. performance? Running speed?
- Line 100-101: RIVE does seem to have applied development for sediment dynamics. Perhaps better to clarify this sentence to “While RIVE model does have applications for sediment dynamics and its interaction with the water column (refs xx and xx), relevant community-centred efforts need to be made in future work, which is not the focus of this study.”
- Line 104: plural: polymers
- Line 105: remove “which” here. Using both “but” and “which” is not correct here.
- Line 107: “uptake” is generally not used as a verb. “takes up” or “utilizes” may be not suitable.
- Line 157: Please add the full name for “NH4+” at its 1st appearance in the text.
- Line 173: Please note that “AUQAPHY” is used here; but in Line 39, “Aquaphy” is used; in Figure 3 caption, “Aquaphy” is used.
- Line 182: Please revise: “The most common way of measuring phytoplankton biomass is using the chlorophyll a concentration”.
- Line 183-189: This part may be misleading. Please consider moving the last sentence that mentions “the initial proportions of different constituents are fixed and used to determined ….” to be before the sentences describing the detailed proportion numbers.
- Line 188: “external inflows” is very confusing. Can you revise it to make the meaning clearer?
- Line 216: Please add the full term for “N”, “P” and “Si” at the first-time use of the abbreviation.
- Line 216-217: This sentence is unnecessarily wordy: ”The nutrients can potentially limit phytoplankton growth if their quantities are insufficient”.
- Line 216 and 223: I understand the authors want to mean “DIN”, “DIP”, and “DSi”, but the use of [N], [P] and [Si] may mean “TN”, “TP” and “TSi”, respectively. Need to clarify these uses to change to the correct terms.
- Line 258: “Disappearance” seems not the most suitable expression here. Please consider “consumption” or another word.
- Line 311, 581: Nutrient cycling
- Line 315-316: Maybe need to specify whether C, N, P, and Si are dissolved inorganic forms. Or are they not?
- Line 387: Here water temperature appears for the first time. But I believe water temperature is (should be) used also in other processes described in other sections.
- Line 395 and Line 370-372: Sediment dynamics can be important e.g. for P dynamics and sediment oxygen demand, and RIVE has been applied for sedimentary dynamics long ago. Can you roughly mention here, e.g., through citations of RIVE with sedimentary dynamics, whether or how much the influence of excluding sediment dynamics is for this RIVE v1.0 version with a focus on the water column? For example, are P and O2 concentrations still well simulated and agree with observations?
- Line 455: Please specify the specific item name in Appendix.
- Captions of Figures 7, 8, 10: Can you add the location (or name of water system/river basin) and time (year or month or date) for the validation figures?
- Section 3.2: Can you describe in this section a little bit the reason why DOM and SHB+LHB are selected to show validation, and validation of other state variables such as DO and nutrients are not shown?
- Line 569-570: Please choose one between “such as” and “for instance”
- Line 568: “depend on different limitations” is confusing. Please consider the use of “limiting factors”.
- Line 673: The name of the first author is not correct for this reference.
Citation: https://doi.org/10.5194/gmd-2023-135-RC1
Shuaitao Wang et al.
Shuaitao Wang et al.
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